Error(s) in re-building vignettes:
  ...
--- re-building ‘vortexRguide.Rmd’ using rmarkdown
Quitting from lines 293-297 (vortexRguide.Rmd) 
Error: processing vignette 'vortexRguide.Rmd' failed with diagnostics:
Some items of .SDcols are not column names: [N]
--- failed re-building ‘vortexRguide.Rmd’

SUMMARY: processing the following file failed:
  ‘vortexRguide.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘test’ ‘testname.rda’ ‘testname.txt’
voss1d: no visible global function definition for ‘approx’
voss1d: no visible global function definition for ‘rnorm’
voss1g: no visible global function definition for ‘dchisq’
voss1g: no visible global function definition for ‘approx’
voss1g: no visible global function definition for ‘rnorm’
voss2d: no visible global function definition for ‘rnorm’
voss2g: no visible global function definition for ‘dchisq’
voss2g: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  approx dchisq rnorm
Consider adding
  importFrom("stats", "approx", "dchisq", "rnorm")
to your NAMESPACE file.
'library' or 'require' call to ‘raster’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
level: no visible global function definition for ‘quantile’
obj.rec: no visible global function definition for ‘txtProgressBar’
obj.rec: no visible global function definition for ‘setTxtProgressBar’
project: no visible global function definition for ‘aggregate’
raster.proj: no visible global function definition for ‘quantile’
raster.proj: no visible global function definition for ‘rasterFromXYZ’
raster.proj: no visible global function definition for ‘plot.new’
raster.proj: no visible global function definition for ‘plot’
raster.proj: no visible global function definition for ‘legend’
sub.obj: no visible global function definition for ‘aggregate’
sub.obj: no visible global function definition for ‘txtProgressBar’
sub.obj: no visible global function definition for ‘setTxtProgressBar’
surface: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  aggregate legend plot plot.new quantile rasterFromXYZ
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "plot", "plot.new")
  importFrom("stats", "aggregate", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
'library' or 'require' call to ‘misc3d’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.vscc: no visible global function definition for ‘rainbow’
plot.vscc: no visible global function definition for ‘pairs’
Undefined global functions or variables:
  pairs rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "pairs")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘vwr-Ex.R’
Packages in Depends field not imported from:
  ‘lattice’ ‘latticeExtra’ ‘stringdist’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ald: no visible global function definition for ‘detectCores’
ald: no visible global function definition for ‘mclapply’
coltheart.N: no visible global function definition for ‘detectCores’
coltheart.N: no visible global function definition for ‘mclapply’
hamming.distance: no visible global function definition for
  ‘stringdist’
ldknn: no visible global function definition for ‘detectCores’
ldknn: no visible global function definition for ‘mclapply’
ldknn.odds: no visible global function definition for ‘glm’
ldknn.odds: no visible binding for global variable ‘binomial’
ldknn.odds: no visible global function definition for ‘coefficients’
levenshtein.damerau.distance: no visible global function definition for
  ‘stringdist’
levenshtein.distance: no visible global function definition for
  ‘stringdist’
plot.ldknn.run: no visible global function definition for ‘histogram’
plot.ldknn.run: no visible global function definition for
  ‘theEconomist.theme’
plot.ldknn.run: no visible global function definition for ‘xyplot’
plot.ldknn.run: no visible global function definition for ‘as.layer’
Undefined global functions or variables:
  as.layer binomial coefficients detectCores glm histogram mclapply
  stringdist theEconomist.theme xyplot
Consider adding
  importFrom("stats", "binomial", "coefficients", "glm")
to your NAMESPACE file.
Package in Depends field not imported from: ‘Rcpp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘waffect/libs/waffect.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘waffect.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
summary.whc: no visible global function definition for ‘printCoefmat’
wahc.fit: no visible global function definition for ‘pt’
wahc.fit: no visible global function definition for ‘cor’
whc: no visible global function definition for ‘model.frame’
whc: no visible global function definition for ‘model.matrix’
whc: no visible global function definition for ‘model.response’
Undefined global functions or variables:
  cor model.frame model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "printCoefmat", "pt")
to your NAMESPACE file.
Found the following files/directories:
  ‘linout.csv’ ‘linout.pdf’ ‘out.csv’ ‘out.pdf’ ‘tabel_out.csv’
Found the following files/directories:
  ‘weisseritz’
Foreign function call to a different package:
  .C("comwr", ..., PACKAGE = "wavethresh")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘rPeaks’
Found the following files/directories:
  ‘ReconstructedData.txt’ ‘ReconstructedDataStDev.txt’
  ‘ResampledReconstructions.txt’
  ‘ResampledReconstructionsStandardVariation.txt’
onesamplemeantest: no visible global function definition for ‘pnorm’
twosamplemeantest: no visible global function definition for ‘pnorm’
wcq: no visible global function definition for ‘var’
wcq: no visible global function definition for ‘pnorm’
wcq.fdrc: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  p.adjust pnorm var
Consider adding
  importFrom("stats", "p.adjust", "pnorm", "var")
to your NAMESPACE file.
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(webddx)
  > 
  > test_check("webddx")
  ── 1. Error: query_fz works for a simple query (@testfz_normal.R#7)  ───────────
  HTTP error 410.
  Backtrace:
   1. webddx::query_fz(...)
   2. jsonlite::fromJSON(query_url)
   3. jsonlite:::parse_and_simplify(...)
   4. jsonlite:::parseJSON(txt, bigint_as_char)
   5. jsonlite:::parse_con(txt, bigint_as_char)
   7. base::open.connection(con, "rb")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: query_fz works for a simple query (@testfz_normal.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Package vignette with placeholder title ‘Vignette Title’:
  ‘weco-vignette.Rmd’
Weighted.Box.test: no visible global function definition for ‘acf’
Weighted.Box.test: no visible binding for global variable ‘na.pass’
Weighted.Box.test: no visible global function definition for ‘pgamma’
Weighted.Box.test: no visible global function definition for ‘pchisq’
Weighted.LM.test: no visible global function definition for ‘acf’
Weighted.LM.test: no visible binding for global variable ‘na.pass’
Weighted.LM.test: no visible global function definition for ‘pgamma’
Undefined global functions or variables:
  acf na.pass pchisq pgamma
Consider adding
  importFrom("stats", "acf", "na.pass", "pchisq", "pgamma")
to your NAMESPACE file.
Bundesliga.Mannschaft: no visible global function definition for ‘data’
Bundesliga.Mannschaft: no visible binding for global variable
  ‘Bundesliga’
Bundesliga.Tabelle: no visible global function definition for ‘data’
Bundesliga.Tabelle: no visible binding for global variable ‘Bundesliga’
Bundesliga.XML: no visible global function definition for ‘data’
Bundesliga.XML: no visible binding for global variable ‘Bundesliga’
sens.spec: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘wikibooks/R/Bundesliga.Mannschaft.R’:
  data(Bundesliga)
File ‘wikibooks/R/Bundesliga.Tabelle.R’:
  data(Bundesliga)
File ‘wikibooks/R/Bundesliga.XML.R’:
  data(Bundesliga)
See section ‘Good practice’ in ‘?data’.
Found the following files/directories:
  ‘Bundesliga.xml’ ‘myfile.xml’
wilcox.selection.split: no visible global function definition for
  ‘pnorm’
wilcox.test2: no visible global function definition for ‘wilcox.test’
Undefined global functions or variables:
  pnorm wilcox.test
Consider adding
  importFrom("stats", "pnorm", "wilcox.test")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘WindCurves_Info.Rmd’
plotTrait: no visible global function definition for ‘plot’
plotTrait: no visible global function definition for ‘points’
plotTrait: no visible global function definition for ‘legend’
test.windex: no visible global function definition for ‘hist’
test.windex: no visible global function definition for ‘abline’
test.windex: no visible global function definition for ‘legend’
windex: no visible global function definition for ‘sd’
windex: no visible global function definition for ‘var’
windex: no visible global function definition for ‘dist’
windex: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline dist hist legend plot points quantile sd var
Consider adding
  importFrom("graphics", "abline", "hist", "legend", "plot", "points")
  importFrom("stats", "dist", "quantile", "sd", "var")
to your NAMESPACE file.
Found the following files/directories:
  ‘foo’
dbayes: no visible global function definition for ‘mahalanobis’
dbayes: no visible global function definition for ‘var’
wmd: no visible global function definition for ‘cor’
wmd: no visible global function definition for ‘var’
Undefined global functions or variables:
  cor mahalanobis var
Consider adding
  importFrom("stats", "cor", "mahalanobis", "var")
to your NAMESPACE file.
fit,Leader: no visible global function definition for ‘lm’
plotfit,Leader: no visible global function definition for ‘par’
plotfit,Leader: no visible global function definition for ‘plot’
Undefined global functions or variables:
  lm par plot
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘plyr’ ‘reshape2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
wordmatch: no visible global function definition for ‘llply’
wordmatch : <anonymous>: no visible global function definition for
  ‘llply’
wordmatch: no visible global function definition for ‘melt’
wordmatch: no visible global function definition for ‘count’
Undefined global functions or variables:
  count llply melt
Found the following files/directories:
  ‘aphiainfo.csv’ ‘tax.csv’
Package unavailable to check Rd xrefs: ‘cleaver’
simul.wsvm: no visible binding for global variable ‘mixture.example’
wsvm.boost: no visible global function definition for ‘plot’
Undefined global functions or variables:
  mixture.example plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘wTOvignette.Rmd’
File
  inst/LICENCE
will install at top-level and is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘CONTENTS’
Found the following files/directories:
  ‘Rout.a1’ ‘Rout.b1’ ‘Rout.d10’ ‘Rout.d11’ ‘Rout.d12’ ‘Rout.dat’
  ‘Rout.ftr’ ‘Rout.html’ ‘Rout.spc’ ‘Rout_Profiler.txt’ ‘Rout_err.html’
  ‘Rout_log.html’ ‘gra_Rout’
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/x13binary.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘RP2_data_1.txt’ ‘RP2_data_4.txt’ ‘RP2_qtl_1.txt’ ‘RP2_qtl_4.txt’
  ‘hp1_effect_qtl.txt’ ‘hp1_freq_mrk.txt’ ‘hp1_freq_qtl.txt’
  ‘hp1_genome.txt’ ‘hp1_last_hp_data.txt’ ‘hp1_lm_mrk.txt’
  ‘hp1_lm_qtl.txt’ ‘hp1_lm_qtl_mrk.txt’ ‘hp1_mrk.txt’ ‘hp1_qtl.txt’
  ‘hp2_effect_qtl.txt’ ‘hp2_freq_mrk.txt’ ‘hp2_freq_qtl.txt’
  ‘hp2_genome.txt’ ‘hp2_last_hp_data.txt’ ‘hp2_lm_mrk.txt’
  ‘hp2_lm_qtl.txt’ ‘hp2_lm_qtl_mrk.txt’ ‘hp2_mrk.txt’ ‘hp2_qtl.txt’
  ‘my_RP_data_1.txt’ ‘my_RP_data_4.txt’ ‘my_RP_mrk_1.txt’
  ‘my_RP_mrk_4.txt’
Found the following files/directories:
  ‘xgb.txt’
quadplot: no visible global function definition for ‘median’
xgobi: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  median write.table
Consider adding
  importFrom("stats", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
XHWE: no visible global function definition for ‘read.table’
result: no visible global function definition for ‘pchisq’
result: no visible global function definition for ‘rbinom’
result: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  pchisq rbinom read.table rmultinom
Consider adding
  importFrom("stats", "pchisq", "rbinom", "rmultinom")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘results.txt’
Found the following files/directories:
  ‘XLConnect.xlsx’ ‘autofilter.xlsx’ ‘cellstyles.xlsx’
  ‘createCellstyles.xlsx’ ‘createName.xlsx’ ‘createSheet.xlsx’
  ‘dataformat.xlsx’ ‘datatype.xlsx’ ‘dollar.xlsx’ ‘earthquake.png’
  ‘earthquake.xlsx’ ‘freezePaneTest.xlsx’ ‘hiddenWorksheet.xlsx’
  ‘iris.xlsx’ ‘mergeCells.xlsx’ ‘missingValue.xlsx’ ‘myDump.xlsx’
  ‘myWorkbook.xlsx’ ‘removePaneTest.xlsx’ ‘saveMe.xlsx’
  ‘setBorder.xlsx’ ‘setCellFormula.xls’ ‘setCellStyle.xlsx’
  ‘setDataFormat.xlsx’ ‘setFillBackgroundColor.xlsx’
  ‘setFillForegroundColor.xlsx’ ‘setFillPattern.xlsx’
  ‘setHyperlink.xlsx’ ‘setWrapText.xlsx’ ‘sheetcolor.xlsx’
  ‘splitPaneTest.xlsx’ ‘styleaction.xlsx’ ‘template-multi-ws.xlsx’
  ‘template-ws.xlsx’ ‘writeNamedRegion.xlsx’ ‘writeWorksheet.xlsx’
R5.value.default: no visible binding for global variable ‘data.table’
R5.value.default: no visible global function definition for
  ‘as.data.table’
R5.value.parse: no visible binding for global variable ‘data.table’
R5.value.parse: no visible global function definition for
  ‘is.data.table’
R5.value.parse: no visible global function definition for
  ‘as.data.table’
stampme: no visible global function definition for ‘flush.console’
stampmsg: no visible global function definition for ‘flush.console’
write.data.table: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  as.data.table data.table flush.console is.data.table write.table
Consider adding
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
LPGM: no visible global function definition for ‘flush.console’
PGM: no visible global function definition for ‘flush.console’
PGM.path.neighborhood: no visible global function definition for
  ‘runif’
PGMSim: no visible global function definition for ‘rpois’
PGMSim: no visible global function definition for ‘par’
WPGMSim: no visible global function definition for ‘rpois’
XMRF.Sim: no visible global function definition for ‘cov2cor’
XMRF.Sim: no visible global function definition for ‘rbinom’
XMRF.Sim: no visible global function definition for ‘rnorm’
glm.generic: no visible global function definition for ‘flush.console’
mymult: no visible global function definition for ‘rmultinom’
plot.GMS: no visible global function definition for ‘pdf’
plot.GMS: no visible global function definition for ‘dev.off’
plotNet: no visible global function definition for ‘pdf’
plotNet: no visible global function definition for ‘dev.off’
print.GMS: no visible global function definition for ‘str’
processSeq: no visible binding for global variable ‘quantile’
processSeq: no visible binding for global variable ‘var’
processSeq: no visible global function definition for ‘ks.test’
rmpois : <anonymous>: no visible global function definition for ‘rpois’
Undefined global functions or variables:
  cov2cor dev.off flush.console ks.test par pdf quantile rbinom
  rmultinom rnorm rpois runif str var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  importFrom("stats", "cov2cor", "ks.test", "quantile", "rbinom",
             "rmultinom", "rnorm", "rpois", "runif", "var")
  importFrom("utils", "flush.console", "str")
to your NAMESPACE file.
Found the following files/directories:
  ‘ggm.fit.net.pdf’
Running ‘testthat.R’ [5s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(xpectr)
  > 
  > test_check("xpectr")
  ── 1. Failure: apply_capture() works as expected (@test_addin_utils.R#50)  ─────
  apply_capture("a_df", dput, envir = current_envir) not equal to c(...).
  Lengths differ: 2 is not 3
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 615 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: apply_capture() works as expected (@test_addin_utils.R#50) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘Xplortext-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: LexHCca
> ### Title: Hierarchical Clustering of Documents on Textual Correspondence
> ###   Analysis Coordinates (LexHCca)
> ### Aliases: LexHCca
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> data(open.question)
> res.TD<-TextData(open.question, var.text=c(9,10), Fmin=10, Dmin=10, stop.word.tm=TRUE,
+         context.quali=c("Gender","Age_Group","Education"), context.quanti=c("Age"))
> res.LexCA<-LexCA(res.TD, graph=FALSE, ncp=8)
Error in which(unlist(lapply(listModa, is.numeric))) : 
  argument to 'which' is not logical
Calls: LexCA -> as.matrix -> t -> tab.disjonctif -> which
Execution halted
Found the following files/directories:
  ‘xSub_ACLED_EGY_adm0_year.csv’
Found the following files/directories:
  ‘xtable.html’ ‘xtable.tex’
Found the following files/directories:
  ‘OPT.csv’ ‘testTecan_defaultLiquid.csv’ ‘testTecan_setLiquid.csv’
Package vignette with placeholder title ‘Vignette Title’:
  ‘xyz-vignette.Rmd’
Non-standard file/directory found at top level:
  ‘CONTRIBUTORS’
big.read.table: no visible global function definition for ‘read.table’
big.read.table: no visible global function definition for ‘object.size’
sparkline: no visible global function definition for ‘is.ts’
sparkline: no visible global function definition for ‘time’
sparkline: no visible global function definition for ‘boxplot’
Undefined global functions or variables:
  boxplot is.ts object.size read.table time
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "is.ts", "time")
  importFrom("utils", "object.size", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘CO2.csv’
Running ‘testthat.R’ [10s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(yardstick)
  For binary classification, the first factor level is assumed to be the event.
  Set the global option `yardstick.event_first` to `FALSE` to change this.
  
  > 
  > test_check("yardstick")
  ── 1. Error: Three class (@test-prob-mn_log_loss.R#14)  ────────────────────────
  `truth` should be a factor but a character was supplied.
  Backtrace:
    1. testthat::expect_equal(...)
   13. yardstick:::metric_fn(...)
   14. yardstick::metric_vec_template(...)
   15. yardstick:::validate_truth_estimate_checks(...)
   16. yardstick:::validate_class(truth, "truth", cls[1])
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 511 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Three class (@test-prob-mn_log_loss.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘yatah-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: taxtree
> ### Title: Taxonomic tree
> ### Aliases: taxtree
> 
> ### ** Examples
> 
> lineage1 <- "k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae"
> lineage2 <- "k__Bacteria|p__Firmicutes|c__Clostridia"
> lineage3 <- "k__Bacteria|p__Firmicutes|c__Bacilli"
> table <- taxtable(c(lineage1, lineage2, lineage3))
> taxtree(table)
Warning in taxtree(table) : NAs introduced by coercion
Warning in taxtree(table) : NAs introduced by coercion
Warning in taxtree(table) : NAs introduced by coercion
Error in kids[[parent[i]]] <- c(kids[[parent[i]]], children[i]) : 
  attempt to select less than one element in integerOneIndex
Calls: taxtree -> read.tree -> write.tree -> .write.tree2
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gammaproteobacteria.Rmd’ using rmarkdown
ggtree v2.1.2  For help: https://yulab-smu.github.io/treedata-book/

If you use ggtree in published research, please cite the most appropriate paper(s):

[36m-[39m Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution 2018, 35(12):3041-3043. doi: 10.1093/molbev/msy194
[36m-[39m Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628



Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 73-75 (gammaproteobacteria.Rmd) 
Error: processing vignette 'gammaproteobacteria.Rmd' failed with diagnostics:
attempt to select less than one element in integerOneIndex
--- failed re-building ‘gammaproteobacteria.Rmd’

SUMMARY: processing the following file failed:
  ‘gammaproteobacteria.Rmd’

Error: Vignette re-building failed.
Execution halted
bootstrapswapcurve: no visible global function definition for ‘ts’
fitted: no visible global function definition for ‘ts’
forwardrates: no visible global function definition for ‘ts’
residuals: no visible global function definition for ‘ts’
tZC_NS: no visible global function definition for ‘cmpfun’
tZC_NS_extra: no visible global function definition for ‘cmpfun’
tZC_SV: no visible global function definition for ‘cmpfun’
tZC_SV_extra: no visible global function definition for ‘cmpfun’
ycextra: no visible global function definition for ‘new’
ycinter: no visible global function definition for ‘new’
ycplot: no visible global function definition for ‘par’
ycplot: no visible global function definition for ‘points’
ycplot: no visible global function definition for ‘abline’
ycplot: no visible global function definition for ‘hist’
ycplot: no visible global function definition for ‘lines’
ycplot: no visible global function definition for ‘density’
ycplot: no visible global function definition for ‘qqnorm’
ycplot: no visible global function definition for ‘qqline’
ycsummary: no visible global function definition for ‘shapiro.test’
ycsummary: no visible global function definition for ‘pf’
Undefined global functions or variables:
  abline cmpfun density hist lines new par pf points qqline qqnorm
  shapiro.test ts
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "par", "points")
  importFrom("methods", "new")
  importFrom("stats", "density", "pf", "qqline", "qqnorm",
             "shapiro.test", "ts")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.NS.estimator: no visible global function definition for ‘lm’
.NS.estimator: no visible global function definition for ‘coef’
.NS.estimator: no visible global function definition for ‘na.omit’
.NS.estimator: no visible global function definition for ‘resid’
.NSS.estimator: no visible global function definition for ‘lm’
.NSS.estimator: no visible global function definition for ‘coef’
.NSS.estimator: no visible global function definition for ‘na.omit’
.NSS.estimator: no visible global function definition for ‘resid’
NSrates: no visible global function definition for ‘time’
Nelson.Siegel: no visible global function definition for ‘optimize’
Srates: no visible global function definition for ‘time’
Svensson: no visible global function definition for ‘median’
Svensson: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  coef lm median na.omit optimize resid time
Consider adding
  importFrom("stats", "coef", "lm", "median", "na.omit", "optimize",
             "resid", "time")
to your NAMESPACE file.
kmeansN: no visible global function definition for ‘kmeans’
kmeansN: no visible global function definition for ‘aggregate’
kmeansN2: no visible global function definition for ‘aggregate’
kmeansN2: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  aggregate kmeans sd
Consider adding
  importFrom("stats", "aggregate", "kmeans", "sd")
to your NAMESPACE file.
Found the following files/directories:
  ‘installed_pkgs.rda’
Running examples in ‘zCompositions-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: LPdata
> ### Title: La Paloma data set
> ### Aliases: LPdata
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(LPdata)
> 
> zPatterns(LPdata,label=0)
Error in data.frame(Pattern = names(table(miss$pat)), ID = 1:nlevels(miss$pat)) : 
  arguments imply differing number of rows: 11, 2
Calls: zPatterns -> data.frame
Execution halted
Missing or unexported object: ‘devtools::use_data’
Package vignette with placeholder title ‘Vignette Title’:
  ‘ZipRadius.Rmd’
S3 methods shown with full name in documentation object 'merge':
  ‘cbind.zoocat’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘DT’ ‘shinydashboard’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.6Mb
Namespaces in Imports field not imported from:
  ‘httr’ ‘progress’
  All declared Imports should be used.
Missing or unexported object: ‘devtools::use_package’
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
File ‘abundant/libs/abundant.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘acc/libs/acc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘rARPACK’ ‘sparseLDA’
  All declared Imports should be used.
File ‘ACDm/libs/ACDm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘acepack/libs/acepack.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
File ‘acrt/libs/acrt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    R  13.6Mb
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
File ‘adagio/libs/adagio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinydashboard’
  All declared Imports should be used.
Missing or unexported object: ‘devtools::clean_source’
asp: no visible global function definition for ‘as.formula’
asp: no visible global function definition for ‘var’
aspm: no visible binding for global variable ‘X.Declan’
aspm: no visible binding for global variable ‘Z.Jaida’
aspm: no visible binding for global variable ‘group.vec.Handan’
aspm: no visible global function definition for ‘as.formula’
aspm: no visible global function definition for ‘glm’
aspm: no visible global function definition for ‘binomial’
aspm: no visible global function definition for ‘poisson’
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘AdaptFit/R/aspm.R’:
  assign("group.vec.Handan", group.vec, pos = 1)
  assign("X.Declan", X, pos = 1)
  assign("Z.Jaida", Z, pos = 1)
Namespace in Imports field not imported from: ‘Benchmarking’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.8Mb
    pictures   2.1Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R       1.3Mb
    data    1.3Mb
    files   1.7Mb
Namespace in Imports field not imported from: ‘filehash’
  All declared Imports should be used.
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    data  20.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
File ‘AdMit/libs/AdMit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
File ‘ADMMnet/libs/ADMMnet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘assertthat’ ‘tibble’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
File ‘ahaz/libs/ahaz.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mixexp’
  All declared Imports should be used.
File ‘AhoCorasickTrie/libs/AhoCorasickTrie.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘randomNames’ ‘tidyr’
  All declared Imports should be used.
File ‘akima/libs/akima.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘taxize’
  All declared Imports should be used.
File ‘AlgDesign/libs/AlgDesign.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘allelic/libs/allelic.so’:
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Object: ‘newallelic.o’
File ‘allelic/libs/allelic.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘tibble’
  All declared Imports should be used.
File ‘alphabetr/libs/alphabetr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    extdata  11.7Mb
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.6Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘gridExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘kernlab’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shinyjs’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘magrittr’
  All declared Imports should be used.
installed size is 29.3Mb
  sub-directories of 1Mb or more:
    libs  27.9Mb
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
File ‘anchors/libs/anchors.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lazyeval’ ‘tibble’
  All declared Imports should be used.
installed size is 63.4Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs    61.8Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   2.0Mb
Namespaces in Imports field not imported from:
  ‘car’ ‘datasets’ ‘dplyr’ ‘ggplot2’ ‘plotly’ ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    testdata   5.0Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘evd’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Namespaces in Imports field not imported from:
  ‘curl’ ‘httr’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(aoos)
  > 
  > test_check("aoos")
  ── 1. Failure: Type inheritance (@test-S4-types.R#75)  ─────────────────────────
  inherits(Child(), "Test2") isn't true.
  
  ── 2. Failure: Type with VIRTUAL (@test-S4-types.R#111)  ───────────────────────
  names(Test(x = 2)) == "x" isn't true.
  
  ── 3. Failure: Type with VIRTUAL (@test-S4-types.R#112)  ───────────────────────
  inherits(Test(), "Type") isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 187 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: Type inheritance (@test-S4-types.R#75) 
  2. Failure: Type with VIRTUAL (@test-S4-types.R#111) 
  3. Failure: Type with VIRTUAL (@test-S4-types.R#112) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘pls’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
File ‘APIS/libs/APIS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
File ‘apple/libs/apple.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
runAPSIM: warning in scan(reports_file[i], "", sep = "", skip =
  length(temp), nline = 1): partial argument match of 'nline' to
  'nlines'
runAPSIM: no visible global function definition for ‘write.table’
runAPSIM: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  am.c:275:9: warning: comparison of array 'readByte' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/aqr.Rcheck/00install.out’ for details.
File ‘aqr/libs/aqr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘purrr’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
File ‘arf3DS4/libs/arf3DS4.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R             2.3Mb
    help          1.1Mb
    testScripts   1.3Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘gmm’ ‘graphics’ ‘sandwich’ ‘stats4’ ‘utils’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.6Mb
File ‘ash/libs/ash.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ASPBay/libs/ASPBay.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘arules’ ‘arulesViz’ ‘dplyr’ ‘methods’ ‘plotly’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
File ‘AssotesteR/libs/AssotesteR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘AtmRay/libs/AtmRay.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   9.6Mb
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/audio.Rcheck/00install.out’ for details.
File ‘audio/libs/audio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘broom’ ‘diptest’ ‘ggplot2’ ‘hexbin’ ‘moments’
  All declared Imports should be used.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R.utils’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    java   7.8Mb
installed size is 67.2Mb
  sub-directories of 1Mb or more:
    java  67.2Mb
Namespace in Imports field not imported from: ‘openssl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘jose’ ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
File ‘BaBooN/libs/BaBooN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   3.3Mb
    libs   3.6Mb
Namespace in Imports field not imported from: ‘glpkAPI’
  All declared Imports should be used.
installed size is 93.4Mb
  sub-directories of 1Mb or more:
    libs  92.2Mb
Package suggested but not available for checking: ‘mzR’
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
File ‘BALD/libs/BALD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘docopt’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ranger’
  All declared Imports should be used.
Found the following files/directories:
  ‘bbsi_tmp.RData’ ‘bbsik_tmp.RData’ ‘identified.txt’
File ‘Barnard/libs/Barnard.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.1Mb
    libs   5.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   3.1Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
File ‘base64enc/libs/base64enc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘BASIX/libs/BASIX.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘batman/libs/batman.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘baycn-Ex.R’ failed
The error most likely occurred in:

> ### Name: mhEdge
> ### Title: mhEdge
> ### Aliases: mhEdge
> 
> ### ** Examples
> 
> # Generate data under topology m1_gv.
> # Use ?simdata for a description and graph of m1_gv.
> data_m1 <- simdata(b0 = 0,
+                    N = 200,
+                    s = 1,
+                    graph = 'm1_gv',
+                    ss = 1,
+                    p = 0.27)
> 
> # Create an adjacency matrix with the true edges.
> am_m1 <- matrix(c(0, 1, 0,
+                   0, 0, 1,
+                   0, 0, 0),
+                 byrow = TRUE,
+                 nrow = 3)
> 
> # Run the Metropolis-Hastings algorithm on the data from m1_gv using the
> # Principle of Mendelian Randomization (PMR) and the true edges as the input.
> mh_m1_pmr <- mhEdge(data = data_m1,
+                     adjMatrix = am_m1,
+                     burnIn = 0.2,
+                     iterations = 1000,
+                     nGV = 1,
+                     pmr = TRUE,
+                     prior = c(0.05,
+                               0.05,
+                               0.9),
+                     progress = FALSE,
+                     thinTo = 200)
Error in `[<-`(`*tmp*`, coordinates[1, e], coordinates[2, e], value = 1) : 
  invalid subscript type 'list'
Calls: mhEdge -> convertAM
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(baycn)
  > 
  > test_check("baycn")
  ── 1. Error: the MHEdge function returns the correct matrix (@testMCMC.R#27)  ──
  invalid subscript type 'list'
  Backtrace:
   1. baycn::mhEdge(...)
   2. baycn:::convertAM(...)
  
  ── 2. Error: MHEdge returns the correct matrix with and without pmr (@testMCMCGV
  invalid subscript type 'list'
  Backtrace:
   1. baycn::mhEdge(...)
   2. baycn:::toAdjMatrix(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 12 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: the MHEdge function returns the correct matrix (@testMCMC.R#27) 
  2. Error: MHEdge returns the correct matrix with and without pmr (@testMCMCGV.R#28) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 78.0Mb
  sub-directories of 1Mb or more:
    libs  76.0Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Found the following significant warnings:
  rcpparma_hello_world.cpp:930:4: warning: explicitly assigning value of variable of type 'arma::colvec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
  rcpparma_hello_world.cpp:930:12: warning: explicitly assigning value of variable of type 'arma::colvec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
  rcpparma_hello_world.cpp:939:4: warning: explicitly assigning value of variable of type 'arma::colvec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
  rcpparma_hello_world.cpp:939:12: warning: explicitly assigning value of variable of type 'arma::colvec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/BayesBD.Rcheck/00install.out’ for details.
File ‘BayesComm/libs/BayesComm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘bayescount/libs/bayescount.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘msm’
  All declared Imports should be used.
installed size is 72.8Mb
  sub-directories of 1Mb or more:
    libs  71.9Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MatrixModels’
  All declared Imports should be used.
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs  15.5Mb
File ‘bayesGARCH/libs/bayesGARCH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘BayesGPfit/libs/BayesGPfit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘bayesianETAS/libs/bayesianETAS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘shinytest’ ‘testthat’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.7Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
File ‘bayesloglin/libs/bayesloglin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespace in Imports field not imported from: ‘FastGP’
  All declared Imports should be used.
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs  29.5Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   4.1Mb
Namespaces in Imports field not imported from:
  ‘HDInterval’ ‘carData’ ‘runjags’
  All declared Imports should be used.
File ‘bayesQR/libs/bayesQR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs  15.4Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    ex-data   4.7Mb
File ‘BayesTree/libs/BayesTree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is 133.8Mb
  sub-directories of 1Mb or more:
    libs  133.7Mb
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘matrixStats’ ‘reshape2’ ‘scales’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘locfit’ ‘secr’
  All declared Imports should be used.
File ‘BCBCSF/libs/BCBCSF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘coda’ ‘knitr’ ‘plyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ellipse’ ‘viridis’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
File ‘Bclim/libs/Bclim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  sparseFactor.cpp:33:10: warning: explicitly assigning value of variable of type 'Rcpp::IntegerVector' (aka 'Vector<13>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/BClustLonG.Rcheck/00install.out’ for details.
File ‘bcpa/libs/bcpa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rlang’
  All declared Imports should be used.
File ‘bcv/libs/bcv.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 108.5Mb
  sub-directories of 1Mb or more:
    libs  106.9Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘chron’ ‘colorspace’ ‘gtable’ ‘htmltools’ ‘htmlwidgets’
  ‘httpuv’ ‘magrittr’ ‘munsell’ ‘plyr’ ‘scales’ ‘stringi’ ‘xtable’
  ‘yaml’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
File ‘BenfordTests/libs/BenfordTests.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 42.6Mb
  sub-directories of 1Mb or more:
    libs  41.6Mb
Running examples in ‘bestglm-Ex.R’ failed
The error most likely occurred in:

> ### Name: oneSDRule
> ### Title: Utility function. Implements the 1-sd rule.
> ### Aliases: oneSDRule
> 
> ### ** Examples
> 
> CV<-c(1.4637799,0.7036285,0.6242480,0.6069406,0.6006877,0.6005472,0.5707958,
+       0.5907897,0.5895489)
> CVsd<-c(0.24878992,0.14160499,0.08714908,0.11376041,0.08522291,
+  0.11897327,0.07960879,0.09235052,0.12860983)
> CVout <- matrix(c(CV,CVsd), ncol=2)
> oneSDRule(CVout)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
bestglm
 --- call from context --- 
oneSDRule(CVout)
 --- call from argument --- 
if (class(CVout) == "train") {
    ans <- CVout
    CVout <- with(ans$results, cbind(RMSE, RMSESD))
}
 --- R stacktrace ---
where 1: oneSDRule(CVout)

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (CVout) 
{
    stopifnot(is.matrix(CVout) || is.data.frame(CVout) || class(CVout) == 
        "train")
    if (class(CVout) == "train") {
        ans <- CVout
        CVout <- with(ans$results, cbind(RMSE, RMSESD))
    }
    cverrs <- CVout[, 1]
    indMin <- which.min(cverrs)
    fmin <- CVout[indMin, 2]
    cutOff <- fmin + cverrs[indMin]
    min(which(cverrs < cutOff))
}
<bytecode: 0x67548b8>
<environment: namespace:bestglm>
 --- function search by body ---
Function oneSDRule in namespace bestglm has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(CVout) == "train") { : the condition has length > 1
Calls: oneSDRule
Execution halted
Namespace in Imports field not imported from: ‘compiler’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘ggplot2’ ‘readxl’ ‘rlist’ ‘shinyBS’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
File ‘betategarch/libs/betategarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Running examples in ‘bgmm-Ex.R’ failed
The error most likely occurred in:

> ### Name: chooseModels
> ### Title: Selecting a subset of fitted models
> ### Aliases: chooseModels chooseOptimal
> 
> ### ** Examples
> 
>  simulated = simulateData(d=2, k=3, n=100, m=50, cov="0", within="E", n.labels=2)
>  
>  models3 = beliefList(X=simulated$X, knowns=simulated$knowns, B=simulated$B,
+                kList=2:4, mean="D", within="D")
>  plotGIC(models3, penalty="BIC")
Error in strsplit((models[[3]])[1:(length(models[[3]])/length(models$kList))],  : 
  non-character argument
Calls: plotGIC -> sapply -> lapply -> strsplit
Execution halted
installed size is 135.0Mb
  sub-directories of 1Mb or more:
    include  134.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
File ‘BiasedUrn/libs/BiasedUrn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    1.9Mb
Namespace in Imports field not imported from: ‘nycflights13’
  All declared Imports should be used.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  10.8Mb
possible bashism in configure line 12 (echo -n):
  echo -n "  checking for Sun Studio compiler..."
  possible bashism in configure line 22 (echo -n):
  echo -n "  checking for OS..."
File ‘biganalytics/libs/biganalytics.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
File ‘bigGP/libs/bigGP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘biglars/libs/biglars.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
File ‘biglm/libs/biglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   2.5Mb
    libs      2.1Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
possible bashism in configure line 14 (echo -n):
  echo -n "  checking for Sun Studio compiler..."
  possible bashism in configure line 24 (echo -n):
  echo -n "  checking for OS..."
File ‘bigReg/libs/bigReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs     10.9Mb
possible bashism in configure line 13 (echo -n):
  echo -n "  checking for Sun Studio compiler..."
  possible bashism in configure line 23 (echo -n):
  echo -n "  checking for OS..."
File ‘bigtabulate/libs/bigtabulate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘lattice’ ‘zoo’
  All declared Imports should be used.
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  17.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
File ‘bild/libs/bild.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.4Mb
Error(s) in re-building vignettes:
--- re-building ‘bimets.Rnw’ using Sweave
Loading required package: xts
Loading required package: zoo

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric

 
bimets is active - version 1.4.2
For help type '?bimets'


Error: processing vignette 'bimets.Rnw' failed with diagnostics:
 chunk 19 
Error in value[[3L]](cond) : 
  LOAD_MODEL(): error while building incidence vector for behavioral cn. .getIncidenceVendogs(): inputs need to be strings

--- failed re-building ‘bimets.Rnw’

SUMMARY: processing the following file failed:
  ‘bimets.Rnw’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘methods’
  All declared Imports should be used.
File ‘binom/libs/binom.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘binostics/libs/binostics.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘msa’
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Package suggested but not available for checking: ‘BiocVersion’
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   8.7Mb
Namespace in Imports field not imported from: ‘fs’
  All declared Imports should be used.
Package suggested but not available for checking: ‘ecospat’

Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
File ‘bioPN/libs/bioPN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    doc       1.3Mb
    extdata   1.7Mb
Found the following files/directories:
  ‘R.pdb’ ‘alignment.fa’ ‘sapiens.pdb’ ‘sapiens.pml’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
File ‘bitops/libs/bitops.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘corrgram’ ‘rpivotTable’ ‘shinyAce’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Package suggested but not available for checking: ‘RQuantLib’
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RGtk2’ ‘cairoDevice’ ‘ergm’ ‘foreign’ ‘gWidgets’ ‘gWidgetsRGtk2’
  ‘haven’ ‘plot3D’ ‘plot3Drgl’ ‘rgl’ ‘sna’ ‘statnet.common’
  All declared Imports should be used.
installed size is 53.2Mb
  sub-directories of 1Mb or more:
    libs  51.3Mb
Package suggested but not available for checking: ‘bigrf’

Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘gtools’ ‘knitr’ ‘nnet’ ‘parallel’ ‘rJava’ ‘reshape’
  ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
Missing or unexported object: ‘xgboost::predict’
installed size is 60.2Mb
  sub-directories of 1Mb or more:
    libs  58.9Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
File ‘blockmodels/libs/blockmodels.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘blockTools/libs/blockTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘ggplot2’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘formula.tools’ ‘plm’
  All declared Imports should be used.
File ‘Bmix/libs/Bmix.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 36.3Mb
  sub-directories of 1Mb or more:
    libs  35.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
File ‘BMRV/libs/BMRV.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘fastDummies’
  All declared Imports should be used.
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.7Mb
installed size is 371.2Mb
  sub-directories of 1Mb or more:
    include    8.8Mb
    lib      362.0Mb
installed size is 81.1Mb
  sub-directories of 1Mb or more:
    libs  80.6Mb
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘psychTools’
  All declared Imports should be used.
File ‘bootruin/libs/bootruin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘tidyr’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
File ‘bqtl/libs/bqtl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘CCA’ ‘brainR’ ‘elasticnet’
  All declared Imports should be used.
File ‘brainwaver/libs/brainwaver.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘connexity_small_world.o’
File ‘brainwaver/libs/brainwaver.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Branching/libs/Branching.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 40.8Mb
  sub-directories of 1Mb or more:
    libs  40.5Mb
Namespace in Imports field not imported from: ‘hexbin’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘profileModel’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R     3.5Mb
    doc   2.6Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    bin    2.7Mb
    doc    1.1Mb
    libs   2.6Mb
Namespaces in Imports field not imported from:
  ‘rworldxtra’ ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
installed size is 41.5Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  39.3Mb
Namespaces in Imports field not imported from:
  ‘mvtnorm’ ‘ssmn’
  All declared Imports should be used.
installed size is 105.5Mb
  sub-directories of 1Mb or more:
    libs  104.7Mb
File ‘BTYDplus/libs/BTYDplus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘modeldata’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
File ‘bvarsv/libs/bvarsv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
File ‘bvls/libs/bvls.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
File ‘bytescircle/libs/bytescircle.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘here’ ‘withr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/Cairo.Rcheck/00install.out’ for details.
File ‘CAMAN/libs/CAMAN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.1Mb
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.5Mb
Namespace in Imports field not imported from: ‘details’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R        1.1Mb
    data     1.5Mb
    models   2.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Namespace in Imports field not imported from: ‘g.data’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘animation’ ‘devtools’ ‘gapminder’ ‘knitr’ ‘rlist’ ‘rmarkdown’
  ‘roxygen2’ ‘sde’ ‘shiny’ ‘tidyverse’ ‘usethis’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘dplyr’ ‘tidyr’
  All declared Imports should be used.
Found the following significant warnings:
  ../inst/include/SignificantIntervalSearchFais.h:97:17: warning: 'saveSignificantInterval' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  ../inst/include/SignificantIntervalSearchFais.h:100:17: warning: 'saveTestableInterval' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
See ‘/data/gannet/ripley/R/packages/tests-clang/CASMAP.Rcheck/00install.out’ for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘broom’ ‘epitools’
  All declared Imports should be used.
File ‘catIrt/libs/catIrt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘cat/libs/cat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘rgdal’ ‘spatialEco’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   1.1Mb
    libs      2.9Mb
Namespace in Imports field not imported from: ‘prettydoc’
  All declared Imports should be used.
File ‘cbird/libs/cbird.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 216.4Mb
  sub-directories of 1Mb or more:
    libs  215.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
estim.regul: warning in matrix(res, nc = length(grid2)): partial
  argument match of 'nc' to 'ncol'
comput: no visible global function definition for ‘cor’
img.estim.regul: no visible global function definition for ‘par’
img.estim.regul: no visible global function definition for ‘image’
img.estim.regul: no visible global function definition for
  ‘heat.colors’
img.estim.regul: no visible global function definition for ‘axis’
img.estim.regul: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘par’
img.matcor: no visible global function definition for ‘image’
img.matcor: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘abline’
img.matcor: no visible global function definition for ‘layout’
loo: no visible global function definition for ‘cor’
matcor: no visible global function definition for ‘cor’
plt.cc: no visible global function definition for ‘par’
plt.cc: no visible global function definition for ‘layout’
plt.indiv: no visible global function definition for ‘plot’
plt.indiv: no visible global function definition for ‘text’
plt.indiv: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘plot’
plt.var: no visible global function definition for ‘points’
plt.var: no visible global function definition for ‘text’
plt.var: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘lines’
rcc: no visible global function definition for ‘var’
rcc: no visible global function definition for ‘cov’
Undefined global functions or variables:
  abline axis box cor cov heat.colors image layout lines par plot
  points text var
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "lines", "par", "plot", "points", "text")
  importFrom("stats", "cor", "cov", "var")
to your NAMESPACE file.
installed size is 21.9Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
File ‘cccp/libs/cccp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’
  All declared Imports should be used.
File ‘CDLasso/libs/CDLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.9Mb
File ‘CDVine/libs/CDVine.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   9.3Mb
File ‘cec2013/libs/cec2013.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.7Mb
    libs   6.9Mb
File ‘censNID/libs/censNID.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
File ‘cents/libs/cents.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘base’ ‘stats’ ‘tidyr’
  All declared Imports should be used.
File ‘cgAUC/libs/cgAUC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘cgh/libs/cgh.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘pwr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Found the following significant warnings:
  costfunctions.c:33:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  costfunctions.c:57:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/changepoint.np.Rcheck/00install.out’ for details.
File ‘changepoint/libs/changepoint.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ChargeTransport/libs/ChargeTransport.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘cheb/libs/cheb.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘foreach’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
File ‘ChIPtest/libs/ChIPtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
Namespace in Imports field not imported from: ‘forcats’
  All declared Imports should be used.
File ‘CHsharp/libs/CHsharp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘stringr’
  All declared Imports should be used.
File ‘CIFsmry/libs/CIFsmry.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘circlize’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   5.6Mb
Namespaces in Imports field not imported from:
  ‘RInside’ ‘circular’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shinyBS’
  All declared Imports should be used.
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
Running examples in ‘clam-Ex.R’ failed
The error most likely occurred in:

> ### Name: add.dates
> ### Title: Add dates to age-depth plots
> ### Aliases: add.dates
> 
> ### ** Examples
> 
>   clam(coredir=tempfile())
The run's files will be put in this folder: /tmp/RtmpqcdhmS/working_dir/RtmpKakeFh/file4d8959c256a3/Example

 Warning, dates spanning beyond the calibration curve will be truncated! 
 Calibrating dates... Error in smp[i, (1:its) + 1, ] <- calibs[[i]][sample(1:length(calibs[[i]][,  : 
  incorrect number of subscripts
Calls: clam -> .smpl
Execution halted
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
Namespaces in Imports field not imported from:
  ‘scales’ ‘sp’
  All declared Imports should be used.
File ‘ClickClust/libs/ClickClust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘climwin-Ex.R’ failed
The error most likely occurred in:

> ### Name: merge_results
> ### Title: Merge two slidingwin analyses.
> ### Aliases: merge_results
> 
> ### ** Examples
> 
> 
> #Simple test example
> #Create data from a subset of our test dataset
> #Just use two years
> biol_data <- Mass[1:2, ]
> clim_data <- MassClimate[grep(pattern = "1979|1986", x = MassClimate$Date), ]
> 
> output <- slidingwin(xvar = list(Temp = clim_data$Temp),
+                     cdate = clim_data$Date, 
+                     bdate = biol_data$Date, 
+                     baseline = lm(Mass ~ 1, data = biol_data),
+                     range = c(1, 0), 
+                     type = "relative", stat = "mean", 
+                     func = c("lin"), cmissing = FALSE, cinterval = "day")
Initialising, please wait...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  ||||||||||||||||||||||||                                               |  33%
  |                                                                            
  |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100%Error in min(modlist$ModelAICc) : invalid 'type' (list) of argument
Calls: slidingwin -> basewin -> %in%
Execution halted
Namespaces in Imports field not imported from:
  ‘car’ ‘emmeans’
  All declared Imports should be used.
File ‘clogitboost/libs/clogitboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘clogitL1/libs/clogitL1.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
possible bashism in cleanup line 15 (brace expansion):
  rm -f src/*.{o,so,mod}
  possible bashism in cleanup line 17 (brace expansion):
  rm -f config.{log,status}
  possible bashism in cleanup line 22 (brace expansion):
  rm -f vignettes/*.{tex,aux,bbl,blg,log,toc,idx,ind,ilg,out,synctex.gz}
File ‘clustering.sc.dp/libs/clustering.sc.dp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘purrr’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
File ‘ClusterStability/libs/ClusterStability.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘clusteval/libs/clusteval.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
File ‘ClustMMDD/libs/ClustMMDD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘datasets’ ‘dplyr’ ‘klaR’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
Found the following significant warnings:
  VCLDefines.c:265:2: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/clv.Rcheck/00install.out’ for details.
File ‘clv/libs/clv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘CMF/libs/CMF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘cmprsk/libs/cmprsk.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘caret’ ‘e1071’ ‘epitools’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
Imports includes 42 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   4.9Mb
File ‘COBRA/libs/COBRA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘codadiags/libs/codadiags.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘graphics’ ‘jsonlite’ ‘pander’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘methods’ ‘readr’
  All declared Imports should be used.
File ‘coenoflex/libs/coenoflex.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘coin’ ‘ggplot2’ ‘plyr’
  All declared Imports should be used.
File ‘collUtils/libs/collUtils.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘grid’ ‘gridExtra’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    extdata   2.1Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
Package suggested but not available for checking: ‘CAM’

Suggests orphaned package: ‘flare’
File ‘compareC/libs/compareC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘stringr’
  All declared Imports should be used.
installed size is 28.5Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs  26.8Mb
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    libs  22.6Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘checkmate’ ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘PearsonDS’ ‘VGAM’ ‘actuar’ ‘fExtremes’ ‘rmutil’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
File ‘ConConPiWiFun/libs/ConConPiWiFun.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘concreg/libs/concreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘compiler’ ‘rlang’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Missing or unexported object: ‘xlsx::CellBlock.default’
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data      6.5Mb
    extdata   2.6Mb
File ‘condSURV/libs/condSURV.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘cli’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reshape’
  All declared Imports should be used.
File ‘constrainedKriging/libs/constrainedKriging.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 70.4Mb
  sub-directories of 1Mb or more:
    libs  69.1Mb
Namespaces in Imports field not imported from:
  ‘geosphere’ ‘igraph’ ‘methods’ ‘rgdal’ ‘sf’
  All declared Imports should be used.
Running ‘testthat.R’ [56s/48s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(contextual)
  > 
  > test_check("contextual")
  ── 1. Error: BasicBernoulliBandit MAB policies (@test_bandits.R#205)  ──────────
  task 1 failed - "invalid 'type' (list) of argument"
  Backtrace:
   1. simulation$run()
   2. `%fun%`(...)
   3. e$fun(obj, substitute(ex), parent.frame(), e$data)
  
  ── 2. Error: BasicBernoulliBandit Long (@test_bandits.R#232)  ──────────────────
  task 1 failed - "invalid 'type' (list) of argument"
  Backtrace:
   1. simulation$run()
   2. `%fun%`(...)
   3. e$fun(obj, substitute(ex), parent.frame(), e$data)
  
  ── 3. Error: ContextualPrecachingBandit MAB policies (@test_bandits.R#259)  ────
  task 1 failed - "invalid 'type' (list) of argument"
  Backtrace:
   1. simulation$run()
   2. `%fun%`(...)
   3. e$fun(obj, substitute(ex), parent.frame(), e$data)
  
  ── 4. Error: (unknown) (@test_history.R#12)  ───────────────────────────────────
  task 1 failed - "invalid 'type' (list) of argument"
  Backtrace:
   1. Simulator$new(agents, horizon = 3, simulations = 3, do_parallel = FALSE, ...
   2. `%fun%`(...)
   3. e$fun(obj, substitute(ex), parent.frame(), e$data)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 105 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 4 ]
  1. Error: BasicBernoulliBandit MAB policies (@test_bandits.R#205) 
  2. Error: BasicBernoulliBandit Long (@test_bandits.R#232) 
  3. Error: ContextualPrecachingBandit MAB policies (@test_bandits.R#259) 
  4. Error: (unknown) (@test_history.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘contoureR/libs/contoureR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘MASS’ ‘geepack’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   5.0Mb
Namespace in Imports field not imported from: ‘mcc’
  All declared Imports should be used.
File ‘cord/libs/cord.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’ ‘re2r’ ‘rmarkdown’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
Running examples in ‘corpus-Ex.R’ failed
The error most likely occurred in:

> ### Name: text_locate
> ### Title: Searching for Terms
> ### Aliases: text_count text_detect text_locate text_match text_sample
> ###   text_subset
> 
> ### ** Examples
> 
> text <- c("Rose is a rose is a rose is a rose.",
+           "A rose by any other name would smell as sweet.",
+           "Snow White and Rose Red")
> 
> text_count(text, "rose")
[1] 4 1 1
> text_detect(text, "rose")
[1] TRUE TRUE TRUE
> text_locate(text, "rose")
Error in sum(colwidths) : invalid 'type' (list) of argument
Calls: <Anonymous> ... print.corpus_text_locate -> format.corpus_text_locate
Execution halted
Running ‘testthat.R’ [12s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(corpus)
  > 
  > test_check("corpus")
  -- 1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161
  invalid 'type' (list) of argument
  Backtrace:
    1. base::strsplit(capture_output(print(loc), width = 76), "\n")
    9. corpus:::print.corpus_text_locate(loc)
   10. corpus:::format.corpus_text_locate(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 612 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘profr’ ‘xtable’
  All declared Imports should be used.
Package suggested but not available for checking: ‘xcms’
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    libs  28.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    help   1.6Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   6.6Mb
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
File ‘COUSCOus/libs/COUSCOus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Namespace in Imports field not imported from: ‘gstat’
  All declared Imports should be used.
File ‘covBM/libs/covBM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘dplyr’ ‘ggridges’ ‘markdown’ ‘shinyjs’ ‘tidyr’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘misc3d’
  All declared Imports should be used.
File ‘CoxBoost/libs/CoxBoost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘coxinterval/libs/coxinterval.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
Namespace in Imports field not imported from: ‘coxme’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
File ‘CoxPlus/libs/CoxPlus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘coxrobust/libs/coxrobust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘grDevices’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘cents’
  All declared Imports should be used.
File ‘cpm/libs/cpm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
Running examples in ‘cptec-Ex.R’ failed
The error most likely occurred in:

> ### Name: prev7dias
> ### Title: Retrieve 7 days weather forecast data from CPTEC/INPE
> ### Aliases: prev7dias
> ### Keywords: brazil forecast weather
> 
> ### ** Examples
> 
> ## Requesting weather forecast from the city of Campo Grande/MS
> prev7dias(225)
Error in open.connection(x, "rb") : HTTP error 404.
Calls: prev7dias ... read_xml.character -> read_xml.connection -> open -> open.connection
Execution halted
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
File ‘cqrReg/libs/cqrReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
Note: found 11 marked Latin-1 strings
  Note: found 57 marked UTF-8 strings
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Namespaces in Imports field not imported from:
  ‘gdistance’ ‘raster’
  All declared Imports should be used.
File ‘credule/libs/credule.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘glue’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘r6extended’
  All declared Imports should be used.
File ‘crrp/libs/crrp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘crrSC/libs/crrSC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘crskdiag/libs/crskdiag.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 29.9Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  27.8Mb
Namespace in Imports field not imported from: ‘qte’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    shp   7.8Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data  10.9Mb
Note: found 59670 marked Latin-1 strings
  Note: found 16 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘epitools’ ‘rpivotTable’ ‘shinyMatrix’
  All declared Imports should be used.
installed size is 113.0Mb
  sub-directories of 1Mb or more:
    R       1.1Mb
    libs  109.9Mb
Namespaces in Imports field not imported from:
  ‘numDeriv’ ‘pkgbuild’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
File ‘cusp/libs/cusp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘rlang’ ‘tidyselect’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lattice’
  All declared Imports should be used.
File ‘cvxbiclustr/libs/cvxbiclustr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘cvxclustr/libs/cvxclustr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  'gurobi', 'Rcplex', 'rcbc'
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    doc    1.2Mb
    help   1.0Mb
    libs   5.6Mb
File ‘cycleRtools/libs/cycleRtools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 26.8Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
Note: found 4 marked Latin-1 strings
  Note: found 21 marked UTF-8 strings
File ‘DALY/libs/DALY.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘expm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘compiler’ ‘dplyr’ ‘magrittr’ ‘mlbench’
  All declared Imports should be used.
File ‘darts/libs/darts.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
Package suggested but not available for checking: ‘aws.s3’

Requires orphaned package: ‘bit’
Namespace in Imports field not imported from: ‘DatabaseConnectorJars’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   4.1Mb
Namespace in Imports field not imported from: ‘miniUI’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘shinyFiles’ ‘shinycssloaders’ ‘shinyjs’ ‘shinythemes’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
.onLoad : <anonymous>: no visible global function definition for
  ‘read.table’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbConnect’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbListTables’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbExistsTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbReadTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbWriteTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbDisconnect’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbRemoveTable’
Undefined global functions or variables:
  dbConnect dbDisconnect dbExistsTable dbListTables dbReadTable
  dbRemoveTable dbWriteTable read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
File ‘datamap/libs/datamap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   5.5Mb
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
installed size is 51.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  49.0Mb
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/datautils.Rcheck/00install.out’ for details.
File ‘dblcens/libs/dblcens.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘dplyr’
  All declared Imports should be used.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
File ‘DCluster/libs/DCluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘CDM’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
File ‘DDHFm/libs/DDHFm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    libs  22.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
File ‘decon/libs/decon.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘UScensus2010’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘UScensus2010’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘JavaGD’ ‘OpenStreetMap’ ‘maptools’ ‘rgdal’ ‘scales’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘deformula/libs/deformula.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘assertthat’
  All declared Imports should be used.
installed size is 87.1Mb
  sub-directories of 1Mb or more:
    libs  84.3Mb
File ‘delt/libs/delt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
File ‘DendSer/libs/DendSer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘denpro/libs/denpro.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc       4.9Mb
    extdata   2.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
File ‘depth/libs/depth.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.8Mb
    help   1.4Mb
    libs   3.2Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
File ‘desire/libs/desire.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.4Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘utils’
  All declared Imports should be used.
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   7.2Mb
File ‘dfphase1/libs/dfphase1.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 53.5Mb
  sub-directories of 1Mb or more:
    libs  52.9Mb
installed size is 26.7Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  24.7Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
File ‘dgof/libs/dgof.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘mgcv’
  All declared Imports should be used.
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    doc           9.7Mb
    htmlwidgets   5.9Mb
File ‘DiceOptim/libs/DiceOptim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 37 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.

Requires orphaned package: ‘clValid’
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb
File ‘diffIRT/libs/diffIRT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘sf’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gplots’
  All declared Imports should be used.
File ‘diffrprojects/libs/diffrprojects.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
File ‘DiffusionRgqd/libs/DiffusionRgqd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘DiffusionRimp/libs/DiffusionRimp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
File ‘DiffusionRjgqd/libs/DiffusionRjgqd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
File ‘dils/libs/dils.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘DIME/libs/DIME.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘sandwich’
  All declared Imports should be used.
File ‘DIRECT/libs/DIRECT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    libs  21.5Mb
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’ ‘splancs’ ‘utils’
  All declared Imports should be used.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
File ‘dismo/libs/dismo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘dissUtils/libs/dissUtils.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘proxy’
  All declared Imports should be used.
File ‘distory/libs/distory.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘distr.Rnw’ using knitr
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "panel.first" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "panel.last" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "panel.first" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "panel.last" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "panel.first" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "panel.last" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "log" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "panel.first" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "panel.last" is not a graphical parameter
Quitting from lines 2500-2529 (distr.Rnw) 
Error: processing vignette 'distr.Rnw' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘distr.Rnw’

SUMMARY: processing the following file failed:
  ‘distr.Rnw’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘distrMod-Ex.R’ failed
The error most likely occurred in:

> ### Name: MCEstimate-class
> ### Title: MCEstimate-class.
> ### Aliases: MCEstimate-class MDEstimate-class MLEstimate-class
> ###   CvMMDEstimate-class criterion criterion,MCEstimate-method
> ###   criterion.fct criterion.fct,MCEstimate-method
> ###   startPar,MCEstimate-method method method,MCEstimate-method optimwarn
> ###   optimwarn,MCEstimate-method optimReturn optimReturn,MCEstimate-method
> ###   criterion<- criterion<-,MCEstimate-method
> ###   coerce,MCEstimate,mle-method show,MCEstimate-method
> ###   profile,MCEstimate-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> ## (empirical) Data
> x <- rgamma(50, scale = 0.5, shape = 3)
> 
> ## parametric family of probability measures
> G <- GammaFamily(scale = 1, shape = 2)
> 
> MDEstimator(x, G)
Evaluations of Minimum Kolmogorov distance estimate  :
------------------------------------------------------
An object of class “MDEstimate” 
generated by call
  MDEstimator(x = x, ParamFamily = G)
samplesize:   50
estimate:
    scale     shape 
0.3398645 4.2654569 
Criterion:
Kolmogorov distance 
         0.06350364 
> (m <- MLEstimator(x, G))
Evaluations of Maximum likelihood estimate:
-------------------------------------------
An object of class “MLEstimate” 
generated by call
  MLEstimator(x = x, ParamFamily = G)
samplesize:   50
estimate:
     scale        shape   
  0.34200800   4.06028564 
 (0.07002713) (0.78099026)
asymptotic (co)variance (multiplied with samplesize):
           scale     shape
scale  0.2451899 -2.568863
shape -2.5688629 30.497289
Criterion:
negative log-likelihood 
                47.9651 
> m.mle <- as(m,"mle")
> par(mfrow=c(1,2))
> profileM <- profile(m)
Error in ixnfix0[[i]] : subscript out of bounds
Calls: profile -> profile -> .local -> profile -> profile -> .local
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
File ‘dkDNA/libs/dkDNA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    include  16.7Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   2.1Mb
    libs   4.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
File ‘DNAtools/libs/DNAtools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘GOstats’ ‘caTools’ ‘fdrtool’
  All declared Imports should be used.
File ‘documair/libs/documair.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs  11.6Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘parallel’ ‘rgdal’ ‘sp’ ‘tensorflow’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/dpglasso.Rcheck/00install.out’ for details.
File ‘dpglasso/libs/dpglasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
installed size is 33.0Mb
  sub-directories of 1Mb or more:
    libs  30.7Mb
Namespaces in Imports field not imported from:
  ‘bit64’ ‘rstudioapi’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Namespaces in Imports field not imported from:
  ‘tools’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘broom’ ‘colorspace’ ‘colourpicker’ ‘cowplot’
  ‘igraph’ ‘magrittr’ ‘shinyBS’ ‘shinyWidgets’ ‘shinydashboard’
  ‘shinythemes’ ‘tidyverse’ ‘visNetwork’
  All declared Imports should be used.
File ‘drmdel/libs/drmdel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘readr’ ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rJava’ ‘tools’ ‘xtable’
  All declared Imports should be used.
File ‘dse/libs/dse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘dsmodels-Ex.R’ failed
The error most likely occurred in:

> ### Name: dscurve
> ### Title: Parametric curves or a graph of functions
> ### Aliases: dscurve
> 
> ### ** Examples
> 
> library(dsmodels)
> 
> fun <- function(X,Y) {
+   list(
+     X/exp(Y),
+     Y/exp(X)
+   )
+ }
> 
> model <- dsmodel(fun, title = "Points on a One-Dimensional Curve")
> range <- dsrange(-2:2,-2:2, discretize = 0.5)
> 
> # Add the graph of a function and its image in blue.
> graphcrv <- dscurve(function(x) x^2,
+                     col = "orange",
+                     image = "blue",
+                     discretize = TRUE,
+                     xlim = c(-2,2))
> model + range +	graphcrv
Error in -rid : invalid argument to unary operator
Calls: +.dsproto ... <Anonymous> -> f -> <Anonymous> -> f -> <Anonymous> -> f
Execution halted
File ‘DStree/libs/DStree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.7Mb
Namespaces in Imports field not imported from:
  ‘digest’ ‘dplyr’
  All declared Imports should be used.
installed size is 38.1Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs  31.7Mb
Namespaces in Imports field not imported from:
  ‘maptools’ ‘tools’
  All declared Imports should be used.
File ‘dynpred/libs/dynpred.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Namespace in Imports field not imported from: ‘desc’
  All declared Imports should be used.
Package suggested but not available for checking: ‘dyndimred’

Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘hdf5r’ ‘jsonlite’
  All declared Imports should be used.
Running examples in ‘dynwrap-Ex.R’ failed
The error most likely occurred in:

> ### Name: add_dimred
> ### Title: Add or create a dimensionality reduction
> ### Aliases: add_dimred is_wrapper_with_dimred get_dimred
> ### Keywords: adapt_trajectory
> 
> ### ** Examples
> 
> dataset <- example_dataset
> dataset <- add_dimred(
+   dataset,
+   dyndimred::dimred_landmark_mds
+ )
Error in loadNamespace(name) : there is no package called ‘dyndimred’
Calls: add_dimred ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   3.5Mb
File ‘EasyABC/libs/EasyABC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’ ‘scales’ ‘xtable’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘base64enc’ ‘knitr’ ‘markdown’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘ebdbNet/libs/ebdbNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘EBEN/libs/EBEN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘EBglmnet/libs/EBglmnet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘methods’ ‘mgcv’ ‘rappdirs’ ‘rgdal’ ‘scales’ ‘tools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
File ‘ecolMod/libs/ecolMod.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘tnet’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dae’ ‘dplyr’
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
installed size is 112.9Mb
  sub-directories of 1Mb or more:
    libs  112.1Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc       5.2Mb
    extdata   5.1Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘eco’
  All declared Imports should be used.
File ‘eiwild/libs/eiwild.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘tidyr’
  All declared Imports should be used.
File ‘elec.strat/libs/elec.strat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
File ‘EL/libs/EL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘AER’ ‘pROC’ ‘pander’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   4.0Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘Rtsne’ ‘uwot’
  All declared Imports should be used.
File ‘EMC/libs/EMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘graphics’ ‘maptools’ ‘rgeos’
  All declared Imports should be used.
File ‘emdist/libs/emdist.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  17.8Mb
'library' or 'require' calls to packages already attached by Depends:
  ‘clusterSim’ ‘earth’
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘clusterSim’ ‘earth’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.9Mb
File ‘emoa/libs/emoa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.5Mb
Note: found 23639 marked Latin-1 strings
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    lib    3.5Mb
    libs   1.2Mb
Running examples in ‘enaR-Ex.R’ failed
The error most likely occurred in:

> ### Name: enaAll
> ### Title: Conduct All Major ENA
> ### Aliases: enaAll
> 
> ### ** Examples
> 
> 
> 
> 
> data(troModels)
> output = enaAll(troModels[[6]])
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
enaR
 --- call from context --- 
structure.statistics(A)
 --- call from argument --- 
if (class(A) != "matrix") {
    warning("A is not a matrix class object")
}
 --- R stacktrace ---
where 1: structure.statistics(A)
where 2: enaStructure(x)
where 3: enaAll(troModels[[6]])

 --- value of length: 2 type: logical ---
[1] FALSE  TRUE
 --- function from context --- 
function (A = "adjacency matrix") 
{
    if (class(A) != "matrix") {
        warning("A is not a matrix class object")
    }
    n <- dim(A)[1]
    L <- sum(A)
    C <- L/n^2
    LD <- L/n
    e <- eigen(A)$values
    aer <- round(abs(e), digits = 7)
    mlam1A <- length(which(aer == aer[1]))
    ppr <- sum(mExp(A, 200))/sum(mExp(A, 199))
    lam1A <- abs(e[1])
    d <- abs(lam1A - LD)
    if ((n - mlam1A) > 0) {
        lam2A <- abs(e[(1 + mlam1A)])
        rho <- lam1A/abs(lam2A)
        R <- abs(e[n]) - abs(e[n - 1])/(abs(e[n - 1]) - abs(e[1]))
    }
    else {
        lam2A <- NA
        rho <- NA
        R <- NA
    }
    sp1 <- as.vector(scc(A)$sp)
    no.scc <- sp1[1]
    no.scc.big <- sp1[2]
    pscc <- sp1[3]
    sp <- cbind(n, L, C, LD, ppr, lam1A, mlam1A, rho, R, d, no.scc, 
        no.scc.big, pscc)
    return(sp)
}
<bytecode: 0x65f5570>
<environment: namespace:enaR>
 --- function search by body ---
Function structure.statistics in namespace enaR has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(A) != "matrix") { : the condition has length > 1
Calls: enaAll -> enaStructure -> structure.statistics
Execution halted
File ‘endogMNP/libs/endogMNP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘bitops’ ‘rjson’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘SPECIES’ ‘ade4’
  All declared Imports should be used.
File ‘EntropyEstimation/libs/EntropyEstimation.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking: 'xcms', 'MSnbase'
Namespaces in Imports field not imported from:
  ‘DT’ ‘broom’ ‘crosstalk’ ‘dplyr’ ‘ggraph’ ‘igraph’ ‘plotly’
  ‘rmarkdown’ ‘shinythemes’
  All declared Imports should be used.
File ‘enviPick/libs/enviPick.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘EnviroStat/libs/EnviroStat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    doc    3.3Mb
    help   3.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
Namespaces in Imports field not imported from:
  ‘readr’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘colorspace’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘htmlwidgets’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘graphics’ ‘knitr’ ‘rmarkdown’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘ggplot2’ ‘knitr’ ‘pander’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘testthat’ ‘tidyr’
  All declared Imports should be used.
Found the following files/directories:
  ‘CATane_4_27_.png’ ‘CATavz_4_37_.png’ ‘CATbaa_4_13_.png’
  ‘CATbko_4_36_.png’ ‘CATbuu_1_45_.png’ ‘CATbuu_4_45_.png’
  ‘CATbuu_5_45_.png’ ‘CATbzp_4_50_.png’ ‘CATbzx_4_29_.png’
  ‘CATdbn_1_18_.png’ ‘CATdbn_3_18_.png’ ‘CATdmq_4_49_.png’
  ‘CATepg_4_44_.png’ ‘CATfgb_4_7_.png’ ‘CATfgb_5_7_.png’
  ‘CATfnu_4_21_.png’ ‘CATfnu_5_21_.png’ ‘CATham_4_14_.png’
  ‘CATham_5_14_.png’ ‘CATipy_4_19_.png’ ‘CATjoj_2_22_.png’
  ‘CATjpz_4_35_.png’ ‘CATjxh_1_31_.png’ ‘CATlbg_4_40_.png’
  ‘CATlkr_4_32_.png’ ‘CATlzh_4_43_.png’ ‘CATntj_4_24_.png’
  ‘CAToti_5_28_.png’ ‘CATppt_4_4_.png’ ‘CATppt_5_4_.png’
  ‘CATpsl_4_23_.png’ ‘CATpyn_4_20_.png’ ‘CATqoq_4_8_.png’
  ‘CATrck_4_26_.png’ ‘CATrjo_4_30_.png’ ‘CATsgu_4_9_.png’
  ‘CATsgu_5_9_.png’ ‘CATtez_4_34_.png’ ‘CATudg_4_16_.png’
  ‘CATuhl_4_39_.png’ ‘CATuhl_5_39_.png’ ‘CATvbb_4_41_.png’
  ‘CATwgo_4_17_.png’ ‘CATwgo_5_17_.png’ ‘CATwrn_4_46_.png’
  ‘CATwwh_4_10_.png’ ‘CATxmc_2_48_.png’ ‘CATxni_5_6_.png’ ‘ID_5_1_.png’
  ‘ae_dotplot_traitxqtl.png’ ‘ae_siplot_traitxqtl.png’
  ‘histogram_controled_etrait.png’ ‘histogram_qtl.png’
  ‘lod_dotplot_traitxqtl.png’ ‘lod_siplot_traitxqtl.png’
File ‘equivalence/libs/equivalence.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘cubature’ ‘rootSolve’
  All declared Imports should be used.
File ‘erboost/libs/erboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘statnet’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.1Mb
Namespace in Imports field not imported from: ‘signal’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘plyr’ ‘sp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘colorRamps’ ‘colourpicker’ ‘dichromat’ ‘leaflet’
  ‘lwgeom’ ‘raster’ ‘shinycssloaders’ ‘shinydashboard’ ‘shinyjs’ ‘tmap’
  ‘viridis’ ‘zip’
  All declared Imports should be used.
File ‘ESGtoolkit/libs/ESGtoolkit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘ESKNN-Ex.R’ failed
The error most likely occurred in:

> ### Name: Predict.esknnClass
> ### Title: Class predictions from ensemble of subset of k-nearest
> ###   neighbours
> ### Aliases: Predict.esknnClass
> ### Keywords: packages
> 
> ### ** Examples
> 
> # Load the data
> 
>   data(hepatitis)
>   data <- hepatitis
> 
> # Spliting the data into testing and training parts.
> 
>   Class <- data[,names(data)=="Class"]
>   data$Class<-as.factor(as.numeric(Class)-1)
>   train <- data[sample(1:nrow(data),0.7*nrow(data)),]
>   test <- data[-(sample(1:nrow(data),0.7*nrow(data))),]
>   ytrain<-train[,names(train)=="Class"]
>   xtrain<-train[,names(train)!="Class"]
>   xtest<-test[,names(test)!="Class"]
>   ytest <- test[,names(test)=="Class"]
>   
> # Trian esknnClass using training data
> 
> model<-esknnClass(xtrain, ytrain,k=NULL)
Error in order(fBS, decreasing = FALSE) : 
  unimplemented type 'list' in 'orderVector1'
Calls: esknnClass -> order
Execution halted
File ‘EstHer/libs/EstHer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    libs  25.7Mb
File ‘etasFLP/libs/etasFLP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘msm’
  All declared Imports should be used.
File ‘evdbayes/libs/evdbayes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Namespaces in Imports field not imported from:
  ‘curl’ ‘openxlsx’ ‘stringr’
  All declared Imports should be used.
File ‘exactLoglinTest/libs/exactLoglinTest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘exif/libs/exif.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘polynom’
  All declared Imports should be used.
print.cdf : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.cdf: warning in get("x", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.cdf: warning in get("y", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.ogive : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.ogive: warning in get("x", env = environment(x)): partial
  argument match of 'env' to 'envir'
print.ogive: warning in get("y", env = environment(x)): partial
  argument match of 'env' to 'envir'
quantile.expert: warning in formatC(paste(100 * probs, "%", sep = ""),
  format = "fg", wid = 1, digits = dig): partial argument match of
  'wid' to 'width'
MS: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘RColorBrewer’ ‘Rcpp’ ‘e1071’ ‘foreach’ ‘gam’ ‘ggplot2’
  ‘glmnet’ ‘nnet’ ‘polspline’ ‘repmis’ ‘splines’ ‘xgboost’
  All declared Imports should be used.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
File ‘extremis/libs/extremis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘extWeibQuant/libs/extWeibQuant.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ezglm/libs/ezglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘factorcpt/libs/factorcpt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘forcats’ ‘formula.tools’
  All declared Imports should be used.
File ‘factorQR/libs/factorQR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.9Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘caTools’ ‘httr’ ‘jsonlite’ ‘rlang’
  All declared Imports should be used.
File ‘falcon/libs/falcon.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fame/libs/fame.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Familias/libs/Familias.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fanc/libs/fanc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘far/libs/far.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   3.5Mb
File ‘fAsianOptions/libs/fAsianOptions.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fastAdaboost/libs/fastAdaboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FastBandChol/libs/FastBandChol.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fastclime/libs/fastclime.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fastcmh/libs/fastcmh.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fastdigest/libs/fastdigest.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.2Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Namespace in Imports field not imported from: ‘RobustGaSP’
  All declared Imports should be used.
installed size is 40.2Mb
  sub-directories of 1Mb or more:
    libs  40.0Mb
File ‘FastGP/libs/FastGP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  15.5Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.4Mb
File ‘fastmatch/libs/fastmatch.so’:
  Found non-API call to R: ‘match5’
File ‘fastmatch/libs/fastmatch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      7.5Mb
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/data/gannet/ripley/R/packages/tests-clang/FastRWeb.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘FastRWeb/libs/null.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fasttime/libs/fasttime.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘whisker’
  All declared Imports should be used.
File ‘fBasics/libs/fBasics.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.1Mb
File ‘FBFsearch/libs/FBFsearch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is 46.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  43.8Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/fdaPDE.Rcheck/00install.out’ for details.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   8.6Mb
Namespaces in Imports field not imported from:
  ‘usethis’ ‘utils’
  All declared Imports should be used.
Note: found 3 marked Latin-1 strings
  Note: found 3 marked UTF-8 strings
File ‘FD/libs/FD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FDRreg/libs/FDRreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fdrtool/libs/fdrtool.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘testthat’
  All declared Imports should be used.
File ‘fechner/libs/fechner.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘rvest’ ‘stringi’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘prettycode’
  All declared Imports should be used.
File ‘FFD/libs/FFD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ff/libs/ff.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Namespace in Imports field not imported from: ‘pROC’
  All declared Imports should be used.
File ‘fGarch/libs/fGarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FGSG/libs/FGSG.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
File ‘FIACH/libs/FIACH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘numDeriv’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rappdirs’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘mapproj’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   2.2Mb
File ‘FisHiCal/libs/FisHiCal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fishMod/libs/fishMod.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘grid’ ‘png’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
File ‘FitARMA/libs/FitARMA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FitAR/libs/FitAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘XML’ ‘gglasso’ ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   3.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
File ‘flars/libs/flars.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘flashClust/libs/flashClust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
File ‘flock/libs/flock.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R   6.4Mb
Namespace in Imports field not imported from: ‘limSolve’
  All declared Imports should be used.
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘stats’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
File ‘fmrs/libs/fmrs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FMStable/libs/FMStable.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fNonlinear/libs/fNonlinear.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
Namespace in Imports field not imported from: ‘grid’
  All declared Imports should be used.
File ‘fOptions/libs/fOptions.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
File ‘forensim/libs/forensim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rgeos’ ‘viridis’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pkgKitten’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘viridis’
  All declared Imports should be used.
File ‘fpow/libs/fpow.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘fable’ ‘fabletools’ ‘feasts’ ‘ggplot2’ ‘lubridate’ ‘tibble’
  ‘tidyr’ ‘tsibble’ ‘tsibbledata’
  All declared Imports should be used.
File ‘fractional/libs/fractional.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘base’ ‘pbapply’ ‘stringr’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   6.0Mb
Namespaces in Imports field not imported from:
  ‘jsonlite’ ‘rhandsontable’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’
  ‘shinythemes’
  All declared Imports should be used.
Found the following significant warnings:
  c_hd_mf.cpp:157:12: warning: explicitly assigning value of variable of type 'Eigen::VectorXd' (aka 'Matrix<double, Dynamic, 1>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/FRegSigCom.Rcheck/00install.out’ for details.
installed size is 67.9Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs  66.2Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   7.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
Package suggested but not available for checking: ‘dggrids’
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    2.1Mb
installed size is 61.3Mb
  sub-directories of 1Mb or more:
    libs  60.9Mb
File ‘frontiles/libs/frontiles.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘class’ ‘mlbench’ ‘neuralnet’ ‘rpart’
  All declared Imports should be used.
Running examples in ‘FSinR-Ex.R’ failed
The error most likely occurred in:

> ### Name: selectDifference
> ### Title: Select difference
> ### Aliases: selectDifference
> 
> ### ** Examples
> 
> ## Select Difference for iris dataset (filter method)
> # Selects features in descending order as long as the difference between them is less than 0.1
> selectDifference(iris, 'Species', chiSquared, 0.1) 
Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length
Calls: selectDifference ... row.names<- -> row.names<-.data.frame -> .rowNamesDF<-
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘FSinR.Rmd’ using rmarkdown
Loading required package: lattice
Loading required package: ggplot2

Attaching package: 'FSinR'

The following object is masked from 'package:stats':

    ts

Quitting from lines 87-88 (FSinR.Rmd) 
Error: processing vignette 'FSinR.Rmd' failed with diagnostics:
invalid subscript type 'list'
--- failed re-building ‘FSinR.Rmd’

--- re-building ‘methods.Rmd’ using rmarkdown
--- finished re-building ‘methods.Rmd’

SUMMARY: processing the following file failed:
  ‘FSinR.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
File ‘ftnonpar/libs/ftnonpar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
File ‘fts/libs/fts.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fugeR/libs/fugeR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    data  16.2Mb
Found the following significant warnings:
  FunctionalNetworks.c:223:17: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/FunctionalNetworks.Rcheck/00install.out’ for details.
File ‘FunctionalNetworks/libs/FunctionalNetworks.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fUnitRoots/libs/fUnitRoots.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 31.6Mb
  sub-directories of 1Mb or more:
    libs  31.4Mb
File ‘futureheatwaves/libs/futureheatwaves.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
fuzzyBHexact: warning in round(pvals, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.minus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.plus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(pvals, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(tau, d = 4): partial argument match of
  'd' to 'digits'
probRejTies: no visible binding for global variable ‘nn’
Undefined global functions or variables:
  nn
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb
File ‘gafit/libs/gafit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘maptools’ ‘rgeos’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
File ‘GAMBoost/libs/GAMBoost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘gamesGA-Ex.R’ failed
The error most likely occurred in:

> ### Name: games_ga
> ### Title: Games genetic algorithm:
> ### Aliases: games_ga
> 
> ### ** Examples
> 
> games_ga(CC = 3, CD = 0, DC = 5, DD = 1, generations = 100, rounds = 100)
Error in strsplit(x = genomes[i], split = " ") : non-character argument
Calls: games_ga -> strsplit
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(gamesGA)
  > 
  > test_check("gamesGA")
  ── 1. Error: Correct column in gamesGA return (@test-gamesGA.R#5)  ─────────────
  non-character argument
  Backtrace:
   1. testthat::expect_equal(...)
   4. gamesGA::games_ga(...)
   5. base::strsplit(x = genomes[i], split = " ")
  
  ── 2. Error: Fitness vector length and type accurate (@test-gamesGA.R#17)  ─────
  non-character argument
  Backtrace:
   1. testthat::expect_equal(...)
   4. gamesGA::games_ga(...)
   5. base::strsplit(x = genomes[i], split = " ")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 18 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: Correct column in gamesGA return (@test-gamesGA.R#5) 
  2. Error: Fitness vector length and type accurate (@test-gamesGA.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘MASS’ ‘gamlss’
  All declared Imports should be used.
finterp.data.frame: no visible global function definition for
  ‘as.formula’
finterp.data.frame: no visible global function definition for ‘terms’
finterp.data.frame: no visible global function definition for
  ‘model.matrix’
finterp.data.frame: no visible global function definition for
  ‘model.frame’
finterp.default: no visible global function definition for ‘terms’
finterp.default: no visible global function definition for
  ‘model.matrix’
finterp.default: no visible global function definition for
  ‘model.frame’
gamlss.nl: no visible global function definition for ‘nlm’
nl: no visible global function definition for ‘is’
nlgamlss: no visible global function definition for ‘NO’
nlgamlss: no visible global function definition for ‘as.gamlss.family’
nlgamlss: no visible global function definition for ‘nlm’
nlgamlss: no visible global function definition for ‘cov2cor’
summary.nlgamlss: no visible global function definition for ‘coef’
summary.nlgamlss: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  NO as.formula as.gamlss.family coef cov2cor is model.frame
  model.matrix nlm pnorm terms
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "as.formula", "coef", "cov2cor", "model.frame",
             "model.matrix", "nlm", "pnorm", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   4.2Mb
installed size is 115.9Mb
  sub-directories of 1Mb or more:
    libs  115.4Mb
Namespaces in Imports field not imported from:
  ‘methods’ ‘rstantools’
  All declared Imports should be used.
installed size is 78.0Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     74.7Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
File ‘gausscov/libs/gausscov.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  18.5Mb
File ‘gbp/libs/gbp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gCat/libs/gCat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘gcbd.Rnw’ using Sweave
Warning in packageDescription("gputools") :
  no package 'gputools' was found
Error: processing vignette 'gcbd.Rnw' failed with diagnostics:
at gcbd.Rnw:860, subscript out of bounds
--- failed re-building ‘gcbd.Rnw’

SUMMARY: processing the following file failed:
  ‘gcbd.Rnw’

Error: Vignette re-building failed.
Execution halted
File ‘gconcord/libs/gconcord.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘GCPM/libs/GCPM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 45.6Mb
  sub-directories of 1Mb or more:
    L8NY18   2.3Mb
    libs    41.9Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
File ‘gdmp/libs/gdmp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘GEEaSPU/libs/GEEaSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
File ‘gelnet/libs/gelnet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
File ‘gemtc/libs/gemtc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘pracma’ ‘rlang’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘NMF’ ‘RColorBrewer’ ‘VennDiagram’ ‘clValid’ ‘data.table’ ‘grid’
  ‘gtools’ ‘pca3d’ ‘rmarkdown’ ‘scales’ ‘shinydashboard’ ‘shinyjs’
  ‘statmod’ ‘stringr’
  All declared Imports should be used.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R  10.2Mb
Namespace in Imports field not imported from: ‘repmis’
  All declared Imports should be used.
File ‘genepi/libs/genepi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  11.6Mb
File ‘GenKern/libs/GenKern.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘genSurv/libs/genSurv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  runMCMCfunc.cpp:40:40: warning: expression result unused [-Wunused-value]
  runMCMCfunc.cpp:41:43: warning: expression result unused [-Wunused-value]
  runMCMCfunc.cpp:55:42: warning: expression result unused [-Wunused-value]
  runMCMCfunc.cpp:56:45: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/geoCount.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   5.5Mb
File ‘geoCount/libs/geoCount.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘phonTools’ ‘rgdal’ ‘rgeos’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.2Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   7.3Mb
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    data  26.0Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R         9.0Mb
    extdata   1.6Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  13.0Mb
Namespace in Imports field not imported from: ‘velociraptr’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    data   3.5Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘utils’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Running examples in ‘gert-Ex.R’ failed
The error most likely occurred in:

> ### Name: fetch
> ### Title: Push and Pull
> ### Aliases: fetch git_fetch git_push git_clone git_pull
> 
> ### ** Examples
> 
> {# Clone a small repository
+ git_dir <- file.path(tempdir(), 'antiword')
+ git_clone('https://github.com/ropensci/antiword', git_dir)
+ 
+ # Change into the repo directory
+ olddir <- getwd()
+ setwd(git_dir)
+ 
+ # Show some stuff
+ git_log()
+ git_branch_list()
+ git_remote_list()
+ 
+ # Add a file
+ write.csv(iris, 'iris.csv')
+ git_add('iris.csv')
+ 
+ # Commit the change
+ jerry <- git_signature("Jerry", "jerry@hotmail.com")
+ git_commit('added the iris file', author = jerry)
+ 
+ # Now in the log:
+ git_log()
+ 
+ # Cleanup
+ setwd(olddir)
+ unlink(git_dir, recursive = TRUE)
+ }

 *** caught segfault ***
address 0xc800010009, cause 'memory not mapped'

Traceback:
 1: git_clone("https://github.com/ropensci/antiword", git_dir)
An irrecoverable exception occurred. R is aborting now ...
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘lubridate’ ‘readr’ ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘bitops’ ‘data.table’ ‘dplyr’ ‘httr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘scales’ ‘stringr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘XML’
  All declared Imports should be used.
File ‘gettz/libs/gettz.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘plotly’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘corrr’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Namespaces in Imports field not imported from:
  ‘GGEBiplotGUI’ ‘gge’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘grDevices’ ‘scales’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘grid’ ‘rstan’
  All declared Imports should be used.
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  18.5Mb
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘lazyeval’ ‘readr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘gtable’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggforce’ ‘webshot’ ‘ztable’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: ‘__var_41_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/gglasso.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘graph’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘sna’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grid’ ‘scales’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘reshape2’ ‘viridisLite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gcookbook’ ‘ggthemes’ ‘moonBook’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘checkmate’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grDevices’
  All declared Imports should be used.
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Formula’ ‘GGally’ ‘Hmisc’ ‘colourpicker’ ‘dplyr’ ‘ggpmisc’
  ‘ggpubr’ ‘ggrepel’ ‘ggstance’ ‘grDevices’ ‘grid’ ‘gridExtra’
  ‘lazyeval’ ‘markdown’ ‘plotly’ ‘quantreg’ ‘rlang’ ‘shinyjs’
  ‘survival’ ‘survminer’ ‘table1’ ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘randomForest’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.9Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
Namespaces in Imports field not imported from:
  ‘reshape2’ ‘rosm’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
File ‘GiRaF/libs/GiRaF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘mockery’
  All declared Imports should be used.
File ‘GLIDE/libs/GLIDE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gllm/libs/gllm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 49.2Mb
  sub-directories of 1Mb or more:
    libs  48.0Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
File ‘GLMaSPU/libs/GLMaSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
File ‘glmgraph/libs/glmgraph.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 40.8Mb
  sub-directories of 1Mb or more:
    libs  40.1Mb
installed size is 46.5Mb
  sub-directories of 1Mb or more:
    libs  45.6Mb
installed size is 49.1Mb
  sub-directories of 1Mb or more:
    doc         1.1Mb
    libs       45.6Mb
    test_data   1.2Mb
Namespaces in Imports field not imported from:
  ‘AER’ ‘MASS’ ‘Matrix’ ‘censReg’ ‘effects’ ‘foreign’ ‘lme4’ ‘lmtest’
  ‘nnet’ ‘pBrackets’ ‘plm’ ‘pscl’ ‘sandwich’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘cplm’ ‘ggplot2’ ‘rlang’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cplexAPI’
File ‘globalOptTests/libs/globalOptTests.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Found the following significant warnings:
  Evaluation.cpp:173:9: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/gnmf.Rcheck/00install.out’ for details.
File ‘gnmf/libs/gnmf.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘FactorMatrix.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘FactorMatrix.o’
File ‘gnmf/libs/gnmf.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘cluster’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rhandsontable’ ‘shiny’ ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘processx’ ‘remotes’ ‘rsconnect’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘methods’ ‘stats’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   5.5Mb
File ‘gplm/libs/gplm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    3.5Mb
File ‘GrammR/libs/GrammR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Imap’ ‘Rdpack’ ‘ade4’ ‘doBy’ ‘mclust’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    help   2.4Mb
    libs   3.1Mb
File ‘graphscan/libs/graphscan.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
Namespace in Imports field not imported from: ‘BiasedUrn’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
File ‘groupRemMap/libs/groupRemMap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    libs  18.9Mb
File ‘grr/libs/grr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gsDesign/libs/gsDesign.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Found the following files/directories:
  ‘ORCDRC.txt’
File ‘gsmoothr/libs/gsmoothr.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gte/libs/gte.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   3.0Mb
File ‘GUILDS/libs/GUILDS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘GWASExactHW/libs/GWASExactHW.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘GWEX/libs/GWEX.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gwfa/libs/gwfa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’ ‘spgwr’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.5Mb
Namespaces in Imports field not imported from:
  ‘broom’ ‘dplyr’ ‘ggrepel’ ‘kableExtra’ ‘knitr’ ‘nnet’ ‘plotROC’
  All declared Imports should be used.
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
installed size is 130.6Mb
  sub-directories of 1Mb or more:
    java  128.5Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘gsubfn’ ‘stringr’
  All declared Imports should be used.
File ‘hapassoc/libs/hapassoc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
Found the following files/directories:
  ‘ROR.sv’ ‘aa.sur’ ‘aa4digit’ ‘aa6digit’ ‘grp.detail’ ‘grp.his’
  ‘newick’
File ‘hashFunction/libs/hashFunction.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
File ‘hashr/libs/hashr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hawkes/libs/hawkes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data  10.0Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    CWrappers_1.10.2   2.7Mb
    CWrappers_1.10.3   2.6Mb
    libs               1.4Mb
File ‘HDGLM/libs/HDGLM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hdlm/libs/hdlm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    libs  37.6Mb
File ‘HDtweedie/libs/HDtweedie.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
installed size is 29.2Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs  23.7Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘purrr’ ‘tidyverse’
  All declared Imports should be used.
File ‘HiCseg/libs/HiCseg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘HiDimDA/libs/HiDimDA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘MCMCpack’
  All declared Imports should be used.
File ‘hierarchicalSets/libs/hierarchicalSets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hierband/libs/hierband.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc           3.7Mb
    htmlwidgets   4.0Mb
File ‘highD2pop/libs/highD2pop.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
    libs   1.0Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    highlight   1.1Mb
    libs        8.7Mb
File ‘hillmakeR/libs/hillmakeR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hint/libs/hint.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
File ‘HI/libs/HI.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   5.6Mb
File ‘hit/libs/hit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hkevp/libs/hkevp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘HKprocess/libs/HKprocess.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘HLMdiag/libs/HLMdiag.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   4.5Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘methods’ ‘rgl’
  All declared Imports should be used.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Rdpack’
  All declared Imports should be used.
File ‘HotDeckImputation/libs/HotDeckImputation.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
File ‘hpa/libs/hpa.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
    Objects: ‘hpaBinary.o’, ‘hpaML.o’, ‘hpaSelection.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   2.5Mb
File ‘hsmm/libs/hsmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hsphase/libs/hsphase.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 67.7Mb
  sub-directories of 1Mb or more:
    libs  67.1Mb
File ‘htdp/libs/htdp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.5Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data   8.3Mb
    doc    2.1Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
File ‘humaniformat/libs/humaniformat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
File ‘HUM/libs/HUM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   5.9Mb
Namespaces in Imports field not imported from:
  ‘rvest’ ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shiny’ ‘wordcloud2’
  All declared Imports should be used.
File ‘HybridMC/libs/HybridMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘ggplot2’ ‘pander’
  All declared Imports should be used.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   5.9Mb
File ‘iBATCGH/libs/iBATCGH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ibdreg/libs/ibdreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ibmcraftr/libs/ibmcraftr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ibm/libs/ibm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Iboot/libs/Iboot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Registration problems:
  symbol ‘nom1’ in the local frame:
   .C(nom1, as.double(xord), as.integer(length(xord)), as.double(yord), 
       as.double(gridbw), as.integer(length(gridbw)), as.integer(effold), 
       as.integer(neffold), double(length(gridbw)), double(length(gridbw)))
  symbol ‘nom2’ in the local frame:
   .C(nom2, as.double(x), as.integer(n), as.double(y), as.double(bandwidth), 
       as.double(x), as.integer(n), double(n), double(1))
  symbol ‘nom2’ in the local frame:
   .C(nom2, as.double(x), as.integer(n), as.double(y), as.double(bandwidth), 
       as.double(x), as.integer(n), double(n), double(1), double(n))
  symbol ‘nom’ in the local frame:
   .C(nom, as.double(x), as.integer(length(x)), as.double(y), as.double(object$bandwidth), 
       as.double(newdata), as.integer(length(newdata)), double(length(newdata)), 
       double(1))
  symbol ‘nom’ in the local frame:
   .C(nom, as.double(x), as.integer(length(x)), as.double(y), as.double(object$bandwidth), 
       as.double(newdata), as.integer(length(newdata)), double(length(newdata)), 
       double(1), double(length(newdata)))
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
File ‘iBST/libs/iBST.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Mmusculus.UCSC.mm10'
Packages unavailable to check Rd xrefs: ‘BSgenome.Hsapiens.1000genomes.hs37d5’, ‘BSgenome.Mmusculus.UCSC.mm10’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
File ‘icapca/libs/icapca.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   6.8Mb
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/icd.Rcheck/00install.out’ for details.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   1.4Mb
    libs   8.1Mb
Namespace in Imports field not imported from: ‘coda’
  All declared Imports should be used.
File ‘icemelt/libs/icemelt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
File ‘icensmis/libs/icensmis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ICE/libs/ICE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 82.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  80.9Mb
installed size is 26.7Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  25.2Mb
File ‘identity/libs/identity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
File ‘ieeeround/libs/ieeeround.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘testit’
  All declared Imports should be used.
File ‘ifa/libs/ifa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ifctools/libs/ifctools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘IFP/libs/IFP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ifs/libs/ifs.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘xtable’
  All declared Imports should be used.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  14.4Mb
File ‘IHSEP/libs/IHSEP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 50.7Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       1.1Mb
    extdata   1.1Mb
    include   3.0Mb
    libs     43.5Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Found the following significant warnings:
  IM4ECpp.cpp:24:54: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:24:65: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:33:54: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:33:65: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:22:62: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:32:62: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:67: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:78: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:67: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:78: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/Immigrate.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘haven’
  All declared Imports should be used.
File ‘imputeMDR/libs/imputeMDR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘count_compare’
File ‘imputeMulti/libs/imputeMulti.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘IM/libs/IM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lme4’ ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘V8’ ‘assertive’ ‘shinydashboard’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   5.3Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rgeos’
  All declared Imports should be used.
File ‘IndependenceTests/libs/IndependenceTests.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    help   1.6Mb
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
File ‘influenceR/libs/influenceR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘infotheo/libs/infotheo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ca’
  All declared Imports should be used.
File ‘INSPIRE/libs/INSPIRE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
File ‘Interact/libs/Interact.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
installed size is 27.4Mb
  sub-directories of 1Mb or more:
    libs  27.1Mb
File ‘intervals/libs/intervals.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
Namespaces in Imports field not imported from:
  ‘chron’ ‘zoo’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘bsplus’ ‘colourpicker’ ‘kableExtra’ ‘markdown’ ‘reshape2’
  ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’
File ‘iotools/libs/iotools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   7.5Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘expm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘GlobalOptions’ ‘dplyr’ ‘testthat’
  All declared Imports should be used.
File ‘ipfp/libs/ipfp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Namespace in Imports field not imported from: ‘seqinr’
  All declared Imports should be used.
File ‘iRafNet/libs/iRafNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  rf.c:492:17: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/iRF.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘irr’
  All declared Imports should be used.
File ‘ISBF/libs/ISBF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘colorRamps’ ‘virtualspecies’
  All declared Imports should be used.
File ‘isingLenzMC/libs/isingLenzMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.0Mb
File ‘isocir/libs/isocir.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘RandomFields’
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
File ‘ISR3/libs/ISR3.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘pangaear’ ‘rcrossref’ ‘rgdal’ ‘stringr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘comtradr’
  All declared Imports should be used.
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          20.6Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘ggExtra’ ‘ggplot2’ ‘grid’ ‘gridExtra’ ‘mcmcplots’
  All declared Imports should be used.
File ‘JASPAR/libs/JASPAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/JavaGD.Rcheck/00install.out’ for details.
File ‘JavaGD/libs/JavaGD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘GA’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘png’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘BurStFin’ ‘MASS’ ‘fAssets’ ‘timeDate’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   7.2Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘GPArotation’ ‘MASS’ ‘PMCMR’ ‘R6’ ‘ROCR’
  ‘afex’ ‘car’ ‘emmeans’ ‘ggridges’ ‘lavaan’ ‘multcomp’ ‘mvnormtest’
  ‘nnet’ ‘psych’ ‘vcd’ ‘vcdExtra’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   4.7Mb
Found the following significant warnings:
  jomo1clmmC.c:105:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo1clmmhrC.c:107:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo2clmmC.c:128:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo2clmmhrC.c:132:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomooprobitC.c:84:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/jomo.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
File ‘jpeg/libs/jpeg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘JRF/libs/JRF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘survC1’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   5.8Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
File ‘kappalab/libs/kappalab.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘kaps/libs/kaps.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stinepack’
  All declared Imports should be used.
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  16.4Mb
File ‘Kendall/libs/Kendall.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lme4’ ‘metafor’ ‘nlme’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
File ‘KERE/libs/KERE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
File ‘KernSmoothIRT/libs/KernSmoothIRT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘KFKSDS/libs/KFKSDS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘kissmig/libs/kissmig.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘kknn/libs/kknn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘kml/libs/kml.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘kmlShape/libs/kmlShape.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘knncat/libs/knncat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Package in Depends field not imported from: ‘cluster’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespaces in Imports field not imported from:
  ‘FNN’ ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘psycho’ ‘rhandsontable’
  ‘shiny’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.9Mb
File ‘kolmim/libs/kolmim.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘mice’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tibble’
  All declared Imports should be used.
File ‘kriging/libs/kriging.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   3.3Mb
File ‘ktspair/libs/ktspair.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  17.6Mb
File ‘labdsv/libs/labdsv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.3Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   8.4Mb
File ‘LakeMetabolizer/libs/LakeMetabolizer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  W_gamma_Cpp.cpp:14:39: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/LambertW.Rcheck/00install.out’ for details.
File ‘LambertW/libs/LambertW.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘LANDD/libs/LANDD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
Namespaces in Imports field not imported from:
  ‘callr’ ‘collections’ ‘repr’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    2.0Mb
    help   1.1Mb
File ‘lars/libs/lars.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘LassoNet/libs/LassoNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lassoshooting/libs/lassoshooting.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Namespaces in Imports field not imported from:
  ‘ReinforcementLearning’ ‘ggplot2’ ‘grDevices’ ‘h2o’ ‘lubridate’
  ‘magrittr’ ‘openssl’ ‘readr’ ‘stringr’
  All declared Imports should be used.
File ‘lbfgsb3/libs/lbfgsb3.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lbfgs/libs/lbfgs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lbiassurv/libs/lbiassurv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lda/libs/lda.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  ./lda_svi.h:1:9: warning: '_lda_svi_guard' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
See ‘/data/gannet/ripley/R/packages/tests-clang/lda.svi.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘tm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘here’ ‘reshape’
  All declared Imports should be used.
File ‘leaderCluster/libs/leaderCluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘htmlwidgets’ ‘jsonlite’ ‘sf’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘leaflet’
  All declared Imports should be used.
File ‘leaps/libs/leaps.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘LearningRlab/libs/LearningRlab.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lgarch/libs/lgarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘LiblineaR.ACF/libs/LiblineaR.ACF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘LiblineaR/libs/LiblineaR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    extdata   1.2Mb
    libs      7.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data      3.8Mb
    extdata   1.1Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘devtools’ ‘e1071’ ‘glmnet’ ‘hash’ ‘pamr’ ‘randomForest’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ddpcr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘data.table’ ‘e1071’ ‘fastmatch’
  All declared Imports should be used.
File ‘linERR/libs/linERR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘linkcomm/libs/linkcomm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  10.4Mb
File ‘listdtr/libs/listdtr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
File ‘ljr/libs/ljr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        2.4Mb
    libs      20.4Mb
    testdata   1.6Mb
lmec: warning in qr.Q(qrZ, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: warning in qr.Q(qra, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: no visible global function definition for ‘lm’
lmec: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘dnorm’
lmec : vtrnorm2: no visible global function definition for ‘runif’
lmec : vtrnorm2: no visible global function definition for ‘qnorm’
lmec : vtrnorm2: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘rnorm’
lmec: no visible global function definition for ‘ar’
Undefined global functions or variables:
  ar dnorm lm pnorm qnorm rnorm runif
Consider adding
  importFrom("stats", "ar", "dnorm", "lm", "pnorm", "qnorm", "rnorm",
             "runif")
to your NAMESPACE file.
File ‘lmeNBBayes/libs/lmeNBBayes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lmeNB/libs/lmeNB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘boot’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
File ‘lmPerm/libs/lmPerm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘localgauss/libs/localgauss.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘locits/libs/locits.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
File ‘loe/libs/loe.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘modules’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘distr’
  All declared Imports should be used.
Package in Depends field not imported from: ‘logcondens’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘logisticPCA/libs/logisticPCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘LogitNet/libs/LogitNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘loglognorm/libs/loglognorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lokern/libs/lokern.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    libs  26.1Mb
Namespace in Imports field not imported from: ‘futile.options’
  All declared Imports should be used.
File ‘lorec/libs/lorec.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lowmemtkmeans/libs/lowmemtkmeans.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
File ‘LPStimeSeries/libs/LPStimeSeries.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘LRcontrast/libs/LRcontrast.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 143 marked Latin-1 strings
  Note: found 833 marked UTF-8 strings
installed size is 51.7Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  49.1Mb
Namespace in Imports field not imported from: ‘lavaan’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tcltk2’
  All declared Imports should be used.
File ‘ltbayes/libs/ltbayes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ltsa/libs/ltsa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.8Mb
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘raster’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.1Mb
    libs   1.8Mb
File ‘lxb/libs/lxb.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘utils’
  All declared Imports should be used.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    TS_files     5.9Mb
    base_files   6.3Mb
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    libs  25.9Mb
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.

Requires orphaned package: ‘etm’
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘cmprsk’ ‘colorspace’ ‘etm’ ‘fracdiff’ ‘gtable’ ‘munsell’
  ‘numDeriv’ ‘plyr’ ‘quadprog’ ‘scales’ ‘timeDate’ ‘tseries’ ‘zoo’
  All declared Imports should be used.
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs   6.9Mb
File ‘magree/libs/magree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs  19.3Mb
File ‘MAMSE/libs/MAMSE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
installed size is 51.1Mb
  sub-directories of 1Mb or more:
    doc           1.2Mb
    htmlwidgets   1.5Mb
    libs         47.1Mb
File ‘mapfit/libs/mapfit.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rgdal’ ‘rlang’ ‘testthat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘brew’ ‘svglite’ ‘uuid’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘betareg’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘kableExtra’ ‘knitr’
  All declared Imports should be used.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  10.3Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs  11.3Mb
File ‘mateable/libs/mateable.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘matie/libs/matie.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘MAT/libs/MAT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
File ‘MaXact/libs/MaXact.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘effsize’ ‘psych’
  All declared Imports should be used.
File ‘mbrglm/libs/mbrglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mcclust/libs/mcclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  12.4Mb
File ‘mcemGLM/libs/mcemGLM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
installed size is 52.1Mb
  sub-directories of 1Mb or more:
    libs  51.1Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
Namespaces in Imports field not imported from:
  ‘parallelMap’ ‘reshape2’
  All declared Imports should be used.
File ‘mco/libs/mco.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘bayesplot’ ‘methods’ ‘purrr’
  All declared Imports should be used.
File ‘mcr/libs/mcr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Depends: includes the non-default packages:
  'lattice', 'locfit', 'maptools', 'quantreg', 'RANN', 'SparseM'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

Suggests orphaned package: ‘mlogit’
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘datasets’ ‘dplyr’ ‘psych’ ‘shiny’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      1.1Mb
File ‘meboot/libs/meboot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 31.1Mb
  sub-directories of 1Mb or more:
    libs  29.5Mb
File ‘MediaK/libs/MediaK.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘ggplot2’ ‘lavaan’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘RGtk2’ ‘RNifti’ ‘cairoDevice’ ‘gtools’ ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘RODBC’ ‘dplyr’ ‘foreign’ ‘formattable’ ‘ggplot2’
  ‘haven’ ‘mem’ ‘openxlsx’ ‘plotly’ ‘readxl’ ‘shinyBS’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringi’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shinyBS’ ‘shinycssloaders’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   2.9Mb
Namespace in Imports field not imported from: ‘urca’
  All declared Imports should be used.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   6.1Mb
installed size is 122.9Mb
  sub-directories of 1Mb or more:
    libs  122.3Mb
Namespaces in Imports field not imported from:
  ‘ggrepel’ ‘reshape’ ‘svglite’
  All declared Imports should be used.
File ‘metafolio/libs/metafolio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘MetaheuristicFPA/libs/MetaheuristicFPA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘DT’ ‘GEOmetadb’ ‘RMySQL’ ‘RSQLite’ ‘gplots’ ‘pheatmap’
  ‘readr’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.1Mb
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘foreign’ ‘gplots’ ‘httr’ ‘jsonlite’ ‘knitr’ ‘lmerTest’
  ‘magrittr’ ‘mgcv’ ‘repmis’ ‘reshape2’ ‘rmarkdown’
  All declared Imports should be used.
installed size is 123.5Mb
  sub-directories of 1Mb or more:
    libs  123.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   2.4Mb
File ‘MEtest/libs/MEtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 28.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.1Mb
    libs  23.6Mb
    misc   1.1Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
File ‘mewAvg/libs/mewAvg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
Namespace in Imports field not imported from: ‘ECoL’
  All declared Imports should be used.
File ‘mgarchBEKK/libs/mgarchBEKK.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘MGL/libs/MGL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘MGSDA/libs/MGSDA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  19.6Mb
File ‘mhsmm/libs/mhsmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘copula’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ggiraph’ ‘ggplot2’ ‘grid’ ‘gtools’ ‘scales’ ‘shinyBS’
  ‘shinyWidgets’ ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mipfp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘softImpute’
  All declared Imports should be used.
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  20.7Mb
Namespaces in Imports field not imported from:
  ‘DiceDesign’ ‘MaxPro’ ‘doSNOW’ ‘gmp’ ‘jpeg’
  All declared Imports should be used.
File ‘minpack.lm/libs/minpack.lm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cdf.pval: no visible global function definition for ‘median’
cdf.pval: no visible binding for global variable ‘ecdf’
find_hits: no visible global function definition for ‘na.omit’
mad.scores: no visible global function definition for ‘as.formula’
mad.scores: no visible binding for global variable ‘median’
mad.scores: no visible binding for global variable ‘mad’
rm.outliers: no visible global function definition for ‘as.formula’
rm.outliers: no visible binding for global variable ‘median’
rm.outliers: no visible binding for global variable ‘mad’
Undefined global functions or variables:
  as.formula ecdf mad median na.omit
Consider adding
  importFrom("stats", "as.formula", "ecdf", "mad", "median", "na.omit")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘dendextend’ ‘npmv’ ‘utils’
  All declared Imports should be used.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   7.7Mb
File ‘MiSPU/libs/MiSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  simcensor.cpp:91:16: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:91:41: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:95:17: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/missDeaths.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘mcmcr’
  All declared Imports should be used.
installed size is 43.7Mb
  sub-directories of 1Mb or more:
    libs  41.4Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
File ‘mixedMem/libs/mixedMem.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mixexp/libs/mixexp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rjags’
  All declared Imports should be used.
File ‘mkde/libs/mkde.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
File ‘mlbench/libs/mlbench.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘iterators’ ‘parallel’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DiscriMiner’ ‘MASS’ ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘klaR’
  ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
File ‘MLEcens/libs/MLEcens.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
File ‘mlmc/libs/mlmc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mlmmm/libs/mlmmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mlogitBMA/libs/mlogitBMA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘classiFunc’

Suggests orphaned packages:
  ‘clValid’ ‘flare’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
    help   1.4Mb
Namespaces in Imports field not imported from:
  ‘QuantPsyc’ ‘corrgram’ ‘dplyr’ ‘forecast’ ‘psych’ ‘shinyAce’
  All declared Imports should be used.
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
Namespace in Imports field not imported from: ‘plotrix’
  All declared Imports should be used.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘e1071’ ‘nnet’ ‘shiny’ ‘stats’
  All declared Imports should be used.
File ‘mnormpow/libs/mnormpow.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mnormt/libs/mnormt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘sads’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rmisc’ ‘amap’ ‘fields’ ‘matrixStats’ ‘mco’ ‘miscTools’ ‘plyr’
  ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DALEX’ ‘DT’ ‘auditor’ ‘breakDown’ ‘drifter’ ‘svglite’
  All declared Imports should be used.
File ‘ModelGood/libs/ModelGood.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘lattice’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘BioStatR’ ‘ggplot2’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    libs   4.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
File ‘MonetDB.R/libs/MonetDB.R.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ratelimitr’
  All declared Imports should be used.
File ‘monreg/libs/monreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘Getting_started.Rmd’ using rmarkdown
Quitting from lines 63-66 (Getting_started.Rmd) 
Error: processing vignette 'Getting_started.Rmd' failed with diagnostics:
assignment of an object of class "NULL" is not valid for @'fun' in an object of class "compareClusterResult"; is(value, "character") is not TRUE
--- failed re-building ‘Getting_started.Rmd’

SUMMARY: processing the following file failed:
  ‘Getting_started.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   9.4Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.4Mb
File ‘mpbart/libs/mpbart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 79.4Mb
  sub-directories of 1Mb or more:
    R             1.1Mb
    libs         75.5Mb
    mathematica   1.5Mb
File ‘mpmi/libs/mpmi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
export.summary.mpm: warning in complex(real = x$Rows[, FdimsR[1]], imag
  = x$Rows[, FdimsR[2]]): partial argument match of 'imag' to
  'imaginary'
export.summary.mpm: warning in complex(real = x$Columns[, FdimsC[1]],
  imag = x$Columns[, FdimsC[2]]): partial argument match of 'imag' to
  'imaginary'
.onAttach: no visible global function definition for
  ‘packageDescription’
export.summary.mpm: no visible global function definition for
  ‘write.table’
mpm: no visible binding for global variable ‘median’
plot.mpm: no visible global function definition for ‘rainbow’
plot.mpm: no visible global function definition for ‘quantile’
plot.mpm: no visible global function definition for ‘par’
plot.mpm: no visible global function definition for ‘points’
plot.mpm: no visible global function definition for ‘smoothScatter’
plot.mpm: no visible global function definition for ‘colorRampPalette’
plot.mpm: no visible global function definition for ‘symbols’
plot.mpm: no visible global function definition for ‘text’
plot.mpm: no visible global function definition for ‘lines’
plot.mpm: no visible global function definition for ‘box’
Undefined global functions or variables:
  box colorRampPalette lines median packageDescription par points
  quantile rainbow smoothScatter symbols text write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
  importFrom("graphics", "box", "lines", "par", "points",
             "smoothScatter", "symbols", "text")
  importFrom("stats", "median", "quantile")
  importFrom("utils", "packageDescription", "write.table")
to your NAMESPACE file.
File ‘mp/libs/mp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
File ‘MRCE/libs/MRCE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  15.2Mb
File ‘mrfse/libs/mrfse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
File ‘MRH/libs/MRH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘MRwarping/libs/MRwarping.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘interfaceRC_warp.o’
File ‘MRwarping/libs/MRwarping.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘msda/libs/msda.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘moments’ ‘mvtnorm’
  All declared Imports should be used.
installed size is 29.6Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.1Mb
    libs  26.6Mb
installed size is 50.7Mb
  sub-directories of 1Mb or more:
    libs  50.2Mb
File ‘MSGLasso/libs/MSGLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘msgps/libs/msgps.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs  18.5Mb
Namespace in Imports field not imported from: ‘amap’
  All declared Imports should be used.
File ‘MTS/libs/MTS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘capushe’ ‘shiny’
  All declared Imports should be used.
File ‘muhaz/libs/muhaz.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
File ‘MultiBD/libs/MultiBD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘MultiCNVDetect/libs/MultiCNVDetect.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘cowsay’
  All declared Imports should be used.
installed size is 83.3Mb
  sub-directories of 1Mb or more:
    libs  83.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
File ‘multinomRob/libs/multinomRob.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘multispatialCCM/libs/multispatialCCM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    libs  28.9Mb
File ‘MVB/libs/MVB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mvcluster/libs/mvcluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mvnmle/libs/mvnmle.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mvrtn/libs/mvrtn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    java  13.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.5Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
File ‘namespace/libs/namespace.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
File ‘nanop/libs/nanop.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.9Mb
Namespace in Imports field not imported from: ‘tuneR’
  All declared Imports should be used.
File ‘nbpMatching/libs/nbpMatching.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘NBPSeq/libs/NBPSeq.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘bookdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Deriv’ ‘compiler’ ‘stringi’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.8Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.
File ‘NeatMap/libs/NeatMap.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘nMDS_R.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘nMDS_R.o’
File ‘NeatMap/libs/NeatMap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ez’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rlang’ ‘tidyselect’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘igraph’
  All declared Imports should be used.
File ‘NetComp/libs/NetComp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘mvrtn’
  All declared Imports should be used.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   8.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
Namespace in Imports field not imported from: ‘clue’
  All declared Imports should be used.
File ‘NetPreProc/libs/NetPreProc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   6.8Mb
Error(s) in re-building vignettes:
--- re-building ‘vignette.Rmd’ using rmarkdown
Quitting from lines 57-64 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'PCIT'
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘stats’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
File ‘networksis/libs/networksis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘networkTomography/libs/networkTomography.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
File ‘neuroim/libs/neuroim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘htmlTable’ ‘lme4’ ‘stringi’
  All declared Imports should be used.
File ‘neuRosim/libs/neuRosim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘xml2’
  All declared Imports should be used.
Running examples in ‘nFactors-Ex.R’ failed
The error most likely occurred in:

> ### Name: eigenComputes
> ### Title: Computes Eigenvalues According to the Data Type
> ### Aliases: eigenComputes
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> # .......................................................
> # Different data types
> # Vector of eigenvalues
>   data(dFactors)
>   x1 <- dFactors$Cliff1$eigenvalues
>   eigenComputes(x1)
 [1]  2.842  1.080  0.640  0.171  0.015 -0.008 -0.008 -0.126 -0.040 -0.066
[11] -0.111 -0.116
>   
> # Data from a data.frame
>   x2 <- data.frame(matrix(20*rnorm(100), ncol=5))
>   eigenComputes(x2, cor=TRUE,  use="everything")
[1] 1.5562290 1.3713228 1.1323986 0.6806224 0.2594272
>   eigenComputes(x2, cor=FALSE, use="everything")
[1] 527.95290 485.38169 365.44540 209.02148  84.80241
>   eigenComputes(x2, cor=TRUE,  use="everything", method="spearman")
[1] 1.486597 1.448541 1.249002 0.625795 0.190065
>   eigenComputes(x2, cor=TRUE,  use="everything", method="kendall")
[1] 1.3682956 1.3334477 1.2159607 0.7120364 0.3702597
> 
> # From a covariance matrix
>   x3 <- cov(x2)
>   eigenComputes(x3, cor=TRUE,  use="everything")
Error in switch(classType, data.frame = "data", matrix = "correlation",  : 
  EXPR must be a length 1 vector
Calls: eigenComputes -> eigenFrom
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
File ‘nice/libs/nice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    CppCode        1.1Mb
    R              6.1Mb
    classic-bugs   1.6Mb
    include        5.7Mb
    libs          17.2Mb
    tests          1.6Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.3Mb
Namespace in Imports field not imported from: ‘deSolve’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘jsonlite’
  All declared Imports should be used.
File ‘nmfgpu4R/libs/nmfgpu4R.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘BiocManager’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘uroot’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘multicool’ ‘mvnfast’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stars’
  All declared Imports should be used.
File ‘nnls/libs/nnls.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘XML’ ‘choroplethr’ ‘choroplethrMaps’ ‘data.table’
  ‘forcats’ ‘hurricaneexposure’ ‘plyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘arrow’
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
File ‘noncompliance/libs/noncompliance.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘e1071’ ‘pROC’ ‘purrr’ ‘randomForest’ ‘rlang’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘nonlinearTseries_quickstart.Rmd’ using rmarkdown
Quitting from lines 91-94 (nonlinearTseries_quickstart.Rmd) 
Error: processing vignette 'nonlinearTseries_quickstart.Rmd' failed with diagnostics:
need finite 'ylim' values
--- failed re-building ‘nonlinearTseries_quickstart.Rmd’

SUMMARY: processing the following file failed:
  ‘nonlinearTseries_quickstart.Rmd’

Error: Vignette re-building failed.
Execution halted
File ‘nontarget/libs/nontarget.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
File ‘norm/libs/norm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘NORMT3/libs/NORMT3.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Namespace in Imports field not imported from: ‘rts’
  All declared Imports should be used.
File ‘NPsimex/libs/NPsimex.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘npst/libs/npst.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘xgboost’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Rdpack’ ‘base’ ‘graphics’ ‘parallel’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘forecast’ ‘rlang’ ‘tsibble’ ‘viridis’
  All declared Imports should be used.
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    doc    7.4Mb
    libs  20.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.3Mb
File ‘nws/R/zzz.R’:
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

blendOptions: warning in assign(names[i], new[[i]], env = options):
  partial argument match of 'env' to 'envir'
docall: warning in get(as.character(fun), env = .GlobalEnv, mode =
  "function"): partial argument match of 'env' to 'envir'
logMsg: no visible global function definition for ‘flush.console’
nwsPkgInfo: no visible global function definition for
  ‘packageDescription’
initialize,nwsServer: no visible global function definition for
  ‘make.socket’
initialize,nwsServer: no visible global function definition for
  ‘close.socket’
Undefined global functions or variables:
  close.socket flush.console make.socket packageDescription
Consider adding
  importFrom("utils", "close.socket", "flush.console", "make.socket",
             "packageDescription")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘nws/R/workerLoop.R’:
  assign("SleighName", displayName, globalenv())
  assign("SleighNws", nws, globalenv())
  assign("SleighUserNws", userNws, globalenv())
  assign("SleighRank", rank, globalenv())
  assign("SleighWorkerCount", workerCount, globalenv())
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘obliclus/libs/obliclus.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘random_cluster_C.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘random_cluster_C.o’
File ‘obliclus/libs/obliclus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘readODS’ ‘xlsx’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.5Mb
    test_files   4.2Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    doc    2.3Mb
    help   2.7Mb
    libs   3.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘graphics’
  All declared Imports should be used.
File ‘olctools/libs/olctools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 36.3Mb
  sub-directories of 1Mb or more:
    libs  34.6Mb
Namespaces in Imports field not imported from:
  ‘e1071’ ‘fs’ ‘pdp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘safer’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.1Mb
File ‘onemap/libs/onemap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘onlinePCA/libs/onlinePCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  All declared Imports should be used.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   6.2Mb
installed size is 211.6Mb
  sub-directories of 1Mb or more:
    R         2.5Mb
    libs    201.5Mb
    models    4.7Mb
Running examples in ‘OpenMx-Ex.R’ failed
The error most likely occurred in:

> ### Name: mxBootstrapEval
> ### Title: Evaluate Values in a bootstrapped MxModel
> ### Aliases: mxBootstrapEval omxBootstrapEvalCov omxBootstrapEval
> ###   omxBootstrapEvalByName mxBootstrapEvalByName
> 
> ### ** Examples
> 
> 
> library(OpenMx)
> # make a unit-weighted 10-row data set of values 1 thru 10
> myData = mxData(data.frame(weight=1.0, value=1:10), "raw", weight = "weight")
> sum(1:10)
[1] 55
> 
> # Model sums data$value (sum(1:10)= 55), subtracts "A", squares the result, 
> # and tries to minimize this (achieved by setting A=55)
> testModel = mxModel(model = "testModel1", myData,
+ 	mxMatrix(name  = "A", "Full", nrow = 1, ncol = 1, values = 1, free=TRUE),
+ 	# nb: filteredDataRow is an auto-generated matrix of
+ 	# non-missing data from the present row.
+ 	# This is placed into the "rowResults" matrix (also auto-generated)
+ 	mxAlgebra(name = "rowAlg", data.weight * filteredDataRow),
+ 	# Algebra to turn the rowResults into a single number
+ 	mxAlgebra(name = "reduceAlg", (sum(rowResults) - A)^2),
+ 	mxFitFunctionRow(
+ 		rowAlgebra    = "rowAlg",
+ 		reduceAlgebra = "reduceAlg",
+ 		dimnames      = "value"
+ 	)
+ 	# no need for an MxExpectation object when using mxFitFunctionRow
+ )
> 
> testModel = mxRun(testModel) # A is estimated at 55, with SE= 1
Error in (function (cl, name, valueClass)  : 
  assignment of an object of class “list” is not valid for @‘dataColumns’ in an object of class “MxFitFunctionRow”; is(value, "numeric") is not TRUE
Calls: mxRun ... convertFitFunctions -> lapply -> FUN -> FUN -> <Anonymous>
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
possible bashism in configure line 52 (test -a/-o):
  if test ${java_version_maj} -ge 5 || \
      test ${java_version_maj} -eq 1 -a ${java_version_min} -ge 5;
possible bashism in configure line 34 ($(OS|MACH)TYPE):
    case "$OSTYPE" in "darwin"*)
  possible bashism in configure line 40 (should be '.', not 'source'):
      source autobrew
  possible bashism in configure line 79 ($(OS|MACH)TYPE):
  case "$OSTYPE" in
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      6.1Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
File ‘OptGS/libs/OptGS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘OptHedging/libs/OptHedging.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘geometry’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.8Mb
Namespaces in Imports field not imported from:
  ‘boot’ ‘splines’
  All declared Imports should be used.
File ‘optpart/libs/optpart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘orca/libs/orca.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nr' to 'nrow'
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nc' to 'ncol'
bgmm: no visible global function definition for ‘ecdf’
bgmm : SplineGMM: no visible global function definition for
  ‘constrOptim’
blr: no visible global function definition for ‘ecdf’
blr: no visible global function definition for ‘constrOptim’
blr: no visible global function definition for ‘lm’
parentcdf : combinations: no visible global function definition for
  ‘combn’
parentcdf : solver: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  combn constrOptim ecdf lm uniroot
Consider adding
  importFrom("stats", "constrOptim", "ecdf", "lm", "uniroot")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
File ‘OriGen/libs/OriGen.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_rewind’, possibly from ‘rewind’ (Fortran)
    Object: ‘OriGen.o’
File ‘OriGen/libs/OriGen.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ORMDR/libs/ORMDR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    nifti   3.8Mb
est.lme : <anonymous>: warning in rank(iru, ties = "min"): partial
  argument match of 'ties' to 'ties.method'
est.lme : <anonymous>: no visible global function definition for ‘lme’
est.lme : <anonymous>: no visible global function definition for
  ‘VarCorr’
guo: no visible global function definition for ‘p.adjust’
guo: no visible global function definition for ‘na.omit’
pttest : ptest: no visible global function definition for ‘na.omit’
srt : <anonymous>: no visible global function definition for
  ‘rowttests’
Undefined global functions or variables:
  VarCorr lme na.omit p.adjust rowttests
Consider adding
  importFrom("stats", "na.omit", "p.adjust")
to your NAMESPACE file.
File ‘orQA/libs/orQA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  18.9Mb
File ‘osDesign/libs/osDesign.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   7.7Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
Running examples in ‘OTE-Ex.R’ failed
The error most likely occurred in:

> ### Name: OTClass
> ### Title: Train the ensemble of optimal trees for classification.
> ### Aliases: OTClass
> ### Keywords: OTClass OptTreesEns
> 
> ### ** Examples
> 
> #load the data
> 
>   data(Body)
>   data <- Body
>   
> #Divide the data into training and test parts
> 
>   set.seed(9123) 
>   n <- nrow(data)
>   training <- sample(1:n,round(2*n/3))
>   testing <- (1:n)[-training]
>   X <- data[,1:24]
>   Y <- data[,25]
>   
> #Train OTClass on the training data
> 
>   Opt.Trees <- OTClass(XTraining=X[training,],YTraining = Y[training],t.initial=200)
Assessing trees for individual performance..............
Error in order(er) : unimplemented type 'list' in 'orderVector1'
Calls: OTClass -> order
Execution halted
Package suggested but not available for checking: ‘Rcplex’
Namespace in Imports field not imported from: ‘quantreg’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   2.7Mb
Namespaces in Imports field not imported from:
  ‘jsonlite’ ‘praise’ ‘withr’
  All declared Imports should be used.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Found the following files/directories:
  ‘plotBoot_nf1_30rep.pdf’ ‘plotCVPred_nf1_30rep.pdf’
  ‘plotPred_nf1.pdf’ ‘plotTDim.pdf’
Namespace in Imports field not imported from: ‘ape’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Namespace in Imports field not imported from: ‘GenomicAlignments’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘network’ ‘scales’ ‘sna’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data        1.6Mb
    localdata   3.1Mb
Namespace in Imports field not imported from: ‘iterators’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘glue’ ‘viridisLite’
  All declared Imports should be used.
File ‘pamr/libs/pamr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘smoothmest’
  All declared Imports should be used.
File ‘PanelCount/libs/PanelCount.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [67s/78s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(panelr)
  Loading required package: lme4
  Loading required package: Matrix
  
  Attaching package: 'panelr'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("panelr")
  ── 1. Error: (unknown) (@test_wbm.R#283)  ──────────────────────────────────────
  could not find function "arma"
  Backtrace:
   1. panelr::wbm_stan(...)
   2. brms::make_stancode(...)
   4. brms:::validate_formula.default(...)
   6. brms:::validate_formula.brmsformula(bf(formula), ...)
   7. brms:::validate_autocor(autocor)
   8. brms:::parse_ac(autocor)
   9. base::lapply(out, eval2)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 271 | SKIPPED: 0 | WARNINGS: 60 | FAILED: 1 ]
  1. Error: (unknown) (@test_wbm.R#283) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘M3C’
Namespace in Imports field not imported from: ‘survey’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘tibble’
  All declared Imports should be used.
File ‘parma/libs/parma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘parmigene/libs/parmigene.so’:
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’
File ‘parmigene/libs/parmigene.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tools’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Namespace in Imports field not imported from: ‘party’
  All declared Imports should be used.
File ‘patchDVI/libs/patchDVI.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   1.2Mb
    doc    2.1Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘glue’ ‘logging’ ‘purrr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘KernSmooth’ ‘Mfuzz’ ‘SelectBoost’ ‘animation’ ‘c060’
  ‘cluster’ ‘gplots’ ‘grid’ ‘jetset’
  All declared Imports should be used.
File ‘pauwels2014/libs/pauwels2014.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘PAWL/libs/PAWL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘pbdNCDF4/libs/pbdNCDF4.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ade4’
  All declared Imports should be used.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    lib  10.0Mb
File ‘pbivnorm/libs/pbivnorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    examples   1.7Mb
File ‘PCA4TS/libs/PCA4TS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
    libs      3.2Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pander’
  All declared Imports should be used.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   7.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
installed size is 156.1Mb
  sub-directories of 1Mb or more:
    doc     2.7Mb
    libs  152.9Mb
File ‘PCICt/libs/PCICt.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    libs  32.8Mb
File ‘pdc/libs/pdc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘PDFEstimator/libs/PDFEstimator.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘pdist/libs/pdist.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘car’ ‘sandwich’
  All declared Imports should be used.
File ‘PDSCE/libs/PDSCE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
File ‘PedCNV/libs/PedCNV.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘pedigree/libs/pedigree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespace in Imports field not imported from: ‘lhs’
  All declared Imports should be used.
File ‘PenCoxFrail/libs/PenCoxFrail.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘penMSM/libs/penMSM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
File ‘peperr/libs/peperr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘perccal/libs/perccal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘PerfMeas/libs/PerfMeas.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rms’
  All declared Imports should be used.
Found the following significant warnings:
  permTest.c:20:3: warning: expression result unused [-Wunused-value]
  permTest.c:62:3: warning: expression result unused [-Wunused-value]
  permTest.c:90:3: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/permDep.Rcheck/00install.out’ for details.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘SnowballC’ ‘cluster’ ‘graph’
  All declared Imports should be used.
File ‘pgee.mixed/libs/pgee.mixed.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘pGMGM/libs/pGMGM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ph2bye/libs/ph2bye.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data       2.3Mb
    examples   2.6Mb
File ‘phenmod/libs/phenmod.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘jsonlite’ ‘memoise’
  All declared Imports should be used.
File ‘pheno/libs/pheno.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
Running ‘testthat.R’ [13s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(phrasemachine)
  phrasemachine: Simple Phrase Extraction
  Version 1.1.2 created on 2017-05-29.
  copyright (c) 2016, Matthew J. Denny, Abram Handler, Brendan O'Connor.
  Type help('phrasemachine') or
  vignette('getting_started_with_phrasemachine') to get started.
  Development website: https://github.com/slanglab/phrasemachine
  > 
  > test_check("phrasemachine")
  ── 1. Error: See if tagging five documents works, and if coarsening works (@test
  unused argument (alist())
  Backtrace:
   1. documents[1:5, ]
  
  ── 2. Error: See if extractor works (@test_extract_phrases.R#7)  ───────────────
  unused argument (alist())
  Backtrace:
   1. documents[1:5, ]
  
  Currently tagging document 1 of 1 
  Extracting phrases from document 1 of 1 
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 10 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: See if tagging five documents works, and if coarsening works (@test_POS_tag_documents.R#7) 
  2. Error: See if extractor works (@test_extract_phrases.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘getting_started_with_phrasemachine.Rmd’ using rmarkdown
Quitting from lines 82-91 (getting_started_with_phrasemachine.Rmd) 
Error: processing vignette 'getting_started_with_phrasemachine.Rmd' failed with diagnostics:
unused argument (alist())
--- failed re-building ‘getting_started_with_phrasemachine.Rmd’

SUMMARY: processing the following file failed:
  ‘getting_started_with_phrasemachine.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  phreeqcpp/transport.cpp:794:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/phreeqc.Rcheck/00install.out’ for details.
installed size is 42.4Mb
  sub-directories of 1Mb or more:
    libs  41.7Mb
Namespaces in Imports field not imported from:
  ‘gplots’ ‘phytools’
  All declared Imports should be used.
File ‘phyloland/libs/phyloland.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
File ‘PhyloMeasures/libs/PhyloMeasures.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘intergraph’
  All declared Imports should be used.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  14.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Namespace in Imports field not imported from: ‘FrF2.catlg128’
  All declared Imports should be used.
File ‘Pijavski/libs/Pijavski.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
File ‘pirate/libs/pirate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘PivotalR/libs/PivotalR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘test-async.R’ [22s/44s]
  Running ‘testthat.R’ [5s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pkgcache)
  > 
  > test_check("pkgcache")
  ── 1. Error: load_primary_pkgs (@test-metadata-cache.R#191)  ───────────────────
  No metadata available
  Backtrace:
   1. pkgcache:::synchronise(get_private(cmc)$load_primary_pkgs(oneday()))
   2. get_private(cmc)$load_primary_pkgs(oneday())
   3. pkgcache:::cmc__load_primary_pkgs(self, private, max_age)
   4. private$update_replica_rds(alert = FALSE)
   5. pkgcache:::cmc__update_replica_rds(self, private, alert)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 305 | SKIPPED: 28 | WARNINGS: 2 | FAILED: 1 ]
  1. Error: load_primary_pkgs (@test-metadata-cache.R#191) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘stringi’
  All declared Imports should be used.
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    libs  25.4Mb
File ‘plac/libs/plac.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘planar/libs/planar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.5Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘RColorBrewer’ ‘arm’ ‘epiDisplay’ ‘foreign’ ‘gbm’
  ‘grid’ ‘lattice’ ‘latticeExtra’ ‘lme4’ ‘nnet’ ‘parallel’ ‘splines’
  ‘survey’ ‘twang’ ‘xtable’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘V8’ ‘devtools’ ‘formatR’ ‘gdata’ ‘rhandsontable’ ‘shinythemes’
  ‘sqldf’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(plethem)
  You are now using PLETHEM.
                          If you have installed PLETHEM for the first time or have just updated it, please run setUserDb() to select an existing database or createUserDb() to create a new one.
  > 
  > test_check("plethem")
  ── 1. Error: Tissue volumes are less than 85% of body weight (@test_physio.R#19)
  invalid 'type' (list) of argument
  Backtrace:
   1. plethem::getLifecourseTissueVolumes(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 8 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: Tissue volumes are less than 85% of body weight (@test_physio.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘plgp/libs/plgp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘PlackettLuce’ ‘StatRank’ ‘pmr’ ‘prefmod’ ‘rankdist’
  All declared Imports should be used.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   7.9Mb
File ‘pln/libs/pln.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘hexbin’ ‘quantreg’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.7Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘stats’
  All declared Imports should be used.
File ‘plugdensity/libs/plugdensity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘png/libs/png.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
File ‘poilog/libs/poilog.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘car’ ‘lubridate’
  All declared Imports should be used.
File ‘poisDoubleSamp/libs/poisDoubleSamp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘poLCA/libs/poLCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘polyfreqs/libs/polyfreqs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R      6.4Mb
    data   4.0Mb
Namespace in Imports field not imported from: ‘combinat’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘StanHeaders’ ‘dplyr’ ‘ggplot2’ ‘gridExtra’ ‘rstan’ ‘tibble’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘ggthemes’ ‘memoise’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘memisc’ ‘shinyWidgets’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    doc  11.8Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
File ‘PPtree/libs/PPtree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lmtest’ ‘sandwich’
  All declared Imports should be used.
File ‘prclust/libs/prclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘class’ ‘forcats’ ‘irr’ ‘lpSolve’ ‘purrr’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.1Mb
Namespaces in Imports field not imported from:
  ‘TH.data’ ‘moonBook’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘ROCR’ ‘ada’ ‘colourpicker’ ‘corrplot’ ‘e1071’ ‘flexdashboard’
  ‘glmnet’ ‘kknn’ ‘neuralnet’ ‘randomForest’ ‘rattle’ ‘rpart’
  ‘shinyAce’ ‘shinyWidgets’ ‘shinydashboardPlus’ ‘shinyjs’ ‘tidyverse’
  ‘xgboost’ ‘zip’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘here’ ‘tidyr’
  All declared Imports should be used.
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
Namespaces in Imports field not imported from:
  ‘datasets’ ‘dplyr’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(preText)
  preText: Diagnostics to Assess the Effects of Text Preprocessing Decisions
  Version 0.6.3 created on 2018-01-12.
  copyright (c) 2017, Matthew J. Denny, Penn State University
                      Arthur Spirling, NYU
  Type vignette('getting_started_with_preText') to get started.
  Development website: https://github.com/matthewjdenny/preText
  > 
  > test_check("preText")
  ── 1. Error: Small example works (@test_factorial_preprocessing.R#6)  ──────────
  unused argument (alist())
  Backtrace:
   1. documents[1:10, ]
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Small example works (@test_factorial_preprocessing.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘getting_started_with_preText.Rmd’ using rmarkdown
Quitting from lines 60-69 (getting_started_with_preText.Rmd) 
Error: processing vignette 'getting_started_with_preText.Rmd' failed with diagnostics:
unused argument (alist())
--- failed re-building ‘getting_started_with_preText.Rmd’

SUMMARY: processing the following file failed:
  ‘getting_started_with_preText.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
File ‘PRIMAL/libs/PRIMAL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘primes/libs/primes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘prim-2d.Rnw’ using Sweave
--- finished re-building ‘prim-2d.Rnw’

--- re-building ‘prim-3d.Rnw’ using Sweave

Error: processing vignette 'prim-3d.Rnw' failed with diagnostics:
 chunk 8 
Error in summ.mat[, 1] * summ.mat[, 2] : 
  non-numeric argument to binary operator

--- failed re-building ‘prim-3d.Rnw’

SUMMARY: processing the following file failed:
  ‘prim-3d.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  15.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    libs  21.2Mb
File ‘ProbitSpatial/libs/ProbitSpatial.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘LaplacesDemon’ ‘epitools’ ‘rpivotTable’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    doc           9.2Mb
    htmlwidgets   2.5Mb
Namespaces in Imports field not imported from:
  ‘expm’ ‘mvtnorm’
  All declared Imports should be used.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    extdata   7.4Mb
    libs      6.3Mb
Package suggested but not available for checking: ‘qtbase’
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/proj4.Rcheck/00install.out’ for details.
File ‘proj4/libs/proj4.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘distcrete’
  All declared Imports should be used.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   3.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   2.9Mb
File ‘prospectr/libs/prospectr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grDevices’
  All declared Imports should be used.
File ‘prototest/libs/prototest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.4Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   2.3Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘readr’
  All declared Imports should be used.
File ‘pRSR/libs/pRSR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘forecast’ ‘knitr’
  All declared Imports should be used.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
File ‘pspearman/libs/pspearman.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Namespace in Imports field not imported from: ‘pbv’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘methods’ ‘performance’ ‘tidyr’
  All declared Imports should be used.
File ‘ptest/libs/ptest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  pinpolyhedronA.cc:594:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  pinpolyhedronA.cc:1766:5: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/ptinpoly.Rcheck/00install.out’ for details.
File ‘ptinpoly/libs/ptinpoly.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    dict   5.1Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc        4.1Mb
    examples   2.6Mb
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘dplyr’
  All declared Imports should be used.
installed size is 51.9Mb
  sub-directories of 1Mb or more:
    libs  51.4Mb
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    libs  34.9Mb
File ‘pullword/libs/pullword.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘FSA’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘fractal’ ‘mgcv’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘hms’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘readr’ ‘tidyverse’
  All declared Imports should be used.
File ‘PWD/libs/PWD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘PWEALL/libs/PWEALL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    gui          1.2Mb
    staticdocs   3.3Mb
installed size is 92.7Mb
  sub-directories of 1Mb or more:
    libs  92.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
File ‘qrencoder/libs/qrencoder.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data  10.8Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘msm’
  All declared Imports should be used.
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
Found the following files/directories:
  ‘Pscdbp.txt’
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.8Mb
    doc       3.0Mb
    libs      1.6Mb
Namespace in Imports field not imported from: ‘MatrixModels’
  All declared Imports should be used.
File ‘QuACN/libs/QuACN.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   1.3Mb
    libs  12.7Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Found the following significant warnings:
  rf.c:454:1: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/quantregForest.Rcheck/00install.out’ for details.
File ‘quantspec/libs/quantspec.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   5.8Mb
File ‘QUIC/libs/QUIC.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘QUIC.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘QUIC.o’
File ‘QUIC/libs/QUIC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘gridExtra’ ‘knitr’
  All declared Imports should be used.
File ‘qVarSel/libs/qVarSel.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘qVarSelH.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘qVarSelH.o’
File ‘qVarSel/libs/qVarSel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lmerTest’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    Output   2.2Mb
    bin      3.6Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Package suggested but not available for checking: ‘batchelor’

Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    5.9Mb
    libs   1.1Mb
Namespace in Imports field not imported from: ‘comat’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
Namespaces in Imports field not imported from:
  ‘KernSmooth’ ‘Matrix’ ‘PharmacoGx’ ‘cluster’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.4Mb
File ‘RAD/libs/RAD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘CGHbase’
  All declared Imports should be used.
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    libs  28.1Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    api           3.2Mb
    htmlwidgets   7.1Mb
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘stringi’
  All declared Imports should be used.
File ‘randaes/libs/randaes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.2Mb
    libs   5.3Mb
Found the following significant warnings:
  rf.c:460:17: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/randomForest.Rcheck/00install.out’ for details.
File ‘randomUniformForest/libs/randomUniformForest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘curl’ ‘jsonlite’
  All declared Imports should be used.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
File ‘RANKS/libs/RANKS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RJDBC’
  All declared Imports should be used.
File ‘rappdirs/libs/rappdirs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs  12.6Mb
File ‘RArcInfo/libs/RArcInfo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘RaschSampler/libs/RaschSampler.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rasterKernelEstimates/libs/rasterKernelEstimates.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    libs   7.4Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    etc    1.9Mb
    po     1.2Mb
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  30.0Mb
File ‘rBeta2009/libs/rBeta2009.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘PZ.bi’ ‘mu_sigma.nc’
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-clang/Rblpapi.Rcheck/00install.out’ for details.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    blp    7.1Mb
    libs   8.2Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
File ‘rbvs/libs/rbvs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘RCassandra/libs/RCassandra.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    cont  23.3Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.0Mb
    po    2.4Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    corpora   7.6Mb
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs  21.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    include   6.0Mb
    libs      1.8Mb
File ‘RcppBDT/libs/RcppBDT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    lib    5.0Mb
    libs   1.6Mb
‘configure’: /bin/bash is not portable
  possible bashism in cleanup line 1 (brace expansion):
  rm -f src/*.{o,so}
  possible bashism in cleanup line 2 (brace expansion):
  rm -f src/cwb/cl/*.{a,o}
  possible bashism in cleanup line 4 (brace expansion):
  rm -f src/cwb/cqp/*.{a,o}
  possible bashism in cleanup line 8 (brace expansion):
  rm -r src/cwb/utils/*.{a,o}
File ‘RcppDL/libs/RcppDL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
installed size is 32.6Mb
  sub-directories of 1Mb or more:
    include   7.9Mb
    libs     24.0Mb
File ‘RcppFaddeeva/libs/RcppFaddeeva.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 57.5Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib      42.4Mb
    libs     12.9Mb
File ‘RcppMLPACK/libs/RcppMLPACK.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    include   7.0Mb
    libs      2.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib       3.1Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    include   6.4Mb
    libs      5.5Mb
Registration problem:
  symbol ‘symbol’ in the local frame:
   .Call(symbol)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    jsonexamples   3.8Mb
    libs           1.3Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
File ‘RcppXts/libs/RcppXts.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘smcure’
  All declared Imports should be used.
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
Found the following significant warnings:
  dist.cpp:19:33: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  dist.cpp:65:33: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  dist.cpp:111:36: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/rdist.Rcheck/00install.out’ for details.
Subdirectory ‘src’ contains:
  CLRApi.hpp CLRFactory.hpp CLRObjectRef.hpp Common.hpp OS.hpp
  RValue.hpp TcpClient.hpp
These are unlikely file names for src files.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
Namespace in Imports field not imported from: ‘digest’
  All declared Imports should be used.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/Rdsdp.Rcheck/00install.out’ for details.
File ‘Rdsdp/libs/Rdsdp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Rdtq/libs/Rdtq.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   9.0Mb
File ‘read.dbc/libs/read.dbc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
Note: found 1 marked Latin-1 string
  Note: found 1 marked UTF-8 string
  Note: found 7 strings marked as "bytes"
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
bestmods: no visible global function definition for ‘abline’
bestmods: no visible global function definition for ‘axis’
bestmods: no visible global function definition for ‘lines’
cic: no visible global function definition for ‘lsfit’
cic: no visible global function definition for ‘var’
cvic: no visible global function definition for ‘lsfit’
cvic: no visible global function definition for ‘lm’
eic: no visible global function definition for ‘lsfit’
eic: no visible global function definition for ‘lm’
ic.min: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘var’
xy: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis lines lm lsfit rnorm var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "lm", "lsfit", "rnorm", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘reams/R/xy.R’:
  assign(xname, X, env = .GlobalEnv)
  assign(yname, y, env = .GlobalEnv)
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   3.5Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.4Mb
Namespaces in Imports field not imported from:
  ‘DBI’ ‘readr’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   5.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.6Mb
Namespaces in Imports field not imported from:
  ‘ROCR’ ‘colourpicker’ ‘corrplot’ ‘e1071’ ‘flexdashboard’ ‘gbm’
  ‘glmnet’ ‘kknn’ ‘neuralnet’ ‘rattle’ ‘rpart’ ‘shinyWidgets’
  ‘shinydashboardPlus’ ‘shinyjs’ ‘xgboost’ ‘zip’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘nnet’ ‘purrr’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘Rcplex’
File ‘relevent/libs/relevent.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gWidgetstcltk’
  All declared Imports should be used.
File ‘remMap/libs/remMap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rEMM/libs/rEMM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘remote/libs/remote.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs   2.4Mb
File ‘ReorderCluster/libs/ReorderCluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
File ‘repolr/libs/repolr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  regalg.cpp:215:10: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
  regalg.cpp:454:10: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/resemble.Rcheck/00install.out’ for details.
File ‘resemble/libs/resemble.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘restrictedMVN/libs/restrictedMVN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs      3.9Mb
    swagger   1.4Mb
Namespace in Imports field not imported from: ‘Rserve’
  All declared Imports should be used.
File ‘retimes/libs/retimes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RTriangle’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
installed size is 23.7Mb
  sub-directories of 1Mb or more:
    libs  23.2Mb
installed size is 59.2Mb
  sub-directories of 1Mb or more:
    libs  57.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    java   5.3Mb
Namespaces in Imports field not imported from:
  ‘prob’ ‘titanic’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       1.4Mb
    extdata   1.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.9Mb
Namespaces in Imports field not imported from:
  ‘leaflet’ ‘pals’ ‘raster’ ‘sp’
  All declared Imports should be used.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc     3.7Mb
    fonts   1.5Mb
    libs    2.7Mb
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/Rgnuplot.Rcheck/00install.out’ for details.
File ‘Rgnuplot/libs/Rgnuplot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking: 'playwith', 'pmg'
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extra   9.4Mb
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  10.5Mb
    libs   9.1Mb
File ‘RGtk2/libs/RGtk2.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_new_custom_connection’,
    ‘Rf_EncodeInteger’, ‘Rf_EncodeLogical’, ‘Rf_EncodeReal’,
    ‘Rf_formatInteger’, ‘Rf_formatLogical’, ‘Rf_formatReal’
File ‘RGtk2/libs/RGtk2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc          10.2Mb
    htmlwidgets   1.2Mb
File ‘RI2by2/libs/RI2by2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gWidgetsRGtk2’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
File ‘RInside/libs/RInside.so’:
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLdo1’, ‘R_ReplDLLinit’,
    ‘R_RunExitFinalizers’, ‘R_SetParams’, ‘R_SignalHandlers’,
    ‘R_TempDir’, ‘Rf_endEmbeddedR’, ‘Rf_initEmbeddedR’
File ‘RInside/libs/RInside.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Rip46/libs/Rip46.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
File ‘rIsing/libs/rIsing.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  22.7Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’
File ‘rJava/libs/rJava.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   4.4Mb
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘RcppProgress’ ‘magrittr’
  All declared Imports should be used.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    datasets  10.2Mb
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    exe  23.8Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘arules’ ‘pmml’ ‘rJava’
  All declared Imports should be used.
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    libs  23.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
File ‘rkvo/libs/rkvo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is 59.1Mb
  sub-directories of 1Mb or more:
    libs  58.4Mb
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    libs  25.4Mb
File ‘rlm/libs/rlm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Rlof/libs/Rlof.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘RLRsim/libs/RLRsim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RCarb’ ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    rmd   8.3Mb
Found the following files/directories:
  ‘dipper.inp’ ‘mark001.inp’ ‘mark001.out’ ‘mark001.res’ ‘mark001.vcv’
  ‘mark002.inp’ ‘mark002.out’ ‘mark002.res’ ‘mark002.vcv’ ‘mark003.inp’
  ‘mark003.out’ ‘mark003.res’ ‘mark003.vcv’ ‘mark004.inp’ ‘mark004.out’
  ‘mark004.res’ ‘mark004.vcv’ ‘mark005.inp’ ‘mark005.out’ ‘mark005.res’
  ‘mark005.vcv’ ‘mark006.inp’ ‘mark006.out’ ‘mark006.res’ ‘mark006.vcv’
  ‘mark007.inp’ ‘mark007.out’ ‘mark007.res’ ‘mark007.vcv’ ‘mark008.inp’
  ‘mark008.out’ ‘mark008.res’ ‘mark008.vcv’ ‘mark009.inp’ ‘mark009.out’
  ‘mark009.res’ ‘mark009.vcv’ ‘mark010.inp’ ‘mark010.out’ ‘mark010.res’
  ‘mark010.vcv’ ‘mark010V.tmp’ ‘mark010X.tmp’ ‘mark010Y.tmp’
  ‘mark011.inp’ ‘mark011.out’ ‘mark011.res’ ‘mark011.vcv’ ‘mark012.inp’
  ‘mark012.out’ ‘mark012.res’ ‘mark012.vcv’ ‘mark013.inp’ ‘mark013.out’
  ‘mark013.res’ ‘mark013.vcv’
installed size is 60.4Mb
  sub-directories of 1Mb or more:
    libs  59.7Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   6.8Mb
installed size is 40.0Mb
  sub-directories of 1Mb or more:
    libs  39.1Mb
installed size is 34.6Mb
  sub-directories of 1Mb or more:
    libs  34.4Mb
File ‘RMKdiscrete/libs/RMKdiscrete.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘statmod’
  All declared Imports should be used.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
File ‘rnetcarto/libs/rnetcarto.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rngSetSeed/libs/rngSetSeed.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rngwell19937/libs/rngwell19937.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doxygen   1.6Mb
    libs      3.5Mb
installed size is 92.6Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     90.4Mb
Namespace in Imports field not imported from: ‘impute’
  All declared Imports should be used.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
Namespaces in Imports field not imported from:
  ‘abind’ ‘foreach’
  All declared Imports should be used.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R  11.2Mb
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  16.0Mb
File ‘robcp/libs/robcp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DEoptimR’ ‘DT’ ‘PerformanceAnalytics’ ‘ggplot2’ ‘graphics’
  ‘gridExtra’ ‘methods’ ‘robust’ ‘shinyjs’ ‘utils’ ‘xts’
  All declared Imports should be used.
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
File ‘robustETM/libs/robustETM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘robustgam/libs/robustgam.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    libs  23.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    libs  33.2Mb
File ‘robustloggamma/libs/robustloggamma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         2.7Mb
    extdata   2.7Mb
Namespace in Imports field not imported from: ‘matrixcalc’
  All declared Imports should be used.
File ‘Rook/libs/Rook.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs  25.2Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘utils’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    libs    2.4Mb
    tests   1.3Mb
File ‘rpartitions/libs/rpartitions.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘robustbase’
  All declared Imports should be used.
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  21.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      4.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘testthat’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
Found the following significant warnings:
  wrapper_Message.cpp:149:25: warning: 'ByteSize' is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations]
  wrapper_Message.cpp:253:49: warning: 'ByteSize' is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/RProtoBuf.Rcheck/00install.out’ for details.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Namespaces in Imports field not imported from:
  ‘ape’ ‘igraph’
  All declared Imports should be used.
File ‘rPython/libs/rPython.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘NatureSounds’
  All declared Imports should be used.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    extdata  12.8Mb
File ‘rredis/libs/rredis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  rf.c:485:1: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/RRF.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘mvMORPH’
  All declared Imports should be used.
File ‘rr/libs/rr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rsae/libs/rsae.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
File ‘rscimark/libs/rscimark.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘RSclient/libs/RSclient.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rsdepth/libs/rsdepth.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘binman’ ‘httr’
  All declared Imports should be used.
Found the following significant warnings:
  Rserv.c:2150:17: warning: 'RSA_generate_key' is deprecated [-Wdeprecated-declarations]
  oc.c:47:33: warning: 'RAND_pseudo_bytes' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/Rserve.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rsgcc/libs/rsgcc.so’:
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’
File ‘rsgcc/libs/rsgcc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
File ‘RSKC/libs/RSKC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘miniUI’ ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘methods’ ‘tcltk’ ‘tools’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
Namespace in Imports field not imported from: ‘h2o’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 46.8Mb
  sub-directories of 1Mb or more:
    libs  46.1Mb
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
Namespace in Imports field not imported from: ‘RSQLite’
  All declared Imports should be used.
installed size is 217.1Mb
  sub-directories of 1Mb or more:
    R       1.6Mb
    doc     4.5Mb
    libs  210.4Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
installed size is 191.4Mb
  sub-directories of 1Mb or more:
    libs  188.6Mb
installed size is 101.9Mb
  sub-directories of 1Mb or more:
    libs  100.5Mb
Namespace in Imports field not imported from: ‘loo’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  14.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
File ‘RSvgDevice/libs/RSvgDevice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘RSVGTipsDevice/libs/RSVGTipsDevice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    Lib  11.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘stats’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
File ‘rtfbs/libs/rtfbs.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       2.7Mb
    projects   2.8Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Namespace in Imports field not imported from: ‘quantmod’
  All declared Imports should be used.
Found the following significant warnings:
  getFunctions.cpp:90:16: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/RTransProb.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘memoise’ ‘tidyr’
  All declared Imports should be used.
installed size is 30.2Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  21.5Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   2.4Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   7.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
Namespace in Imports field not imported from: ‘RGtk2’
  All declared Imports should be used.
installed size is 57.8Mb
  sub-directories of 1Mb or more:
    libs  57.1Mb
File ‘rvgtest/libs/rvgtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
rvideopoker: warning in rp.radiogroup(mypanel, var =
  state$penny.nickel.quarter.dollar, initval = 1, values = c(1, 5, 25,
  100), title = "Bet (in Cents)", action = setbet): partial argument
  match of 'var' to 'variable'
rvideopoker: warning in rp.slider(mypanel, var = state$no.of.credits,
  from = 1, to = 5, initval = 1, title = "How many Credits?",
  resolution = 1, action = creditset, showvalue = TRUE): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC1, action = card1check, title = "Keep Card 1?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC2, action = card2check, title = "Keep Card 2?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC3, action = card3check, title = "Keep Card 3?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC4, action = card4check, title = "Keep Card 4?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC5, action = card5check, title = "Keep Card 5?"): partial
  argument match of 'var' to 'variable'
rvideopoker : plotFrame: no visible global function definition for
  ‘par’
rvideopoker : showBack: no visible global function definition for
  ‘title’
rvideopoker : showCardsInitially: no visible global function definition
  for ‘title’
Undefined global functions or variables:
  par title
Consider adding
  importFrom("graphics", "par", "title")
to your NAMESPACE file.
Package suggested but not available for checking: ‘gpuR’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    include   5.3Mb
installed size is 57.6Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs     53.3Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/RVowpalWabbit.Rcheck/00install.out’ for details.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
File ‘rwfec/libs/rwfec.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  qwiener.c:60:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  qwiener.c:69:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/RWiener.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'SnakeCharmR', 'installr'

Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs    8.5Mb
    yacas   1.5Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs    9.2Mb
    yacas   1.6Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  15.1Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
possible bashism in configure line 34 ($(OS|MACH)TYPE):
    case "$OSTYPE" in "darwin"*)
  possible bashism in configure line 40 (should be '.', not 'source'):
      source autobrew
Namespace in Imports field not imported from: ‘spanel’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘mgcv’
  All declared Imports should be used.
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/SafeBayes.Rcheck/00install.out’ for details.
File ‘SafeBayes/libs/SafeBayes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘shinybusy’
  All declared Imports should be used.
File ‘SALES/libs/SALES.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs  13.0Mb
Namespaces in Imports field not imported from:
  ‘gdistance’ ‘methods’
  All declared Imports should be used.
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
File ‘sampling/libs/sampling.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   3.7Mb
File ‘sanitizers/libs/sanitizers.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘purrr’ ‘tidyr’
  All declared Imports should be used.
File ‘sapa/libs/sapa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SAPP/libs/SAPP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 63.0Mb
  sub-directories of 1Mb or more:
    extdata  62.6Mb
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
File ‘saturnin/libs/saturnin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SAVE/libs/SAVE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sbfc/libs/sbfc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sBIC/libs/sBIC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sbioPN/libs/sbioPN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sbmSDP/libs/sbmSDP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sbrl/libs/sbrl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SBSA/libs/SBSA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'
Namespace in Imports field not imported from: ‘pvclust’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘methods’
  All declared Imports should be used.
File ‘scar/libs/scar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘cowplot’ ‘ggplot2’ ‘ggridges’ ‘ggstance’ ‘jmvcore’
  All declared Imports should be used.
File ‘SCEPtERbinary/libs/SCEPtERbinary.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
File ‘SCEPtER/libs/SCEPtER.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘spData’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘stringi’ ‘stringr’ ‘tibble’ ‘tidyr’ ‘tidytext’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/scio.Rcheck/00install.out’ for details.
File ‘scio/libs/scio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘scorer/libs/scorer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘scout/libs/scout.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SDDE/libs/SDDE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sde/libs/sde.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’ ‘tidyr’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R   7.1Mb
File ‘SearchTrees/libs/SearchTrees.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  16.4Mb
Namespaces in Imports field not imported from:
  ‘ForeCA’ ‘Mcomp’ ‘repmis’
  All declared Imports should be used.
File ‘segmag/libs/segmag.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking: 'flowMerge', 'flowClust'
Packages unavailable to check Rd xrefs: ‘flowClust’, ‘flowMerge’
Found the following significant warnings:
  BinNegative.cpp:108:5: warning: assigning field to itself [-Wself-assign-field]
See ‘/data/gannet/ripley/R/packages/tests-clang/Segmentor3IsBack.Rcheck/00install.out’ for details.
File ‘Segmentor3IsBack/libs/Segmentor3IsBack.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘cluster’ ‘factoextra’ ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘FD’
  All declared Imports should be used.
predict.SEL: warning in splineDesign(newdata, knots = knts, ord =
  object$nord, deriv = rep(deriv, length(newdata)), outer.ok = TRUE):
  partial argument match of 'deriv' to 'derivs'
getbinPost: no visible binding for global variable ‘dbeta’
getbinPost: no visible binding for global variable ‘pbeta’
getbinPost : fu: no visible global function definition for ‘dbinom’
getbinPost : fu: no visible global function definition for ‘predict’
getbinPost: no visible global function definition for ‘integrate’
getbinPost: no visible global function definition for ‘splinefun’
int.funct: no visible global function definition for ‘integrate’
int.funct2: no visible global function definition for ‘integrate’
min.abs: no visible global function definition for ‘uniroot’
plot.SEL: no visible global function definition for ‘plot’
print.SEL: no visible global function definition for ‘integrate’
print.summary.SEL : foo1: no visible global function definition for
  ‘predict’
print.summary.SEL : foo2: no visible global function definition for
  ‘predict’
print.summary.SEL: no visible global function definition for
  ‘integrate’
quantSEL: no visible global function definition for ‘predict’
quantSEL: no visible global function definition for ‘splinefun’
rvSEL: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbeta dbinom integrate pbeta plot predict runif splinefun uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dbeta", "dbinom", "integrate", "pbeta", "predict",
             "runif", "splinefun", "uniroot")
to your NAMESPACE file.
File ‘SEL/libs/SEL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lavaan’ ‘psych’ ‘semPlot’ ‘semTools’ ‘shinyAce’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
Namespaces in Imports field not imported from:
  ‘htmlTable’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘SemNetCleaner’ ‘grid’ ‘purrr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘expm’ ‘matrixStats’ ‘matrixcalc’
  All declared Imports should be used.
File ‘semver/libs/semver.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sensitivityPStrat/libs/sensitivityPStrat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.9Mb
Running examples in ‘sEparaTe-Ex.R’ failed
The error most likely occurred in:

> ### Name: lrt2d_svc
> ### Title: Unbiased modified likelihood ratio test for simple separability
> ###   of a variance-covariance matrix.
> ### Aliases: lrt2d_svc
> 
> ### ** Examples
> 
> #To reduce the time elapsed, this example uses only 160 simulations.
> #8000 simulations or more are recommended in an example like this.
> output <- lrt2d_svc(value2d~Id1+Id2, rep = "K", data = data2d, n.simul = 160)
Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) : 
  'x' must be atomic
Calls: lrt2d_svc ... quantile.default -> sort -> sort.default -> sort.int
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs  14.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Package suggested but not available for checking: ‘muscle’
File ‘seqMeta/libs/seqMeta.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    libs  25.6Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
File ‘sequences/libs/sequences.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
capture: no visible binding for global variable ‘resultText’
restore.session: no visible binding for global variable
  ‘.save.session.packages’
restore.session: no visible binding for global variable
  ‘.save.session.search’
save.session: no visible global function definition for ‘dev.list’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.search’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.packages’
Undefined global functions or variables:
  .save.session.packages .save.session.search dev.list resultText
Consider adding
  importFrom("grDevices", "dev.list")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'loomR', 'SDMTools', 'MAST', 'monocle'

Imports includes 36 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   7.9Mb
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    doc     12.0Mb
    libs     9.4Mb
    sqlite   1.5Mb
File ‘sgeostat/libs/sgeostat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.4Mb
Namespaces in Imports field not imported from:
  ‘parallel’ ‘plyr’
  All declared Imports should be used.
File ‘sharpData/libs/sharpData.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
Namespace in Imports field not imported from: ‘shinydashboard’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘htmlwidgets’ ‘jsonlite’ ‘viridis’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘VGAM’ ‘data.table’ ‘ggdendro’ ‘gridExtra’ ‘knitr’
  ‘latticeExtra’ ‘msm’ ‘plotly’ ‘shinyBS’ ‘shinydashboard’ ‘xtable’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘getPass’ ‘svglite’ ‘websocket’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘shiny’ ‘shinyjs’
  All declared Imports should be used.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    www   8.3Mb
Namespaces in Imports field not imported from:
  ‘CARE1’ ‘LCMCR’ ‘coda’ ‘conting’ ‘dga’ ‘future’ ‘ggplot2’ ‘ipc’
  ‘promises’ ‘reshape’ ‘shinycssloaders’ ‘testthat’
  All declared Imports should be used.
File ‘siar/libs/siar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘coda’ ‘ellipse’ ‘viridis’
  All declared Imports should be used.
File ‘signal/libs/signal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.2Mb
Namespaces in Imports field not imported from:
  ‘KernSmooth’ ‘MASS’ ‘class’ ‘cluster’ ‘lattice’ ‘nnet’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘grid’
  All declared Imports should be used.
File ‘simFrame/libs/simFrame.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  12.9Mb
Running examples in ‘SIMMS-Ex.R’ failed
The error most likely occurred in:

> ### Name: SIMMS-package
> ### Title: SIMMS - Subnetwork Integration for Multi-Modal Signatures
> ### Aliases: SIMMS-package SIMMS
> ### Keywords: package
> 
> ### ** Examples
> 
> 
> options("warn" = -1);
> 
> # get data directory 
> data.directory <- get.program.defaults(networks.database = "test")[["test.data.dir"]];
> 
> # initialise params
> output.directory <- ".";
> data.types <- c("mRNA");
> feature.selection.datasets <- c("Breastdata1");
> training.datasets <- c("Breastdata1");
> validation.datasets <- c("Breastdata2");
> feature.selection.p.thresholds <- c(0.5);
> feature.selection.p.threshold <- 0.5;
> learning.algorithms <- c("backward", "forward", "glm");
> top.n.features <- 5;
> 
> # compute network HRs for all the subnet features
> derive.network.features(
+   data.directory = data.directory,
+   output.directory = output.directory,
+   data.types = data.types,
+   feature.selection.datasets = feature.selection.datasets,
+   feature.selection.p.thresholds = feature.selection.p.thresholds,
+   networks.database = "test"
+   );
Error in order(x[, 1], decreasing = TRUE) : 
  unimplemented type 'list' in 'orderVector1'
Calls: derive.network.features -> as.matrix -> order
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Using-SIMMS.Rmd’ using rmarkdown
Loading required package: survival
Loading required package: MASS
Loading required package: glmnet
Loading required package: Matrix
Loaded glmnet 3.0-2

Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Quitting from lines 125-232 (Using-SIMMS.Rmd) 
Error: processing vignette 'Using-SIMMS.Rmd' failed with diagnostics:
unimplemented type 'list' in 'orderVector1'

--- failed re-building ‘Using-SIMMS.Rmd’

SUMMARY: processing the following file failed:
  ‘Using-SIMMS.Rmd’

Error: Vignette re-building failed.
Execution halted
File ‘simplexreg/libs/simplexreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.3Mb
File ‘SimReg/libs/SimReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  23.0Mb
Namespace in Imports field not imported from: ‘pracma’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘psych’ ‘stringr’
  All declared Imports should be used.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   8.0Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
File ‘skda/libs/skda.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘car’ ‘het.test’ ‘lmtest’ ‘lubridate’ ‘magrittr’ ‘tibble’ ‘tseries’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/skeleSim.Rcheck/00install.out’ for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.6Mb
File ‘skm/libs/skm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 34.4Mb
  sub-directories of 1Mb or more:
    libs  32.8Mb
File ‘sld/libs/sld.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
Found the following significant warnings:
  slfm_MDN.cpp:26:38: warning: expression result unused [-Wunused-value]
  slfm_MNN.cpp:26:38: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/slfm.Rcheck/00install.out’ for details.
File ‘SLHD/libs/SLHD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘viridisLite’
  All declared Imports should be used.
File ‘SLOPE/libs/SLOPE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘slp/libs/slp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 15 marked Latin-1 strings
  Note: found 2 marked UTF-8 strings
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Namespaces in Imports field not imported from:
  ‘Amelia’ ‘Boruta’ ‘DMwR’ ‘MVN’ ‘NoiseFiltersR’ ‘VIM’ ‘adaptiveGPCA’
  ‘class’ ‘clusterSim’ ‘denoiseR’ ‘discretization’ ‘imbalance’ ‘lle’
  ‘missForest’ ‘missMDA’ ‘outliers’ ‘unbalanced’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
Namespace in Imports field not imported from: ‘covr’
  All declared Imports should be used.
Imports includes 36 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.

Requires orphaned package: ‘clues’
File ‘SMC/libs/SMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘smds/libs/smds.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  11.2Mb
Found the following significant warnings:
  ./Scythe_IDE.cpp:70:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:107:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:108:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:109:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:147:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:148:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:149:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:189:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:211:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:212:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:262:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:265:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:266:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/data/gannet/ripley/R/packages/tests-clang/smoothSurv.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘ggplot2’
  All declared Imports should be used.
File ‘snipEM/libs/snipEM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘snnR/libs/snnR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SnowballC/libs/SnowballC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.8Mb
File ‘snpStatsWriter/libs/snpStatsWriter.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘raster’ ‘rlang’ ‘sp’ ‘usethis’
  All declared Imports should be used.
File ‘SocialNetworks/libs/SocialNetworks.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SoDA/libs/SoDA.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘softImpute/libs/softImpute.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    data  11.7Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘nnet’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘AGread’ ‘caret’
  All declared Imports should be used.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.6Mb
    libs   6.5Mb
File ‘som/libs/som.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SoundexBR/libs/SoundexBR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
Namespaces in Imports field not imported from:
  ‘gtools’ ‘hashmap’ ‘reshape2’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
File ‘SpaCCr/libs/SpaCCr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘space/libs/space.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘spacodiR/libs/spacodiR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘rstudioapi’
  All declared Imports should be used.
installed size is 35.5Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    libs  33.0Mb
Imports includes 28 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
File ‘sparcl/libs/sparcl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SparseFactorAnalysis/libs/SparseFactorAnalysis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
File ‘sparseLTSEigen/libs/sparseLTSEigen.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sparsereg/libs/sparsereg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sparseSEM/libs/sparseSEM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SparseTSCGM/libs/SparseTSCGM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
File ‘spate/libs/spate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘fasterize’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘SpatialEpi’ ‘dplyr’ ‘dygraphs’ ‘ggplot2’
  ‘htmlwidgets’ ‘knitr’ ‘leaflet’ ‘mapproj’ ‘maptools’ ‘rgdal’ ‘rgeos’
  ‘rmarkdown’ ‘shinyjs’ ‘spdep’ ‘xts’
  All declared Imports should be used.
File ‘spatialfil/libs/spatialfil.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.1Mb
Note: found 25 marked Latin-1 strings
  Note: found 658 marked UTF-8 strings
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  19.4Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
File ‘SpaTimeClus/libs/SpaTimeClus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘spatstat.Knet/libs/spatstat.Knet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    R      5.3Mb
    doc    4.9Mb
    help   5.2Mb
    libs   2.1Mb
installed size is 34.2Mb
  sub-directories of 1Mb or more:
    libs  33.3Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
    libs  11.4Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
File ‘spcr/libs/spcr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.2Mb
File ‘SPECIES/libs/SPECIES.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   2.7Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘usethis’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pdftools’
  All declared Imports should be used.
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nr' to 'nrow'
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nc' to 'ncol'
spe: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
File ‘spe/libs/spe.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’
  All declared Imports should be used.
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    libs  22.6Mb
File ‘spikeslab/libs/spikeslab.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Namespaces in Imports field not imported from:
  ‘GGally’ ‘tibble’ ‘webshot’
  All declared Imports should be used.
File ‘splus2R/libs/splus2R.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘spm12r-Ex.R’ failed
The error most likely occurred in:

> ### Name: install_spm12
> ### Title: Install SPM12 file into directory
> ### Aliases: install_spm12
> 
> ### ** Examples
> 
> tdir = tempfile()
> dir.create(tdir)
> in_ci <- function() {
+ nzchar(Sys.getenv("CI"))
+ }
> if (.Platform$OS.type == "unix" | in_ci()) { # windows problem
+ res = install_spm12(install_dir = tdir)
+ res = install_spm12(install_dir = tdir)
+ }
cloning into '/tmp/Rtmpk78bLc/working_dir/RtmpaSTNvF/file1c785bf1e3c9/spm12'...

 *** caught segfault ***
address 0xc800010009, cause 'memory not mapped'

Traceback:
 1: git2r::clone("https://github.com/muschellij2/spm12r", branch = "gh-pages",     local_path = out_path, progress = verbose)
 2: install_spm12(install_dir = tdir)
An irrecoverable exception occurred. R is aborting now ...
Namespace in Imports field not imported from: ‘biomod2’
  All declared Imports should be used.
File ‘SPODT/libs/SPODT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 8 marked Latin-1 strings
  Note: found 83 marked UTF-8 strings
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs  10.0Mb
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘ggplot2’
  All declared Imports should be used.
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs  13.7Mb
Namespaces in Imports field not imported from:
  ‘BayesX’ ‘BayesXsrc’ ‘automap’ ‘plyr’ ‘rgdal’ ‘splines’
  All declared Imports should be used.
File ‘sROC/libs/sROC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘shinyFiles’
  All declared Imports should be used.
possible bashism in configure line 19 ('command' with option other than -p):
  if [ $(command -v pkg-config) ]; then
  possible bashism in configure line 33 ($(OS|MACH)TYPE):
  elif [[ "$OSTYPE" == "darwin"* ]]; then
  possible bashism in configure line 33 (alternative test command ([[ foo ]] should be [ foo ])):
  elif [[ "$OSTYPE" == "darwin"* ]]; then
  possible bashism in configure line 33 (should be 'b = a'):
  elif [[ "$OSTYPE" == "darwin"* ]]; then
  possible bashism in configure line 34 ('command' with option other than -p):
    if [ $(command -v brew) ]; then
  possible bashism in configure line 38 (should be '.', not 'source'):
      source autobrew
installed size is 79.8Mb
  sub-directories of 1Mb or more:
    libs  79.4Mb
File ‘sspline/libs/sspline.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stabledist’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘stacomir.Rmd’ using rmarkdown
Quitting from lines 281-303 (stacomir.Rmd) 
Error: processing vignette 'stacomir.Rmd' failed with diagnostics:
round(sum(datasub$value, na.rm = TRUE), 2) and round(sum(datasub2$value, na.rm = TRUE), 2) are not equal:
  Mean relative difference: 0.000996741
--- failed re-building ‘stacomir.Rmd’

SUMMARY: processing the following file failed:
  ‘stacomir.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘potato_distance.txt’
stkde: no visible global function definition for ‘npudensbw’
stkde: no visible global function definition for ‘npudens’
stkde: no visible global function definition for ‘quantile’
stkde: no visible global function definition for ‘heat.colors’
stkde: no visible global function definition for ‘par’
stkde: no visible global function definition for ‘image’
stkde: no visible global function definition for ‘contour’
stkde.base: no visible global function definition for ‘npudensbw’
stkde.base: no visible global function definition for ‘npudens’
stkde.sig: no visible global function definition for ‘SpatialPoints’
stkde.sig: no visible global function definition for ‘spsample’
stkde.sig: no visible global function definition for ‘bbox’
stkde.sig: no visible global function definition for ‘quantile’
stkde.sig: no visible global function definition for ‘heat.colors’
stkde.sig: no visible global function definition for ‘par’
stkde.sig: no visible global function definition for ‘image’
stkde.sig: no visible global function definition for ‘contour’
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    include  10.3Mb
    lib       3.0Mb
File ‘starma/libs/starma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   4.9Mb
File ‘STAR/libs/STAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    doc  10.3Mb
    nc    4.5Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   5.1Mb
File ‘staTools/libs/staTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gbm’ ‘ggfortify’ ‘tibble’ ‘tidyverse’
  All declared Imports should be used.
File ‘STB/libs/STB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   4.9Mb
File ‘steadyICA/libs/steadyICA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘rlist’ ‘tm’ ‘zoo’
  All declared Imports should be used.
File ‘steepness/libs/steepness.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
File ‘stepwise/libs/stepwise.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘StepwiseTest/libs/StepwiseTest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘stlplus/libs/stlplus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘tm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘huge’ ‘readr’ ‘scales’ ‘shinyjs’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R          2.1Mb
    datasets   2.6Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.6Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Namespace in Imports field not imported from: ‘knitcitations’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘BSgenome’ ‘BiocManager’
  All declared Imports should be used.
Running examples in ‘strandCet-Ex.R’ failed
The error most likely occurred in:

> ### Name: HP.pred
> ### Title: Prediction of Heligman-Pollard model.
> ### Aliases: HP.pred
> ### Keywords: Heligman-Pollard mortality prediction
> 
> ### ** Examples
> 
> 
> lifeN <- life.tab(cetaceans)
Error in life$Sx/d : non-numeric argument to binary operator
Calls: life.tab
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   3.2Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘Hmisc’ ‘RColorBrewer’ ‘Rcpp’ ‘readr’
  All declared Imports should be used.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Namespace in Imports field not imported from: ‘bnlearn’
  All declared Imports should be used.
File ‘strat/libs/strat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ks’
  All declared Imports should be used.
Found the following significant warnings:
  BIRCH/CFTree.cpp:18:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/stream.Rcheck/00install.out’ for details.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  11.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘broom’ ‘car’ ‘lmerTest’ ‘pbkrtest’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
File ‘strum/libs/strum.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gWidgets2tcltk’
  All declared Imports should be used.
File ‘stsm/libs/stsm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘pls’ ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘UpSetR’ ‘alluvial’ ‘gridBase’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘V8’ ‘bsplus’ ‘colourpicker’ ‘dplyr’ ‘grDevices’ ‘graphics’
  ‘jsonlite’ ‘shinyjs’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lwgeom’
  All declared Imports should be used.
File ‘SummaryLasso/libs/SummaryLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.4Mb
File ‘Sunder/libs/Sunder.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘supclust/libs/supclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R.matlab’ ‘fBasics’ ‘spls’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘mvtnorm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DiceOptim’ ‘GPareto’ ‘rgenoud’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘learnr’
  All declared Imports should be used.
File ‘survAUC/libs/survAUC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘survC1/libs/survC1.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    libs   1.8Mb
File ‘surveybootstrap/libs/surveybootstrap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 156.8Mb
  sub-directories of 1Mb or more:
    libs  155.2Mb
File ‘survIDINRI/libs/survIDINRI.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   3.2Mb
    doc    3.3Mb
File ‘survivalROC/libs/survivalROC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
File ‘survSNP/libs/survSNP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘stats’ ‘survival’ ‘utils’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   6.8Mb
File ‘svcm/libs/svcm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘svmadmm/libs/svmadmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SVMMatch/libs/SVMMatch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘svmpath/libs/svmpath.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘_gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi30spec.o’, ‘mi35mps.o’,
      ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘_gfortran_st_rewind’, possibly from ‘rewind’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi10unix.o’, ‘mi35mps.o’, ‘mi40bfil.o’
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’
File ‘svmpath/libs/svmpath.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lazyeval’ ‘lubridate’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘magrittr’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
File ‘SynchWave/libs/SynchWave.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
Namespaces in Imports field not imported from:
  ‘gee’ ‘survival’
  All declared Imports should be used.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    java  11.5Mb
File ‘tagcloud/libs/tagcloud.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘devEMF’ ‘segmented’ ‘smoother’ ‘tools’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   5.3Mb
Namespace in Imports field not imported from: ‘jiebaR’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘dplyr’ ‘igraph’ ‘tm’ ‘wordcloud2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘drat’ ‘plyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘lazyeval’ ‘rlang’ ‘tidyr’
  All declared Imports should be used.
File ‘tbart/libs/tbart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘PerformanceAnalytics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘glmnet’ ‘quadprog’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    tklibs   4.9Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.9Mb
    libs   1.0Mb
installed size is 33.7Mb
  sub-directories of 1Mb or more:
    libs  32.3Mb
File ‘TDboost/libs/TDboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.

Requires orphaned package: ‘d3heatmap’
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    apps   2.8Mb
    libs   8.4Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘tidyr’
  All declared Imports should be used.
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  16.9Mb
Running examples in ‘TempleMetrics-Ex.R’ failed
The error most likely occurred in:

> ### Name: Fycondx.DR
> ### Title: Fycondx.DR
> ### Aliases: Fycondx.DR
> 
> ### ** Examples
> 
> data(igm)
> yvals <- seq(quantile(igm$lcfincome,.05,type=1),
+  quantile(igm$lcfincome,.95, type=1), length.out=100)
> dres <- distreg(lcfincome ~ lfincome + HEDUC, igm, yvals)
> xdf <- data.frame(lfincome=10, HEDUC=c("LessHS","HS"))
> d <- Fycondx(dres, yvals, xdf)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
TempleMetrics
 --- call from context --- 
Fycondx.DR(dres, yvals, xdf)
 --- call from argument --- 
if (class(predmat) == "numeric") {
    predmat <- t(predmat)
}
 --- R stacktrace ---
where 1: Fycondx.DR(dres, yvals, xdf)
where 2: Fycondx(dres, yvals, xdf)

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (object, yvals, xdf) 
{
    drobj <- object
    yvals <- drobj$yvals
    glmlist <- drobj$glmlist
    predmat <- sapply(glmlist, function(g) {
        predict(g, newdata = xdf, type = "response")
    })
    if (class(predmat) == "numeric") {
        predmat <- t(predmat)
    }
    out <- lapply(1:nrow(predmat), function(i) {
        makeDist(yvals, predmat[i, ], rearrange = TRUE)
    })
    out
}
<bytecode: 0x2729978>
<environment: namespace:TempleMetrics>
 --- function search by body ---
Function Fycondx.DR in namespace TempleMetrics has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(predmat) == "numeric") { : 
  the condition has length > 1
Calls: Fycondx -> Fycondx.DR
Execution halted
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
File ‘tensorA/libs/tensorA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
possible bashism in configure line 34 ($(OS|MACH)TYPE):
    case "$OSTYPE" in "darwin"*)
  possible bashism in configure line 42 (should be '.', not 'source'):
      source autobrew
File ‘TESS/libs/TESS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘par-7269706c6579’
Namespaces in Imports field not imported from:
  ‘stringi’ ‘utils’
  All declared Imports should be used.
File ‘testforDEP/libs/testforDEP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    2.9Mb
    libs   4.9Mb
Note: found 10051 marked UTF-8 strings
  Note: found 10523 strings marked as "bytes"
Namespace in Imports field not imported from: ‘lexicon’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘parallel’ ‘tidyr’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   8.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
Running ‘testthat.R’ [17s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(textrecipes)
  Loading required package: recipes
  Loading required package: dplyr
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  
  Attaching package: 'recipes'
  
  The following object is masked from 'package:stats':
  
      step
  
  > 
  > test_check("textrecipes")
  ── 1. Failure: step_tfidf works as intended (@test-tfidf.R#44)  ────────────────
  as.matrix(rec_answer) not equal to as.matrix(manual_answer).
  29/68 mismatches (average diff: 0.123)
  [4]  0.201 - 0.0866 == 0.115
  [7]  0.201 - 0.0866 == 0.115
  [10] 0.268 - 0.1155 == 0.153
  [16] 0.201 - 0.0866 == 0.115
  [17] 0.106 - 0.0000 == 0.106
  [18] 0.141 - 0.0000 == 0.141
  [19] 0.106 - 0.0000 == 0.106
  [23] 0.201 - 0.0866 == 0.115
  [27] 0.201 - 0.0866 == 0.115
  ...
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 88 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 1 ]
  1. Failure: step_tfidf works as intended (@test-tfidf.R#44) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘textreuse/libs/textreuse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  16.5Mb
File ‘tgp/libs/tgp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    rda    7.1Mb
Namespace in Imports field not imported from: ‘proxy’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘splancs’ ‘tidyverse’
  All declared Imports should be used.
installed size is 31.5Mb
  sub-directories of 1Mb or more:
    libs  31.1Mb
Namespace in Imports field not imported from: ‘mix’
  All declared Imports should be used.
Running ‘testthat.R’ [15s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidytext)
  > 
  > test_check("tidytext")
  ── 3. Error: (unknown) (@test-corpus-tidiers.R#33)  ────────────────────────────
  Internal error: Trace data is not square.
  Backtrace:
    1. testthat::test_check("tidytext")
    2. testthat:::test_package_dir(...)
    3. testthat::test_dir(...)
    4. testthat:::test_files(...)
   10. base::lapply(...)
   11. testthat:::FUN(X[[i]], ...)
   17. testthat::source_file(...)
   18. testthat:::test_code(NULL, exprs, env)
   27. [ base::eval(...) ] with 1 more call
   29. testthat::test_that(...)
       ...
   40. testthat:::o_apply(...)
   41. base::lapply(objects, function(x) x[[method]](...))
   42. testthat:::FUN(X[[i]], ...)
   43. x[[method]](...)
   47. testthat:::failure_summary(result, self$n_fail)
   50. testthat:::format.expectation(x)
   51. testthat:::format_with_trace(x)
   53. rlang:::format.rlang_trace(...)
   54. rlang:::trace_format_branch(x, max_frames, dir, srcrefs)
   55. rlang:::branch_uncollapse_pipe(trace)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 274 | SKIPPED: 1 | WARNINGS: 2 | FAILED: 3 ]
  1. Error: Can tidy corpus from quanteda using accessor functions (@test-corpus-tidiers.R#38) 
  2. Error: Can tidy corpus from quanteda using accessor functions (@test-corpus-tidiers.R#33) 
  3. Error: (unknown) (@test-corpus-tidiers.R#33) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   4.4Mb
Namespaces in Imports field not imported from:
  ‘curl’ ‘keyring’ ‘nlme’ ‘rgdal’ ‘stringi’ ‘usethis’
  All declared Imports should be used.
Found the following significant warnings:
  ref.cpp:24:14: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
  ref.cpp:35:14: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
  ref.cpp:50:16: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
  ref.cpp:61:16: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/tidyxl.Rcheck/00install.out’ for details.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
File ‘tidyxl/libs/tidyxl.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
    Object: ‘xlex.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tiff/libs/tiff.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘timma/libs/timma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘broom’ ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘snow’
  All declared Imports should be used.
File ‘TKF/libs/TKF.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tkrplot/libs/tkrplot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    examples  15.0Mb
    include    3.0Mb
installed size is 25.4Mb
  sub-directories of 1Mb or more:
    libs  25.1Mb
File ‘tmg/libs/tmg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tmvnsim/libs/tmvnsim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tmvtnorm/libs/tmvtnorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggplot2’ ‘jsonlite’
  All declared Imports should be used.
File ‘TopKLists/libs/TopKLists.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Running examples in ‘tosca-Ex.R’ failed
The error most likely occurred in:

> ### Name: as.textmeta.corpus
> ### Title: Transform corpus to textmeta
> ### Aliases: as.textmeta.corpus
> ### Keywords: manip
> 
> ### ** Examples
> 
> texts <- c("Give a Man a Fish, and You Feed Him for a Day.
+  Teach a Man To Fish, and You Feed Him for a Lifetime",
+  "So Long, and Thanks for All the Fish",
+  "A very able manipulative mathematician, Fisher enjoys a real mastery
+  in evaluating complicated multiple integrals.")
> 
> corp <- quanteda::corpus(x = texts)
> obj <- as.textmeta.corpus(corp, addMetadata = FALSE)
NOTE: No ID-column "id", set to ascending numbers
NOTE: No date-column "date", set to NA
NOTE: No title-column "title", set to NA
success
number of observations in text: 3 

NAs in text:
 NA.abs NA.rel
      0      0
---------------------------------------------------------------------- 

meta: 3 observations of 3 variables

NAs in meta:
      abs rel
id      0   0
date    3   1
title   3   1
---------------------------------------------------------------------- 

NAs in date: 3 (1)
> 
> quanteda::docvars(corp, "title") <- c("Fishing", "Don't panic!", "Sir Ronald")
> quanteda::docvars(corp, "date") <- c("1885-01-02", "1979-03-04", "1951-05-06")
> quanteda::docvars(corp, "id") <- c("A", "B", "C")
> quanteda::docvars(corp, "additionalVariable") <- 1:3
> 
> obj <- as.textmeta.corpus(corp)
Error in matrix(rep(tmp, each = length(tmpid)), nrow = length(tmpid)) : 
  'data' must be of a vector type, was 'NULL'
Calls: as.textmeta.corpus -> matrix
Execution halted
Namespaces in Imports field not imported from:
  ‘R6’ ‘jmvcore’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Note: found 64 marked Latin-1 strings
  Note: found 548 marked UTF-8 strings
File ‘tpr/libs/tpr.so’:
  Found ‘_ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’
File ‘tpr/libs/tpr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 153 marked Latin-1 strings
  Note: found 108 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘V8’ ‘colorspace’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.7Mb
Namespace in Imports field not imported from: ‘neuralnet’
  All declared Imports should be used.
File ‘trapezoid/libs/trapezoid.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    extdata   1.4Mb
    libs     12.3Mb
File ‘treeperm/libs/treeperm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is 126.8Mb
  sub-directories of 1Mb or more:
    doc     4.1Mb
    libs  121.8Mb
File ‘TrialSize/libs/TrialSize.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
File ‘triebeard/libs/triebeard.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  rfmod.c:467:1: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/trimTrees.Rcheck/00install.out’ for details.
File ‘trimTrees/libs/trimTrees.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tripack/libs/tripack.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.4Mb
Namespaces in Imports field not imported from:
  ‘here’ ‘htmltools’ ‘scales’ ‘stringr’
  All declared Imports should be used.
File ‘truncgof/libs/truncgof.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
File ‘tsc/libs/tsc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   7.6Mb
File ‘tseriesChaos/libs/tseriesChaos.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘tsibble’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.6Mb
covTranspose11: warning in glasso(sc, 2 * rhoc/n, wi.init = gc$wi,
  w.init = gc$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
covTranspose11: warning in glasso(sr, 2 * rhor/p, wi.init = gr$wi,
  w.init = gr$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
.help.ESS: no visible global function definition for ‘index.search’
TransSphere : ttin: no visible global function definition for ‘t.test’
TransSphere: no visible global function definition for ‘sd’
TransSphere: no visible global function definition for ‘quantile’
TransSphere: no visible global function definition for ‘pt’
Undefined global functions or variables:
  index.search pt quantile sd t.test
Consider adding
  importFrom("stats", "pt", "quantile", "sd", "t.test")
to your NAMESPACE file.
File ‘tspmeta/libs/tspmeta.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘forecastHybrid’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘shinyAce’ ‘shinyjs’
  All declared Imports should be used.
File ‘tvd/libs/tvd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘TwoCop/libs/TwoCop.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘TwoPhaseInd/libs/TwoPhaseInd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc     6.4Mb
    ubinc   2.0Mb
File ‘ucminf/libs/ucminf.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘plotly’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’
  ‘shinythemes’ ‘zip’
  All declared Imports should be used.
installed size is 33.2Mb
  sub-directories of 1Mb or more:
    doc         6.9Mb
    dummydata   1.4Mb
    libs       23.5Mb
File ‘udunits2/libs/udunits2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
Namespaces in Imports field not imported from:
  ‘extraDistr’ ‘logitnorm’ ‘nakagami’ ‘tibble’
  All declared Imports should be used.
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.6Mb
    libs   9.4Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespace in Imports field not imported from: ‘mcmcplots’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
Running examples in ‘upwaver-Ex.R’ failed
The error most likely occurred in:

> ### Name: storypoints_and_status
> ### Title: Calculate storypoints ans status of the Cards of a specific
> ###   Board
> ### Aliases: storypoints_and_status
> 
> ### ** Examples
> 
> upwaver::storypoints_and_status("4597", 14351, "807a0c3451c04602b4dbfdc0338a65f7")
No encoding supplied: defaulting to UTF-8.
Error in cards[[i]] : subscript out of bounds
Calls: <Anonymous>
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(upwaver)
  > 
  > test_check("upwaver")
  ── 1. Failure: list_cards() works (@test-upwaver.R#53)  ────────────────────────
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 1 - 4 == -3
  
  ── 2. Error: storypoints() works (@test-upwaver.R#71)  ─────────────────────────
  subscript out of bounds
  Backtrace:
   1. upwaver::storypoints_and_status("4597", 14351, "807a0c3451c04602b4dbfdc0338a65f7")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 20 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: list_cards() works (@test-upwaver.R#53) 
  2. Error: storypoints() works (@test-upwaver.R#71) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘upwaver.Rmd’ using rmarkdown
No encoding supplied: defaulting to UTF-8.
No encoding supplied: defaulting to UTF-8.
No encoding supplied: defaulting to UTF-8.
No encoding supplied: defaulting to UTF-8.
Quitting from lines 106-109 (upwaver.Rmd) 
Error: processing vignette 'upwaver.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘upwaver.Rmd’

SUMMARY: processing the following file failed:
  ‘upwaver.Rmd’

Error: Vignette re-building failed.
Execution halted
File ‘urca/libs/urca.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    data  26.4Mb
Imports includes 32 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   6.4Mb
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘stringdist’ ‘utils’
  All declared Imports should be used.
File ‘uuid/libs/uuid.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
File ‘validatejsonr/libs/validatejsonr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘valorate/libs/valorate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Namespaces in Imports field not imported from:
  ‘rstudioapi’ ‘testthat’
  All declared Imports should be used.
File ‘varband/libs/varband.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘matrixcalc’ ‘saemix’
  All declared Imports should be used.
File ‘vbdm/libs/vbdm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘vbsr/libs/vbsr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
File ‘Vdgraph/libs/Vdgraph.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘vdg/libs/vdg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘freetypeharfbuzz’
  All declared Imports should be used.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  16.9Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    doc    1.2Mb
    help   2.9Mb
Namespaces in Imports field not imported from:
  ‘sp’ ‘viridis’
  All declared Imports should be used.
File ‘VIFCP/libs/VIFCP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘VIGoR/libs/VIGoR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 50.4Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  49.2Mb
File ‘vines/libs/vines.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘DT’ ‘plyr’ ‘reshape’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
installed size is 27.1Mb
  sub-directories of 1Mb or more:
    libs  26.4Mb
Namespace in Imports field not imported from: ‘sqldf’
  All declared Imports should be used.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc           4.3Mb
    docjs         1.4Mb
    htmlwidgets   4.0Mb
File ‘vita/libs/vita.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ingredients’
  All declared Imports should be used.
installed size is 46.2Mb
  sub-directories of 1Mb or more:
    libs  45.8Mb
Namespaces in Imports field not imported from:
  ‘iterators’ ‘knitr’ ‘purrr’ ‘testthat’
  All declared Imports should be used.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘XML’ ‘checkmate’ ‘gstat’ ‘intervals’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘EnvStats’ ‘shiny’ ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tibble’
  All declared Imports should be used.
File ‘waffect/libs/waffect.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘waffect.o’
File ‘waffect/libs/waffect.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 63.0Mb
  sub-directories of 1Mb or more:
    libs  61.7Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ENMeval’ ‘RColorBrewer’ ‘XML’ ‘dismo’ ‘dplyr’ ‘leaflet.extras’
  ‘maptools’ ‘raster’ ‘rgdal’ ‘rgeos’ ‘rmarkdown’ ‘shinyjs’
  ‘shinythemes’ ‘spThin’ ‘spocc’ ‘testthat’ ‘zip’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   6.4Mb
Namespaces in Imports field not imported from:
  ‘raster’ ‘reshape2’
  All declared Imports should be used.
File ‘wavelets/libs/wavelets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘waveslim/libs/waveslim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘wavethresh/libs/wavethresh.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘zoo’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(webddx)
  > 
  > test_check("webddx")
  ── 1. Error: query_fz works for a simple query (@testfz_normal.R#7)  ───────────
  HTTP error 410.
  Backtrace:
   1. webddx::query_fz(...)
   2. jsonlite::fromJSON(query_url)
   3. jsonlite:::parse_and_simplify(...)
   4. jsonlite:::parseJSON(txt, bigint_as_char)
   5. jsonlite:::parse_con(txt, bigint_as_char)
   7. base::open.connection(con, "rb")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: query_fz works for a simple query (@testfz_normal.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    client   9.6Mb
    doc      1.0Mb
File ‘webreadr/libs/webreadr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘shiny’ ‘tidyselect’
  All declared Imports should be used.
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘later’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    doc   11.9Mb
    libs   1.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Found the following significant warnings:
  t_region.cpp:78:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:115:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:120:7: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/WhopGenome.Rcheck/00install.out’ for details.
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
Namespaces in Imports field not imported from:
  ‘drc’ ‘imputeTestbench’
  All declared Imports should be used.
File ‘wingui/libs/wingui.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    bn   7.1Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘DescTools’ ‘HydeNet’ ‘RBGL’ ‘Rgraphviz’ ‘arules’ ‘bnlearn’
  ‘dplyr’ ‘graph’ ‘igraph’ ‘linkcomm’ ‘missRanger’ ‘parallel’ ‘psych’
  ‘rhandsontable’ ‘rintrojs’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’
  ‘shinycssloaders’ ‘shinydashboard’ ‘tools’ ‘visNetwork’
  All declared Imports should be used.
File ‘WMCapacity/libs/WMCapacity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
possible bashism in configure line 49 (test -a/-o):
  if test ${java_version_maj} -ge 5 || \
      test ${java_version_maj} -eq 1 -a ${java_version_min} -ge 5;
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.7Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
Package suggested but not available for checking: ‘ROTS’
Packages unavailable to check Rd xrefs: ‘cleaver’, ‘ROTS’
File ‘wskm/libs/wskm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   6.9Mb
Namespace in Imports field not imported from: ‘simts’
  All declared Imports should be used.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-clang/x13binary.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    bin   5.4Mb
installed size is 23.7Mb
  sub-directories of 1Mb or more:
    libs  22.9Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    java  19.0Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    java   9.8Mb
possible bashism in configure line 31 ($(OS|MACH)TYPE):
      if echo $OSTYPE | grep -q '^darwin1[567]'; then
File ‘XMRF/libs/XMRF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘XNomial/libs/XNomial.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘ggdendro’
  All declared Imports should be used.
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  27.1Mb
File ‘xseq/libs/xseq.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    include   3.5Mb
    libs      1.8Mb
File ‘yakmoR/libs/yakmoR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘miniUI’ ‘shinyBS’
  All declared Imports should be used.
installed size is 41.4Mb
  sub-directories of 1Mb or more:
    libs  41.1Mb
Namespace in Imports field not imported from: ‘ghyp’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   3.3Mb
Namespaces in Imports field not imported from:
  ‘Amelia’ ‘MatchIt’ ‘WhatIf’
  All declared Imports should be used.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘testthat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘moonBook’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
asp: no visible global function definition for ‘as.formula’
asp: no visible global function definition for ‘var’
aspm: no visible binding for global variable ‘X.Declan’
aspm: no visible binding for global variable ‘Z.Jaida’
aspm: no visible binding for global variable ‘group.vec.Handan’
aspm: no visible global function definition for ‘as.formula’
aspm: no visible global function definition for ‘glm’
aspm: no visible global function definition for ‘binomial’
aspm: no visible global function definition for ‘poisson’
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/adegenet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/adephylo.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/adespatial.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/adhoc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/adiv.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/AHMbook.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/AICcmodavg.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/AMModels.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/AMOEBA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/angstroms.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/anipaths.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/antaresViz.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [6s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(aoos)
  > 
  > test_check("aoos")
  ── 1. Failure: Type inheritance (@test-S4-types.R#75)  ─────────────────────────
  inherits(Child(), "Test2") isn't true.
  
  ── 2. Failure: Type with VIRTUAL (@test-S4-types.R#111)  ───────────────────────
  names(Test(x = 2)) == "x" isn't true.
  
  ── 3. Failure: Type with VIRTUAL (@test-S4-types.R#112)  ───────────────────────
  inherits(Test(), "Type") isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 187 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: Type inheritance (@test-S4-types.R#75) 
  2. Failure: Type with VIRTUAL (@test-S4-types.R#111) 
  3. Failure: Type with VIRTUAL (@test-S4-types.R#112) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/apex.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/APSIM.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/audio.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/BAT.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘adaptation_level.Rmd’ using rmarkdown
Loading required package: Rcpp

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 85-87 (adaptation_level.Rmd) 
Error: processing vignette 'adaptation_level.Rmd' failed with diagnostics:
result would be too long a vector
--- failed re-building ‘adaptation_level.Rmd’

--- re-building ‘afterimages.Rmd’ using rmarkdown
Loading required package: Rcpp

********************************************************
Note: As of version 1.0.0, cowplot does not change the
  default ggplot2 theme anymore. To recover the previous
  behavior, execute:
  theme_set(theme_cowplot())
********************************************************


Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

--- finished re-building ‘afterimages.Rmd’

--- re-building ‘flanker.Rmd’ using rmarkdown
Loading required package: Rcpp

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Warning in y1 - y2 :
  longer object length is not a multiple of shorter object length
Warning in y1 - y2 :
  longer object length is not a multiple of shorter object length
--- finished re-building ‘flanker.Rmd’

--- re-building ‘stroop.Rmd’ using rmarkdown
Loading required package: Rcpp
Scale for 'fill' is already present. Adding another scale for 'fill', which will replace the existing scale.
--- finished re-building ‘stroop.Rmd’

SUMMARY: processing the following file failed:
  ‘adaptation_level.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/beadplexr.Rcheck/00install.out’ for details.
Running examples in ‘bestglm-Ex.R’ failed
The error most likely occurred in:

> ### Name: oneSDRule
> ### Title: Utility function. Implements the 1-sd rule.
> ### Aliases: oneSDRule
> 
> ### ** Examples
> 
> CV<-c(1.4637799,0.7036285,0.6242480,0.6069406,0.6006877,0.6005472,0.5707958,
+       0.5907897,0.5895489)
> CVsd<-c(0.24878992,0.14160499,0.08714908,0.11376041,0.08522291,
+  0.11897327,0.07960879,0.09235052,0.12860983)
> CVout <- matrix(c(CV,CVsd), ncol=2)
> oneSDRule(CVout)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
bestglm
 --- call from context --- 
oneSDRule(CVout)
 --- call from argument --- 
if (class(CVout) == "train") {
    ans <- CVout
    CVout <- with(ans$results, cbind(RMSE, RMSESD))
}
 --- R stacktrace ---
where 1: oneSDRule(CVout)

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (CVout) 
{
    stopifnot(is.matrix(CVout) || is.data.frame(CVout) || class(CVout) == 
        "train")
    if (class(CVout) == "train") {
        ans <- CVout
        CVout <- with(ans$results, cbind(RMSE, RMSESD))
    }
    cverrs <- CVout[, 1]
    indMin <- which.min(cverrs)
    fmin <- CVout[indMin, 2]
    cutOff <- fmin + cverrs[indMin]
    min(which(cverrs < cutOff))
}
<bytecode: 0x7ba5058>
<environment: namespace:bestglm>
 --- function search by body ---
Function oneSDRule in namespace bestglm has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(CVout) == "train") { : the condition has length > 1
Calls: oneSDRule
Execution halted
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/bfast.Rcheck/00install.out’ for details.
bigglm.RODBC: no visible global function definition for ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘sqlGetResults’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbSendQuery’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbSendQuery’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘fetch’
Undefined global functions or variables:
  dbClearResult dbSendQuery fetch odbcQuery sqlGetResults
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/biogeo.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/Biolinv.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/BIOMASS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/biomod2.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/biotools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/blockCV.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/BSPADATA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/Cairo.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/camtrapR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  catnet_rexport.cpp:207:63: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:211:34: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:218:45: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:221:65: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:222:36: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:225:36: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:236:63: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:237:36: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  rcatnet.cpp:368:104: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
See ‘/data/gannet/ripley/R/packages/tests-devel/catnet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/ccafs.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/cdlTools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/CENFA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/ceramic.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/chillR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/chronosphere.Rcheck/00install.out’ for details.
Running examples in ‘clam-Ex.R’ failed
The error most likely occurred in:

> ### Name: add.dates
> ### Title: Add dates to age-depth plots
> ### Aliases: add.dates
> 
> ### ** Examples
> 
>   clam(coredir=tempfile())
The run's files will be put in this folder: /tmp/RtmpnoMH4f/working_dir/RtmpVhcaos/file100261b8979a/Example

 Warning, dates spanning beyond the calibration curve will be truncated! 
 Calibrating dates... Error in smp[i, (1:its) + 1, ] <- calibs[[i]][sample(1:length(calibs[[i]][,  : 
  incorrect number of subscripts
Calls: clam -> .smpl
Execution halted
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/clhs.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/climateStability.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/ClimMobTools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/ClustGeo.Rcheck/00install.out’ for details.
Found the following significant warnings:
  VCLDefines.c:265:2: warning: statement with no effect [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/clv.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/CommEcol.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/Compind.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [58s/186s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(contextual)
  > 
  > test_check("contextual")
  ── 1. Error: BasicBernoulliBandit MAB policies (@test_bandits.R#205)  ──────────
  task 1 failed - "invalid 'type' (list) of argument"
  Backtrace:
   1. simulation$run()
   2. `%fun%`(...)
   3. e$fun(obj, substitute(ex), parent.frame(), e$data)
  
  ── 2. Error: BasicBernoulliBandit Long (@test_bandits.R#232)  ──────────────────
  task 1 failed - "invalid 'type' (list) of argument"
  Backtrace:
   1. simulation$run()
   2. `%fun%`(...)
   3. e$fun(obj, substitute(ex), parent.frame(), e$data)
  
  ── 3. Error: ContextualPrecachingBandit MAB policies (@test_bandits.R#259)  ────
  task 1 failed - "invalid 'type' (list) of argument"
  Backtrace:
   1. simulation$run()
   2. `%fun%`(...)
   3. e$fun(obj, substitute(ex), parent.frame(), e$data)
  
  ── 4. Error: (unknown) (@test_history.R#12)  ───────────────────────────────────
  task 1 failed - "invalid 'type' (list) of argument"
  Backtrace:
   1. Simulator$new(agents, horizon = 3, simulations = 3, do_parallel = FALSE, ...
   2. `%fun%`(...)
   3. e$fun(obj, substitute(ex), parent.frame(), e$data)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 105 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 4 ]
  1. Error: BasicBernoulliBandit MAB policies (@test_bandits.R#205) 
  2. Error: BasicBernoulliBandit Long (@test_bandits.R#232) 
  3. Error: ContextualPrecachingBandit MAB policies (@test_bandits.R#259) 
  4. Error: (unknown) (@test_history.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/coreCT.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [13s/37s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(corpus)
  > 
  > test_check("corpus")
  -- 1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161
  invalid 'type' (list) of argument
  Backtrace:
    1. base::strsplit(capture_output(print(loc), width = 76), "\n")
    9. corpus:::print.corpus_text_locate(loc)
   10. corpus:::format.corpus_text_locate(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 612 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/cruts.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/cubeview.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/DAMisc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  DTDataFile.cpp:145:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/DataGraph.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/datautils.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/DClusterm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/DCluster.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/decisionSupport.Rcheck/00install.out’ for details.
Found the following significant warnings:
  DEploid/vcfReader.cpp:57:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/DEploid.Rcheck/00install.out’ for details.
Found the following significant warnings:
  clipper.cpp:721:34: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct ClipperLib::TEdge’; use assignment or value-initialization instead [-Wclass-memaccess]
  /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
  shpopen.c:1769:22: warning: ‘. Probably broken SHP file’ directive output may be truncated writing 26 bytes into a region of size between 25 and 48 [-Wformat-truncation=]
See ‘/data/gannet/ripley/R/packages/tests-devel/dggridR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/Digiroo2.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/dismo.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/dissever.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/DiversityOccupancy.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/DNLC.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/downscale.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/dpglasso.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/DRHotNet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  fintegrate.c:350:5: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
  gibbsEM.c:417:9: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/eco.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/eixport.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/EmissV.Rcheck/00install.out’ for details.
Running examples in ‘enaR-Ex.R’ failed
The error most likely occurred in:

> ### Name: enaAll
> ### Title: Conduct All Major ENA
> ### Aliases: enaAll
> 
> ### ** Examples
> 
> 
> 
> 
> data(troModels)
> output = enaAll(troModels[[6]])
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
enaR
 --- call from context --- 
structure.statistics(A)
 --- call from argument --- 
if (class(A) != "matrix") {
    warning("A is not a matrix class object")
}
 --- R stacktrace ---
where 1: structure.statistics(A)
where 2: enaStructure(x)
where 3: enaAll(troModels[[6]])

 --- value of length: 2 type: logical ---
[1] FALSE  TRUE
 --- function from context --- 
function (A = "adjacency matrix") 
{
    if (class(A) != "matrix") {
        warning("A is not a matrix class object")
    }
    n <- dim(A)[1]
    L <- sum(A)
    C <- L/n^2
    LD <- L/n
    e <- eigen(A)$values
    aer <- round(abs(e), digits = 7)
    mlam1A <- length(which(aer == aer[1]))
    ppr <- sum(mExp(A, 200))/sum(mExp(A, 199))
    lam1A <- abs(e[1])
    d <- abs(lam1A - LD)
    if ((n - mlam1A) > 0) {
        lam2A <- abs(e[(1 + mlam1A)])
        rho <- lam1A/abs(lam2A)
        R <- abs(e[n]) - abs(e[n - 1])/(abs(e[n - 1]) - abs(e[1]))
    }
    else {
        lam2A <- NA
        rho <- NA
        R <- NA
    }
    sp1 <- as.vector(scc(A)$sp)
    no.scc <- sp1[1]
    no.scc.big <- sp1[2]
    pscc <- sp1[3]
    sp <- cbind(n, L, C, LD, ppr, lam1A, mlam1A, rho, R, d, no.scc, 
        no.scc.big, pscc)
    return(sp)
}
<bytecode: 0x6a919e0>
<environment: namespace:enaR>
 --- function search by body ---
Function structure.statistics in namespace enaR has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(A) != "matrix") { : the condition has length > 1
Calls: enaAll -> enaStructure -> structure.statistics
Execution halted
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/ENiRG.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/ENMeval.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/esmisc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/exactextractr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/expp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/fasterize.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/data/gannet/ripley/R/packages/tests-devel/FastRWeb.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/fgdr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/FlexScan.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/foto.Rcheck/00install.out’ for details.
Found the following significant warnings:
  /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/freeknotsplines.Rcheck/00install.out’ for details.
Found the following significant warnings:
  FunctionalNetworks.c:223:17: warning: statement with no effect [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/FunctionalNetworks.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/gasfluxes.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/gdalUtilities.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/gdm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  runMCMCfunc.cpp:40:40: warning: left operand of comma operator has no effect [-Wunused-value]
  runMCMCfunc.cpp:41:43: warning: left operand of comma operator has no effect [-Wunused-value]
  runMCMCfunc.cpp:55:42: warning: left operand of comma operator has no effect [-Wunused-value]
  runMCMCfunc.cpp:56:45: warning: left operand of comma operator has no effect [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/geoCount.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/geostatsp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/geozoning.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_41_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/gglasso.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/ggvoronoi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/gimms.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/glacierSMBM.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/graticule.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/grec.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/gwer.Rcheck/00install.out’ for details.
normalweight: no visible binding for global variable ‘NW_above’
normalweight: no visible binding for global variable ‘NW_below’
obese: no visible global function definition for ‘data’
obese: no visible binding for global variable ‘OB_above’
obese: no visible binding for global variable ‘OB_below’
overweight: no visible global function definition for ‘data’
overweight: no visible binding for global variable ‘OW_above’
overweight: no visible binding for global variable ‘OW_below’
Undefined global functions or variables:
  NW_above NW_below OB_above OB_below OW_above OW_below data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/GWmodel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/HACSim.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/HierDpart.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/hierfstat.Rcheck/00install.out’ for details.
PlotOptPower: no visible global function definition for ‘bmp’
PlotOptPower: no visible global function definition for
  ‘filled.contour’
PlotOptPower: no visible global function definition for ‘title’
PlotOptPower: no visible global function definition for ‘grey.colors’
PlotOptPower: no visible global function definition for ‘axis’
PlotOptPower: no visible global function definition for ‘polygon’
PlotOptPower: no visible global function definition for ‘legend’
PlotOptPower: no visible global function definition for ‘mtext’
PlotOptPower: no visible global function definition for ‘dev.off’
PlotOptPower: no visible global function definition for
  ‘terrain.colors’
ShowOptDesign: no visible global function definition for ‘head’
diffVariantError: no visible global function definition for ‘pbinom’
predictPoolNCP: no visible global function definition for ‘data’
probDetEqual3: no visible global function definition for ‘dbinom’
probDetEqual3: no visible global function definition for ‘pbinom’
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/horizon.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/hypervolume.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/ibeemd.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/icd.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/IceCast.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/INLABMA.Rcheck/00install.out’ for details.
Interpol: no visible global function definition for ‘splinefun’
Undefined global functions or variables:
  splinefun
Consider adding
  importFrom("stats", "splinefun")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/intkrige.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/isocat.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/IsoriX.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/itcSegment.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/JavaGD.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/kehra.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/kissmig.Rcheck/00install.out’ for details.
comp.npci: no visible global function definition for ‘qnorm’
epband.fun: no visible global function definition for ‘data’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.90’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.95’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.99’
hall.wellner.fun: no visible global function definition for ‘data’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.90’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.95’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.99’
lrt.confints: no visible global function definition for ‘qchisq’
rothman.fun: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  critical.value.hall.90 critical.value.hall.95 critical.value.hall.99
  critical.value.nair.90 critical.value.nair.95 critical.value.nair.99
  data qchisq qnorm
Consider adding
  importFrom("stats", "qchisq", "qnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
Found the following significant warnings:
  matrix.c:827:1: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  matrix.c:833:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  matrix.c:843:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  matrix.c:979:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  matrix.c:1007:1: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  matrix.c:1051:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  matrix.c:1101:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  matrix.c:1155:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/knncat.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/lagsarlmtree.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/landscapemetrics.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/latticeDensity.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/lazyraster.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/leafem.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/lgcp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/lmSupport.Rcheck/00install.out’ for details.
Found the following significant warnings:
  /data/gannet/ripley/R/test-4.0/BH/include/boost/container/detail/copy_move_algo.hpp:182:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘value_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /data/gannet/ripley/R/test-4.0/BH/include/boost/container/detail/copy_move_algo.hpp:896:16: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /data/gannet/ripley/R/test-4.0/BH/include/boost/container/detail/copy_move_algo.hpp:196:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/data/gannet/ripley/R/packages/tests-devel/lolog.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/LS2Wstat.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/lulcc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/Luminescence.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Manifolds/SmartSpace.cpp:147:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
See ‘/data/gannet/ripley/R/packages/tests-devel/ManifoldOptim.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/mapmisc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/mapview.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/maxlike.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/mclcar.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/mdsOpt.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/MetaLandSim.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/meteoForecast.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/mgwrsar.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/mkde.Rcheck/00install.out’ for details.
listGenoToTable: no visible binding for global variable ‘dummy’
Undefined global functions or variables:
  dummy
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/mmod.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/monographaR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/mptools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/multimark.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/ncdf.tools.Rcheck/00install.out’ for details.
Running examples in ‘netdiffuseR-Ex.R’ failed
The error most likely occurred in:

> ### Name: exposure
> ### Title: Ego exposure
> ### Aliases: exposure
> ### Keywords: univar
> 
> ### ** Examples
> 
> # Calculating lagged exposure -----------------------------------------------
> 
> set.seed(8)
> graph <- rdiffnet(20, 4)
> 
> expo0 <- exposure(graph)
> expo1 <- exposure(graph, lags = 1)
> 
> # These should be equivalent
> stopifnot(all(expo0[, -4] == expo1[, -1])) # No stop!
> 
> 
> # Calculating the exposure based on Structural Equivalence ------------------
> set.seed(113132)
> graph <- rdiffnet(100, 10)
> 
> SE <- lapply(struct_equiv(graph), "[[", "SE")
> SE <- lapply(SE, function(x) {
+    x <- 1/x
+    x[!is.finite(x)] <- 0
+    x
+ })
> 
> 
> # These three lines are equivalent to:
> expo_se2 <- exposure(graph, alt.graph="se", valued=TRUE)
> # Notice that we are setting valued=TRUE, but this is not necesary since when
> # alt.graph = "se" the function checks this to be setted equal to TRUE
> 
> # Weighted Exposure using degree --------------------------------------------
> eDE <- exposure(graph, attrs=dgr(graph))
> 
> # Which is equivalent to
> graph[["deg"]] <- dgr(graph)
> eDE2 <- exposure(graph, attrs="deg")
> 
> # Comparing using incoming edges -------------------------------------------
> eIN <- exposure(graph, outgoing=FALSE)
Error in sys.call() : 
  GC encountered a node (0x98ac170) with an unknown SEXP type: 12 at memory.c:1787
Calls: exposure ... initialize -> callNextMethod -> .nextMethod -> callGeneric
Execution halted
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/nmixgof.Rcheck/00install.out’ for details.
File ‘nws/R/zzz.R’:
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

blendOptions: warning in assign(names[i], new[[i]], env = options):
  partial argument match of 'env' to 'envir'
docall: warning in get(as.character(fun), env = .GlobalEnv, mode =
  "function"): partial argument match of 'env' to 'envir'
logMsg: no visible global function definition for ‘flush.console’
nwsPkgInfo: no visible global function definition for
  ‘packageDescription’
initialize,nwsServer: no visible global function definition for
  ‘make.socket’
initialize,nwsServer: no visible global function definition for
  ‘close.socket’
Undefined global functions or variables:
  close.socket flush.console make.socket packageDescription
Consider adding
  importFrom("utils", "close.socket", "flush.console", "make.socket",
             "packageDescription")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/oceanis.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/oceanmap.Rcheck/00install.out’ for details.
mapvar: no visible global function definition for ‘data’
mapvar: no visible binding for global variable ‘state.fips’
mapvar: no visible global function definition for ‘rgb’
mapvar: no visible global function definition for ‘rect’
mapvar: no visible global function definition for ‘text’
rowScrape: no visible global function definition for ‘tail’
rowScrape: no visible global function definition for ‘head’
scrapeTable: no visible binding for global variable ‘tail’
Undefined global functions or variables:
  data head rect rgb state.fips tail text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "rect", "text")
  importFrom("utils", "data", "head", "tail")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/openCR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  rcpp_nativecont.cpp:30:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  rcpp_nativecont.cpp:34:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  rcpp_segBreedComp.cpp:42:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  rcpp_segBreedComp.cpp:45:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  rcpp_segN.cpp:48:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/optiSel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/osc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/outbreaker.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/ouxy.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/paleobioDB.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [65s/93s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(panelr)
  Loading required package: lme4
  Loading required package: Matrix
  
  Attaching package: 'panelr'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("panelr")
  ── 1. Error: (unknown) (@test_wbm.R#283)  ──────────────────────────────────────
  could not find function "arma"
  Backtrace:
   1. panelr::wbm_stan(...)
   2. brms::make_stancode(...)
   4. brms:::validate_formula.default(...)
   6. brms:::validate_formula.brmsformula(bf(formula), ...)
   7. brms:::validate_autocor(autocor)
   8. brms:::parse_ac(autocor)
   9. base::lapply(out, eval2)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 271 | SKIPPED: 0 | WARNINGS: 60 | FAILED: 1 ]
  1. Error: (unknown) (@test_wbm.R#283) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/PatternClass.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/pegas.Rcheck/00install.out’ for details.
Found the following significant warnings:
  permTest.c:20:3: warning: statement with no effect [-Wunused-value]
  permTest.c:62:3: warning: statement with no effect [-Wunused-value]
  permTest.c:90:3: warning: statement with no effect [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/permDep.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/PersomicsArray.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Serialize.h:64:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
  Serialize.h:66:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
  Serialize.h:68:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
  mbart.cpp:512:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
  mbart.cpp:513:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/pgbart.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/phenopix.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [11s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(phrasemachine)
  phrasemachine: Simple Phrase Extraction
  Version 1.1.2 created on 2017-05-29.
  copyright (c) 2016, Matthew J. Denny, Abram Handler, Brendan O'Connor.
  Type help('phrasemachine') or
  vignette('getting_started_with_phrasemachine') to get started.
  Development website: https://github.com/slanglab/phrasemachine
  > 
  > test_check("phrasemachine")
  ── 1. Error: See if tagging five documents works, and if coarsening works (@test
  unused argument (alist())
  Backtrace:
   1. documents[1:5, ]
  
  ── 2. Error: See if extractor works (@test_extract_phrases.R#7)  ───────────────
  unused argument (alist())
  Backtrace:
   1. documents[1:5, ]
  
  Currently tagging document 1 of 1 
  Extracting phrases from document 1 of 1 
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 10 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: See if tagging five documents works, and if coarsening works (@test_POS_tag_documents.R#7) 
  2. Error: See if extractor works (@test_extract_phrases.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/phyloclim.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/phylosignal.Rcheck/00install.out’ for details.
Running ‘test-async.R’ [22s/54s]
  Running ‘testthat.R’ [4s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pkgcache)
  > 
  > test_check("pkgcache")
  ── 1. Error: load_primary_pkgs (@test-metadata-cache.R#191)  ───────────────────
  No metadata available
  Backtrace:
   1. pkgcache:::synchronise(get_private(cmc)$load_primary_pkgs(oneday()))
   2. get_private(cmc)$load_primary_pkgs(oneday())
   3. pkgcache:::cmc__load_primary_pkgs(self, private, max_age)
   4. private$update_replica_rds(alert = FALSE)
   5. pkgcache:::cmc__update_replica_rds(self, private, alert)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 305 | SKIPPED: 28 | WARNINGS: 2 | FAILED: 1 ]
  1. Error: load_primary_pkgs (@test-metadata-cache.R#191) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/plotdap.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/poppr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/popprxl.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/PrevMap.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/prioritizrdata.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/prioritizr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/prism.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/proj4.Rcheck/00install.out’ for details.
Compilation used the following non-portable flag(s):
  ‘-Wp,-D_GLIBCXX_ASSERTIONS’
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/QRAGadget.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/qrencoder.Rcheck/00install.out’ for details.
Found the following significant warnings:
  /data/gannet/ripley/R/packages/tests-devel/qtbase/src/EventLoop.cpp:103:12: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
  /data/gannet/ripley/R/packages/tests-devel/qtbase/src/EventLoop.cpp:92:7: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/qtbase.Rcheck/00install.out’ for details.
Found the following file(s) containing GNU extensions:
  src-build/Makefile
  tools/kdebindings-build/Makefile
  tools/kdebindings-build/generator/Makefile
  tools/kdebindings-build/generator/generators/Makefile
  tools/kdebindings-build/generator/generators/dump/Makefile
  tools/kdebindings-build/generator/generators/smoke/Makefile
  tools/kdebindings-build/generator/parser/Makefile
  tools/kdebindings-build/smoke/Makefile
  tools/kdebindings-build/smoke/qt/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable
packages’ in the ‘Writing R Extensions’ manual.
Note: information on .o files is not available
File ‘qtpaint/libs/qtpaint.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/quadmesh.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Routines/xml_file_read.cc:154:9: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  Routines/xml_file_read.cc:243:9: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/R2GUESS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/raincpc.Rcheck/00install.out’ for details.
Running examples in ‘randNames-Ex.R’ failed
The error most likely occurred in:

> ### Name: rand_names
> ### Title: Random name generator
> ### Aliases: rand_names
> 
> ### ** Examples
> 
> data <- rand_names(5)
No encoding supplied: defaulting to UTF-8.
Error: lexical error: invalid char in json text.
                                       <!DOCTYPE html> <!--[if lt IE 7
                     (right here) ------^
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(randNames)
  > 
  > test_check("randNames")
  ── 1. Error: Random names work (@test_rand_names.R#4)  ─────────────────────────
  lexical error: invalid char in json text.
                                         <!DOCTYPE html> <!--[if lt IE 7
                       (right here) ------^
  Backtrace:
   1. testthat::expect_is(rand_names(1), "data.frame")
   4. randNames::rand_names(1)
   5. jsonlite::fromJSON(...)
   6. jsonlite:::parse_and_simplify(...)
   7. jsonlite:::parseJSON(txt, bigint_as_char)
   8. jsonlite:::parse_string(txt, bigint_as_char)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Random names work (@test_rand_names.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
.disableThreads: no visible global function definition for
  ‘stopCluster’
.enableThreads: no visible global function definition for ‘detectCores’
.enableThreads: no visible global function definition for
  ‘makePSOCKcluster’
.enableThreads: no visible global function definition for
  ‘clusterExport’
.enableThreads: no visible global function definition for ‘clusterCall’
.forwardSelection: no visible binding for global variable ‘var’
.forwardSelection: no visible global function definition for ‘glm’
.forwardSelection: no visible global function definition for ‘formula’
.forwardSelection: no visible global function definition for ‘binomial’
.forwardSelection: no visible global function definition for ‘lm’
.forwardSelection: no visible global function definition for ‘predict’
.predict.internal: no visible global function definition for ‘predict’
randomGLM: no visible binding for global variable ‘cor’
randomGLM: no visible binding for global variable ‘sd’
randomGLM: no visible global function definition for ‘var’
thinRandomGLM: no visible global function definition for ‘glm’
thinRandomGLM: no visible global function definition for ‘binomial’
thinRandomGLM: no visible global function definition for ‘lm’
Undefined global functions or variables:
  binomial clusterCall clusterExport cor detectCores formula glm lm
  makePSOCKcluster predict sd stopCluster var
Consider adding
  importFrom("stats", "binomial", "cor", "formula", "glm", "lm",
             "predict", "sd", "var")
to your NAMESPACE file.
Found the following significant warnings:
  /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:1453:29: warning: ‘%4.4d’ directive writing between 4 and 10 bytes into a region of size 5 [-Wformat-overflow=]
  avc_binwr.c:1553:28: warning: ‘%s’ directive writing up to 39 bytes into a region of size between 38 and 77 [-Wformat-overflow=]
  avc_e00write.c:386:30: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  avc_e00write.c:387:30: warning: ‘-ID’ directive writing 3 bytes into a region of size between 1 and 40 [-Wformat-overflow=]
  avc_e00write.c:401:61: warning: ‘%s’ directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:397:61: warning: ‘%s’ directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:409:39: warning: ‘%s’ directive writing up to 39 bytes into a region of size 33 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/RArcInfo.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/rasterKernelEstimates.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/rasterList.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/rasterVis.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/rbgm.Rcheck/00install.out’ for details.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-devel/Rblpapi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/RchivalTag.Rcheck/00install.out’ for details.
Found the following significant warnings:
  bits.c:1247:23: warning: array subscript 8 is outside array bounds of ‘unsigned int[1]’ [-Warray-bounds]
  bits.c:1265:18: warning: array subscript 9 is outside array bounds of ‘unsigned int[1]’ [-Warray-bounds]
See ‘/data/gannet/ripley/R/packages/tests-devel/RDieHarder.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
  Rreadsdpa.c:496:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  Rreadsdpa.c:504:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  Rreadsdpa.c:528:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  Rreadsdpa.c:540:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  Rreadsdpa.c:549:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  Rreadsdpa.c:554:55: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  Rreadsdpa.c:560:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  Rreadsdpa.c:602:54: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  Rreadsdpa.c:607:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  Rreadsdpa.c:1028:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 3999 bytes from a string of length 3999 [-Wstringop-truncation]
  dsdpsetoptions.c:161:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/Rdsdp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/rdwplus.Rcheck/00install.out’ for details.
Found the following significant warnings:
  compile.cc:292:69: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class re2::Prog::Inst’; use assignment or value-initialization instead [-Wclass-memaccess]
  regexp.cc:343:33: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
  regexp.cc:344:32: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
See ‘/data/gannet/ripley/R/packages/tests-devel/re2r.Rcheck/00install.out’ for details.
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
bestmods: no visible global function definition for ‘abline’
bestmods: no visible global function definition for ‘axis’
bestmods: no visible global function definition for ‘lines’
cic: no visible global function definition for ‘lsfit’
cic: no visible global function definition for ‘var’
cvic: no visible global function definition for ‘lsfit’
cvic: no visible global function definition for ‘lm’
eic: no visible global function definition for ‘lsfit’
eic: no visible global function definition for ‘lm’
ic.min: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘var’
xy: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis lines lm lsfit rnorm var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "lm", "lsfit", "rnorm", "var")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/redist.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/redlistr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/regrrr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/remote.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [106s/101s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(restatapi)
  restatapi: - config file with the API version 1 loaded from GitHub (the 'current' API version number is 1).
             - 4 from the 24 cores are used for parallel computing.
             - 'libcurl' will be used for file download.
             - the Table of contents (TOC) was not pre-loaded into the deafult cache ('.restatapi_env').
  > 
  > test_check("restatapi")
  ── 1. Failure: test of the get_eurostat_raw/bulk/data functions (@test-all.R#84)
  `rt1 <- get_eurostat_raw(id, verbose = FALSE)` did not produce any messages.
  
  ── 2. Error: test of the get_eurostat_raw/bulk/data functions (@test-all.R#85)  
  'target' and 'current' must both be data.tables
  Backtrace:
   1. testthat::expect_equal(rt1, NULL)
   3. testthat:::compare.default(act$val, exp$val, ...)
   5. data.table:::all.equal.data.table(x, y, ...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 67 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: test of the get_eurostat_raw/bulk/data functions (@test-all.R#84) 
  2. Error: test of the get_eurostat_raw/bulk/data functions (@test-all.R#85) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/RFmerge.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/Rgnuplot.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-devel/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’
File ‘rJava/libs/rJava.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/rleafmap.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/rLiDAR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/RLumModel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/RLumShiny.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/rmetasim.Rcheck/00install.out’ for details.
Found the following significant warnings:
  graph_io_chac.c:106:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  graph_io_chac.c:179:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  graph_io_chac.c:208:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/rmumps.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/rPAex.Rcheck/00install.out’ for details.
Found the following significant warnings:
  bgc_hmm.c:241:15: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  bgc_hmm.c:242:13: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  bgc_hmm.c:241:31: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
  /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/rphast.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/rpostgisLT.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/rpostgis.Rcheck/00install.out’ for details.
Found the following significant warnings:
  rng.cpp:43:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/Rsampletrees.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rserv.c:2150:3: warning: ‘RSA_generate_key’ is deprecated [-Wdeprecated-declarations]
  Rserv.c:816:4: warning: ignoring return value of ‘setgid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:817:3: warning: ignoring return value of ‘setuid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:820:22: warning: ignoring return value of ‘setgid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:821:22: warning: ignoring return value of ‘setuid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:372:2: warning: ignoring return value of ‘chown’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:375:3: warning: ignoring return value of ‘chown’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:2342:3: warning: ignoring return value of ‘chdir’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:3351:4: warning: ignoring return value of ‘chdir’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:3358:3: warning: ignoring return value of ‘chdir’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:2088:7: warning: ignoring return value of ‘setgid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:2090:7: warning: ignoring return value of ‘setuid’, declared with attribute warn_unused_result [-Wunused-result]
  oc.c:47:5: warning: ‘RAND_pseudo_bytes’ is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-devel/Rserve.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-devel/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/rsMove.Rcheck/00install.out’ for details.
Math.Sym: no visible binding for global variable ‘transtab’
jythonStart: no visible global function definition for ‘.jinit’
jythonStart: no visible global function definition for ‘.jnew’
jythonStart: no visible binding for global variable ‘.Jython’
sympy: no visible binding for global variable ‘.Jython’
sympy: no visible global function definition for ‘.jstrVal’
sympyStart: no visible binding for global variable ‘.Jython’
Undefined global functions or variables:
  .Jython .jinit .jnew .jstrVal transtab
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/Rtrack.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/rts.Rcheck/00install.out’ for details.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-devel/RVowpalWabbit.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/rwc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/sabre.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/saeSim.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/sampSurf.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/satellite.Rcheck/00install.out’ for details.
prime.factor: no visible global function definition for ‘data’
prime.factor: no visible binding for global variable ‘primlist’
Undefined global functions or variables:
  data primlist
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/scio.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/SDALGCP.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/SDLfilter.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/sdm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/SDMtune.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/sdmvspecies.Rcheck/00install.out’ for details.
Found the following significant warnings:
  catnet_rexport.cpp:222:63: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:226:34: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:233:45: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:236:65: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:237:36: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:240:36: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:251:63: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:252:36: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  rcatnet_prob.cpp:49:104: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
See ‘/data/gannet/ripley/R/packages/tests-devel/sdnet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/secrdesign.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/sen2r.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'loomR', 'SDMTools', 'MAST', 'monocle'
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/shadow.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/sharpshootR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/siland.Rcheck/00install.out’ for details.
Found the following significant warnings:
  /data/gannet/ripley/R/test-4.0/BH/include/boost/graph/detail/adjacency_list.hpp:2239:43: warning: ‘p.Edge::color’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/SimilaR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/sirad.Rcheck/00install.out’ for details.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/skeleSim.Rcheck/00install.out’ for details.
Found the following significant warnings:
  slfm_MDN.cpp:26:38: warning: left operand of comma operator has no effect [-Wunused-value]
  slfm_MNN.cpp:26:38: warning: left operand of comma operator has no effect [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/slfm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/slga.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/slideview.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/smapr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/smoothr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/soilDB.Rcheck/00install.out’ for details.
Warning: namespace 'rgdal' is not available and has been replaced
  by .GlobalEnv when processing object '<unknown>'
  Warning: namespace 'rgdal' is not available and has been replaced
  by .GlobalEnv when processing object '<unknown>'
  Warning: namespace 'rgdal' is not available and has been replaced
  by .GlobalEnv when processing object '<unknown>'
  Warning: namespace 'rgdal' is not available and has been replaced
  by .GlobalEnv when processing object '<unknown>'
  Warning: namespace 'rgdal' is not available and has been replaced
  by .GlobalEnv when processing object '<unknown>'
  Warning: namespace 'rgdal' is not available and has been replaced
  by .GlobalEnv when processing object '<unknown>'
  Warning: namespace 'rgdal' is not available and has been replaced
  by .GlobalEnv when processing object '<unknown>'
  Warning: namespace 'rgdal' is not available and has been replaced
  by .GlobalEnv when processing object '<unknown>'
  Warning: namespace 'rgdal' is not available and has been replaced
  by .GlobalEnv when processing object '<unknown>'
  Warning: namespace 'rgdal' is not available and has been replaced
  by .GlobalEnv when processing object '<unknown>'
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/spANOVA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/SpatialEpi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/SpatialKDE.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/SpatialPosition.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/spatialprobit.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/spatialreg.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/spc4sts.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/spData.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/spdep.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/spdynmod.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/spectral.methods.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/spemd.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/spex.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/spfrontier.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/spGARCH.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/spgwr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/sphet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/spider.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/splm.Rcheck/00install.out’ for details.
Running examples in ‘spm12r-Ex.R’ failed
The error most likely occurred in:

> ### Name: install_spm12
> ### Title: Install SPM12 file into directory
> ### Aliases: install_spm12
> 
> ### ** Examples
> 
> tdir = tempfile()
> dir.create(tdir)
> in_ci <- function() {
+ nzchar(Sys.getenv("CI"))
+ }
> if (.Platform$OS.type == "unix" | in_ci()) { # windows problem
+ res = install_spm12(install_dir = tdir)
+ res = install_spm12(install_dir = tdir)
+ }
cloning into '/tmp/RtmpFySBiu/working_dir/Rtmpm8Ymvg/filea3ba687a7184/spm12'...

 *** caught segfault ***
address 0xc800010009, cause 'memory not mapped'

Traceback:
 1: git2r::clone("https://github.com/muschellij2/spm12r", branch = "gh-pages",     local_path = out_path, progress = verbose)
 2: install_spm12(install_dir = tdir)
An irrecoverable exception occurred. R is aborting now ...
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/spMaps.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/spmoran.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/spsur.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/SSDM.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/ssfa.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/StAMPP.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/steps.Rcheck/00install.out’ for details.
Found the following significant warnings:
  MaxChi.c:468:20: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  Phylpro.c:457:24: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  init.c:63:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  init.c:64:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  init.c:95:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  init.c:100:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  init.c:132:3: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
  init.c:142:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
  init.c:153:3: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
  init.c:156:3: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/stepwise.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/stplanr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/strataG.Rcheck/00install.out’ for details.
Found the following significant warnings:
  computeQ.cpp:75:15: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
  computeQ.cpp:134:15: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
  computeQ.cpp:142:17: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
See ‘/data/gannet/ripley/R/packages/tests-devel/strum.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/SurfaceTortoise.Rcheck/00install.out’ for details.
Found the following significant warnings:
  lineariadmm.c:189:17: warning: value computed is not used [-Wunused-value]
  lineariadmm.c:190:17: warning: value computed is not used [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/svmadmm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/tabularaster.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/tanaka.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/tangles.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/telefit.Rcheck/00install.out’ for details.
Running examples in ‘TempleMetrics-Ex.R’ failed
The error most likely occurred in:

> ### Name: Fycondx.DR
> ### Title: Fycondx.DR
> ### Aliases: Fycondx.DR
> 
> ### ** Examples
> 
> data(igm)
> yvals <- seq(quantile(igm$lcfincome,.05,type=1),
+  quantile(igm$lcfincome,.95, type=1), length.out=100)
> dres <- distreg(lcfincome ~ lfincome + HEDUC, igm, yvals)
> xdf <- data.frame(lfincome=10, HEDUC=c("LessHS","HS"))
> d <- Fycondx(dres, yvals, xdf)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
TempleMetrics
 --- call from context --- 
Fycondx.DR(dres, yvals, xdf)
 --- call from argument --- 
if (class(predmat) == "numeric") {
    predmat <- t(predmat)
}
 --- R stacktrace ---
where 1: Fycondx.DR(dres, yvals, xdf)
where 2: Fycondx(dres, yvals, xdf)

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (object, yvals, xdf) 
{
    drobj <- object
    yvals <- drobj$yvals
    glmlist <- drobj$glmlist
    predmat <- sapply(glmlist, function(g) {
        predict(g, newdata = xdf, type = "response")
    })
    if (class(predmat) == "numeric") {
        predmat <- t(predmat)
    }
    out <- lapply(1:nrow(predmat), function(i) {
        makeDist(yvals, predmat[i, ], rearrange = TRUE)
    })
    out
}
<bytecode: 0x19b1008>
<environment: namespace:TempleMetrics>
 --- function search by body ---
Function Fycondx.DR in namespace TempleMetrics has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(predmat) == "numeric") { : 
  the condition has length > 1
Calls: Fycondx -> Fycondx.DR
Execution halted
Running ‘testthat.R’ [17s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(textrecipes)
  Loading required package: recipes
  Loading required package: dplyr
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  
  Attaching package: 'recipes'
  
  The following object is masked from 'package:stats':
  
      step
  
  > 
  > test_check("textrecipes")
  ── 1. Failure: step_tfidf works as intended (@test-tfidf.R#44)  ────────────────
  as.matrix(rec_answer) not equal to as.matrix(manual_answer).
  29/68 mismatches (average diff: 0.123)
  [4]  0.201 - 0.0866 == 0.115
  [7]  0.201 - 0.0866 == 0.115
  [10] 0.268 - 0.1155 == 0.153
  [16] 0.201 - 0.0866 == 0.115
  [17] 0.106 - 0.0000 == 0.106
  [18] 0.141 - 0.0000 == 0.141
  [19] 0.106 - 0.0000 == 0.106
  [23] 0.201 - 0.0866 == 0.115
  [27] 0.201 - 0.0866 == 0.115
  ...
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 88 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 1 ]
  1. Failure: step_tfidf works as intended (@test-tfidf.R#44) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘tidyquant-Ex.R’ failed
The error most likely occurred in:

> ### Name: geom_bbands
> ### Title: Plot Bollinger Bands using Moving Averages
> ### Aliases: geom_bbands geom_bbands_
> 
> ### ** Examples
> 
> # Load libraries
> library(tidyquant)
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:xts’:

    first, last

The following objects are masked from ‘package:lubridate’:

    intersect, setdiff, union

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> library(ggplot2)
> 
> 
> AAPL <- tq_get("AAPL")
> 
> # SMA
> AAPL %>%
+     ggplot(aes(x = date, y = close)) +
+     geom_line() +           # Plot stock price
+     geom_bbands(aes(high = high, low = low, close = close), ma_fun = SMA, n = 50) +
+     coord_x_date(xlim = c(today() - years(1), today()), ylim = c(80, 130))
Error in if (zero_range(range)) zero_width else diff(range) : 
  missing value where TRUE/FALSE needed
Calls: <Anonymous> ... f -> train_cartesian -> scale_range -> expand_range
Execution halted
Running ‘testthat.R’ [14s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidytext)
  > 
  > test_check("tidytext")
  ── 3. Error: (unknown) (@test-corpus-tidiers.R#33)  ────────────────────────────
  Internal error: Trace data is not square.
  Backtrace:
    1. testthat::test_check("tidytext")
    2. testthat:::test_package_dir(...)
    3. testthat::test_dir(...)
    4. testthat:::test_files(...)
   10. base::lapply(...)
   11. testthat:::FUN(X[[i]], ...)
   17. testthat::source_file(...)
   18. testthat:::test_code(NULL, exprs, env)
   27. [ base::eval(...) ] with 1 more call
   29. testthat::test_that(...)
       ...
   40. testthat:::o_apply(...)
   41. base::lapply(objects, function(x) x[[method]](...))
   42. testthat:::FUN(X[[i]], ...)
   43. x[[method]](...)
   47. testthat:::failure_summary(result, self$n_fail)
   50. testthat:::format.expectation(x)
   51. testthat:::format_with_trace(x)
   53. rlang:::format.rlang_trace(...)
   54. rlang:::trace_format_branch(x, max_frames, dir, srcrefs)
   55. rlang:::branch_uncollapse_pipe(trace)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 274 | SKIPPED: 1 | WARNINGS: 2 | FAILED: 3 ]
  1. Error: Can tidy corpus from quanteda using accessor functions (@test-corpus-tidiers.R#38) 
  2. Error: Can tidy corpus from quanteda using accessor functions (@test-corpus-tidiers.R#33) 
  3. Error: (unknown) (@test-corpus-tidiers.R#33) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/TLdating.Rcheck/00install.out’ for details.
File ‘tpr/libs/tpr.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’
File ‘tpr/libs/tpr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/treespace.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/trip.Rcheck/00install.out’ for details.
Found the following significant warnings:
  /usr/include/bits/string_fortified.h:136:10: warning: ‘__builtin___strncat_chk’ output may be truncated copying between 0 and 199 bytes from a string of length 199 [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/TukeyRegion.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/unmarked.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/usdm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<> >::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::MemoryPoolAllocator<> >’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<> >’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::CrtAllocator>’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/data/gannet/ripley/R/packages/tests-devel/validatejsonr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  vic/drivers/shared_all/src/compress_files.c:49:5: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result]
  vic/drivers/shared_all/src/forcing_utils.c:140:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  vic/drivers/shared_all/src/forcing_utils.c:161:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  vic/drivers/shared_all/src/get_parameters.c:43:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  vic/drivers/shared_all/src/get_parameters.c:51:17: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  vic/drivers/shared_all/src/get_parameters.c:540:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  vic/drivers/shared_all/src/input_tools.c:77:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  vic/drivers/shared_all/src/input_tools.c:101:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  vic/drivers/shared_all/src/open_file.c:89:17: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  vic/drivers/shared_all/src/open_file.c:98:17: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/VICmodel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: namespace ‘rgdal’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/virtualspecies.Rcheck/00install.out’ for details.
Bundesliga.Mannschaft: no visible global function definition for ‘data’
Bundesliga.Mannschaft: no visible binding for global variable
  ‘Bundesliga’
Bundesliga.Tabelle: no visible global function definition for ‘data’
Bundesliga.Tabelle: no visible binding for global variable ‘Bundesliga’
Bundesliga.XML: no visible global function definition for ‘data’
Bundesliga.XML: no visible binding for global variable ‘Bundesliga’
sens.spec: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-devel/x13binary.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown
Quitting from lines 78-85 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building 'vignette.Rmd'

SUMMARY: processing the following file failed:
  'vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    R  14.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/AcuityView.Rcheck/00install.out' for details.
asp: no visible global function definition for 'as.formula'
asp: no visible global function definition for 'var'
aspm: no visible binding for global variable 'X.Declan'
aspm: no visible binding for global variable 'Z.Jaida'
aspm: no visible binding for global variable 'group.vec.Handan'
aspm: no visible global function definition for 'as.formula'
aspm: no visible global function definition for 'glm'
aspm: no visible global function definition for 'binomial'
aspm: no visible global function definition for 'poisson'
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.7Mb
    pictures   2.1Mb
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    data  20.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/AFM.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/AIG.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/alphashape3d.Rcheck/00install.out' for details.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    extdata  11.3Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    data  15.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs     4.2Mb
annot : annotlist: no visible global function definition for
  'read.table'
annot : annotlist: no visible global function definition for
  'write.table'
annot: no visible global function definition for 'flush.console'
annot: no visible global function definition for 'read.table'
annot: no visible global function definition for 'choose.dir'
Undefined global functions or variables:
  choose.dir flush.console read.table write.table
Consider adding
  importFrom("utils", "choose.dir", "flush.console", "read.table",
             "write.table")
to your NAMESPACE file.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   1.8Mb
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
installed size is 73.0Mb
  sub-directories of 1Mb or more:
    gdal   3.8Mb
    libs  68.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/archiDART.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'annual-maps.Rmd' using rmarkdown
Some values in the specified facet_geo column 'BUYER_STATE' do not
  match the 'code' column of the specified grid and will be removed:
  AE, GU, MP, PR, PW, VI
--- finished re-building 'annual-maps.Rmd'

--- re-building 'county-analysis.Rmd' using rmarkdown
Joining, by = c("year", "countyfips")
Quitting from lines 121-137 (county-analysis.Rmd) 
Error: processing vignette 'county-analysis.Rmd' failed with diagnostics:
Can't join on 'year' x 'year' because of incompatible types (character / integer)
--- failed re-building 'county-analysis.Rmd'

--- re-building 'per-capita-pharmacies.Rmd' using rmarkdown
--- finished re-building 'per-capita-pharmacies.Rmd'

SUMMARY: processing the following file failed:
  'county-analysis.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   1.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Arothron.Rcheck/00install.out' for details.
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    R      3.2Mb
    libs  24.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.5Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    bin   12.0Mb
    misc   2.1Mb
Package which this enhances but not available for checking: 'rPython'
installed size is 56.6Mb
  sub-directories of 1Mb or more:
    libs  55.8Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
Running examples in 'AWR.Kinesis-Ex.R' failed
The error occurred in:


R Under development (unstable) (2020-01-28 r77738) -- "Unsuffered Consequences"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> pkgname <- "AWR.Kinesis"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> library('AWR.Kinesis')
> 
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
> cleanEx()
Error: connections left open:
	stdin (file)
Execution halted
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   3.3Mb
    libs   1.8Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
trying URL 'https://downloads.lightbend.com/scala/2.13.1/scala-2.13.1.tgz'
Content type 'application/octet-stream' length 19685743 bytes (18.8 MB)
==================================================
downloaded 18.8 MB
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.1Mb
    libs   2.0Mb
Packages which this enhances but not available for checking:
  'doMC', 'rPython'
Package suggested but not available for checking: 'doMC'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/BAT.Rcheck/00install.out' for details.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.7/bayesCL.Rcheck/00install.out' for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs   2.1Mb
NeedsCompilation field should likely be 'yes'
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   4.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   4.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   3.7Mb
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    libs  23.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.3Mb
Packages suggested but not available for checking: 'bcmapsdata', 'doMC'
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 133.1Mb
  sub-directories of 1Mb or more:
    include  132.2Mb
Found the following significant warnings:
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0/biganalytics.Rcheck/00install.out' for details.
bigglm.RODBC: no visible global function definition for 'odbcQuery'
bigglm.RODBC : chunk: no visible global function definition for
  'odbcQuery'
bigglm.RODBC : chunk: no visible global function definition for
  'sqlGetResults'
bigglm,ANY-DBIConnection: no visible global function definition for
  'dbSendQuery'
bigglm,ANY-DBIConnection: no visible global function definition for
  'dbClearResult'
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for 'dbClearResult'
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for 'dbSendQuery'
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for 'fetch'
Undefined global functions or variables:
  dbClearResult dbSendQuery fetch odbcQuery sqlGetResults
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   2.5Mb
    libs      1.7Mb
Found the following significant warnings:
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0/bigmemory.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.9Mb
Found the following significant warnings:
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0/bigtabulate.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   1.9Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   8.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    doc       1.3Mb
    extdata   1.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   1.5Mb
Depends: includes the non-default packages:
  'colorspace', 'deldir', 'rgl', 'tcltk', 'tcltk2', 'tkrplot'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'colorspace'
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  'deldir' 'rgl' 'tcltk' 'tcltk2' 'tkrplot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in 'blandr-Ex.R' failed
The error most likely occurred in:

> ### Name: blandr.dataset.fibre
> ### Title: Function to load D'arbela mean velocity of circumferential fibre
> ###   shortening dataset from internet
> ### Aliases: blandr.dataset.fibre
> 
> ### ** Examples
> 
> blandr.dataset.fibre()
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in file(con, "r") : cannot open the connection
Calls: blandr.dataset.fibre -> readLines -> file
Execution halted
install_blat: no visible global function definition for 'download.file'
install_blat: no visible global function definition for 'unzip'
Undefined global functions or variables:
  download.file unzip
Consider adding
  importFrom("utils", "download.file", "unzip")
to your NAMESPACE file.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/BonEV.Rcheck/00install.out' for details.
installed size is 59.5Mb
  sub-directories of 1Mb or more:
    include   8.5Mb
    lib      50.6Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
File 'brainwaver/libs/i386/brainwaver.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'connexity_small_world.o'
File 'brainwaver/libs/x64/brainwaver.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'connexity_small_world.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Foreign function calls to a different package:
  .C("CharArray", ..., PACKAGE = "libOpenBUGS")
  .C("CmdInterpreter", ..., PACKAGE = "libOpenBUGS")
  .C("Integer", ..., PACKAGE = "libOpenBUGS")
  .C("RealArray", ..., PACKAGE = "libOpenBUGS")
  .C("SetTempDir", ..., PACKAGE = "libOpenBUGS")
  .C("SetWorkingDir", ..., PACKAGE = "libOpenBUGS")
Undeclared package in foreign function calls:
   'libOpenBUGS'
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Brundle.Rcheck/00install.out' for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.0Mb
Package which this enhances but not available for checking: 'FastRWeb'
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R        1.1Mb
    data     1.5Mb
    models   2.4Mb
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.2Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.7Mb
    libs   2.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Found the following significant warnings:
  VCLDefines.c:265:2: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/clv.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/cmaesr.Rcheck/00install.out' for details.
Running examples in 'cobalt-Ex.R' failed
The error most likely occurred in:

> ### Name: bal.tab.mimids
> ### Title: Balance Statistics for MatchThem Objects
> ### Aliases: bal.tab.mimids bal.tab.wimids
> ### Keywords: tables
> 
> ### ** Examples
> 
> library(MatchThem)
Loading required package: MatchIt

Attaching package: 'MatchIt'

The following object is masked from 'package:cobalt':

    lalonde

Loading required package: WeightIt
> library(mice)

Attaching package: 'mice'

The following objects are masked from 'package:MatchThem':

    complete, pool

The following objects are masked from 'package:base':

    cbind, rbind

> data("lalonde_mis", package = "cobalt")
> 
> #Imputing the missing data
> imp <- mice(lalonde_mis, m = 5)

 iter imp variable
  1   1  married  re74  re75
  1   2  married  re74  re75
  1   3  married  re74  re75
  1   4  married  re74  re75
  1   5  married  re74  re75
  2   1  married  re74  re75
  2   2  married  re74  re75
  2   3  married  re74  re75
  2   4  married  re74  re75
  2   5  married  re74  re75
  3   1  married  re74  re75
  3   2  married  re74  re75
  3   3  married  re74  re75
  3   4  married  re74  re75
  3   5  married  re74  re75
  4   1  married  re74  re75
  4   2  married  re74  re75
  4   3  married  re74  re75
  4   4  married  re74  re75
  4   5  married  re74  re75
  5   1  married  re74  re75
  5   2  married  re74  re75
  5   3  married  re74  re75
  5   4  married  re74  re75
  5   5  married  re74  re75
> 
> #Matching using within-imputation propensity scores
> mt.out1 <- matchthem(treat ~ age + educ + race + 
+                        married + nodegree + re74 + re75, 
+                        data = imp, approach = "within")
Error in mice::is.mids(object) : 
  argument "object" is missing, with no default
Calls: matchthem ... complete.mids -> <Anonymous> -> complete.mids -> <Anonymous>
Execution halted
Running examples in 'colorspace-Ex.R' failed
The error most likely occurred in:

> ### Name: scale_colour_continuous_diverging
> ### Title: HCL-Based Continuous Diverging Color Scales for ggplot2
> ### Aliases: scale_colour_continuous_diverging
> ###   scale_color_continuous_diverging scale_fill_continuous_diverging
> 
> ### ** Examples
> 
> # adapted from stackoverflow: https://stackoverflow.com/a/20127706/4975218
> 
> library("ggplot2")
> 
> # generate dataset and base plot
> set.seed(100)
> df <- data.frame(country = LETTERS, V = runif(26, -40, 40))
> df$country = factor(LETTERS, LETTERS[order(df$V)]) # reorder factors
> gg <- ggplot(df, aes(x = country, y = V, fill = V)) +
+   geom_bar(stat = "identity") +
+   labs(y = "Under/over valuation in %", x = "Country") +
+   coord_flip() + theme_minimal()
>   
> # plot with default diverging scale
> gg + scale_fill_continuous_diverging()
Error in if (!alpha || all(lab_in[, 4] == 1)) { : 
  missing value where TRUE/FALSE needed
Calls: scale_fill_continuous_diverging ... <Anonymous> -> ggproto -> <Anonymous> -> colour_ramp
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    extdata   2.0Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   5.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.2Mb
    libs      1.5Mb
Package suggested but not available for checking: 'ProData'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    help   1.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/CovTools.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.7/cplexAPI.Rcheck/00install.out' for details.
Running examples in 'cptec-Ex.R' failed
The error most likely occurred in:

> ### Name: condicoes_tempo
> ### Title: Data frame containing "tempo" descriptions
> ### Aliases: condicoes_tempo
> ### Keywords: brazil forecast weather
> 
> ### ** Examples
> 
> condicoes_tempo()
Error in open.connection(x, "rb") : 
  Timeout was reached: [servicos.cptec.inpe.br] Resolving timed out after 10000 milliseconds
Calls: condicoes_tempo -> <Anonymous> -> read_html.default
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   5.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    shp   7.8Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   4.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/curl.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'cutpointr.Rmd' using rmarkdown
Quitting from lines 181-184 (cutpointr.Rmd) 
Error: processing vignette 'cutpointr.Rmd' failed with diagnostics:
there is no package called 'registry'
--- failed re-building 'cutpointr.Rmd'

SUMMARY: processing the following file failed:
  'cutpointr.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    doc    1.2Mb
    help   1.0Mb
    libs   1.9Mb
Running examples in 'DALEXtra-Ex.R' failed
The error most likely occurred in:

> ### Name: explain_scikitlearn
> ### Title: Wrapper for Python Scikit-Learn Models
> ### Aliases: explain_scikitlearn
> 
> ### ** Examples
> 
> library("DALEXtra")
> if(DALEXtra:::is_conda()) {
+    # Explainer build (Keep in mind that 18th column is target)
+    titanic_test <- read.csv(system.file("extdata", "titanic_test.csv", package = "DALEXtra"))
+    # Keep in mind that when pickle is being built and loaded,
+    # not only Python version but libraries versions has to match aswell
+    explainer <- explain_scikitlearn(system.file("extdata", "scikitlearn.pkl", package = "DALEXtra"),
+    yml = system.file("extdata", "testing_environment.yml", package = "DALEXtra"),
+    data = titanic_test[,1:17], y = titanic_test$survived)
+    plot(model_performance(explainer))
+ 
+    # Predictions with newdata
+    predict(explainer, titanic_test[1:10,1:17])
+ 
+ } else {
+   print('Conda is required.')
+ }
There already exists environment named the same as it is specified in .yml file - myenv. It will be used
Warning in system2(command = python, args = paste0("\"", config_script,  :
  running command '"C:/Users/CRAN/AppData/Local/r-miniconda/envs/myenv/python.exe" "D:/RCompile/CRANpkg/lib/4.0/reticulate/config/config.py"' had status 2
Warning: Error in python_config(python_version, required_module, python_version, : Error 2 occurred running C:/Users/CRAN/AppData/Local/r-miniconda/envs/myenv/python.exe 

Error: Yours environment has to match environment where pickle file was created. It also includes encoding, python version, and libraries version. Specifying .yml file or path to virtual environment may help. For more information look warnings() and then ?explain_scikitlearn
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/DandEFA.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   1.9Mb
.onLoad : <anonymous>: no visible global function definition for
  'read.table'
.onLoad : <anonymous>: no visible global function definition for
  'dbConnect'
.onLoad : <anonymous>: no visible global function definition for
  'dbListTables'
.onLoad : <anonymous>: no visible global function definition for
  'dbExistsTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbReadTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbWriteTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbDisconnect'
.onLoad : <anonymous>: no visible global function definition for
  'dbRemoveTable'
Undefined global functions or variables:
  dbConnect dbDisconnect dbExistsTable dbListTables dbReadTable
  dbRemoveTable dbWriteTable read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   5.1Mb
Running examples in 'DCD-Ex.R' failed
The error most likely occurred in:

> ### Name: DCD
> ### Title: Differential Community Detection for Paired Biological Networks,
> ###   for e.g. case vs control
> ### Aliases: DCD
> 
> ### ** Examples
> 
> 
> DCD_output <- DCD()
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
> ## Not run: 
> ##D library(igraph)
> ##D g_A <- sample_grg(200, 0.15, torus=FALSE, coords = FALSE)
> ##D g_B <- permute(g_A,c(sample(20),21:200))
> ##D ground_truth <- c(rep(1,20),rep(0,180))
> ##D DCD_output2 <- DCD(g_A = g_A, g_B = g_B, method = "Spectral", mink = 7,
> ##D                    ground_truth = ground_truth, plot_flag = 1, color = "red",
> ##D                    iter = 1, cores = 1 )
> ##D   
> ## End(Not run)
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11828 (sockconn)
Execution halted
.makeICCDialog: no visible global function definition for 'J'
.makeICCDialog: no visible global function definition for 'new'
.makeICCDialog: no visible global function definition for '.jnull'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'new'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'J'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'toJava'
.makeNewLDADialog: no visible global function definition for 'new'
.makeNewLDADialog: no visible global function definition for 'J'
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for 'new'
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for 'toJava'
.makeNewLDADialog: no visible global function definition for 'toJava'
.makeNewReliabilityDialog: no visible global function definition for
  'new'
.makeNewReliabilityDialog: no visible global function definition for
  'toJava'
.onLoad: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for 'winMenuAdd'
.onLoad: no visible global function definition for 'winMenuAddItem'
.onLoad: no visible global function definition for 'jgr.getMenuNames'
.onLoad: no visible global function definition for 'jgr.insertMenu'
.onLoad: no visible global function definition for 'jgr.addMenu'
.onLoad: no visible global function definition for 'jgr.addMenuItem'
Undefined global functions or variables:
  .jnull J jgr.addMenu jgr.addMenuItem jgr.getMenuNames jgr.insertMenu
  new toJava winMenuAdd winMenuAddItem
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "winMenuAdd", "winMenuAddItem")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/DeducerSpatial.Rcheck/00install.out' for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.8Mb
    help   1.4Mb
    libs   1.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.7Mb
Running examples in 'dgmb-Ex.R' failed
The error most likely occurred in:

> ### Name: dgmb-package
> ### Title: Simulating Data for PLS Mode B Structural Models
> ### Aliases: dgmb-package dgmb
> ### Keywords: package
> 
> ### ** Examples
> 
> dgmbGui()
 --------------------------------------------------
| Simulating Data for PLS Mode B Structural Models |
| Version: 1.2                                     |
| Depends: abind, tcltk, MASS                      |
| Licence: GPL >= 2                                |
| System Requirements: tktable, BWidget            |
 --------------------------------------------------
Warning in tclRequire("Tktable") : Tcl package 'Tktable' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "table".
Calls: dgmbGui -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb
Running examples in 'DiffNet-Ex.R' failed
The error most likely occurred in:

> ### Name: diffnet
> ### Title: Detection of Statistically Significant Changes in Paired
> ###   Biological Networks
> ### Aliases: diffnet
> 
> ### ** Examples
> 
> library("DiffNet")
> # this step is optional, it helps speed up calculations, run in parallel on 2 processors
> library(doParallel)
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> registerDoParallel(2)
> # Run the differential network analysis tehcnique on sample data
> p <- diffnet()
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11724 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11724 (sockconn)
Execution halted
Running examples in 'DiffNet-Ex.R' failed
The error most likely occurred in:

> ### Name: diffnet
> ### Title: Detection of Statistically Significant Changes in Paired
> ###   Biological Networks
> ### Aliases: diffnet
> 
> ### ** Examples
> 
> library("DiffNet")
> # this step is optional, it helps speed up calculations, run in parallel on 2 processors
> library(doParallel)
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> registerDoParallel(2)
> # Run the differential network analysis tehcnique on sample data
> p <- diffnet()
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11768 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11768 (sockconn)
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    5.1Mb
    libs   1.4Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    5.6Mb
    libs   1.4Mb
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    include  15.9Mb
    libs      1.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   2.1Mb
    libs   2.0Mb
Package suggested but not available for checking: 'rPython'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.1Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs   5.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.5Mb
    libs   1.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/ecr.Rcheck/00install.out' for details.
Found the following significant warnings:
  lpkit.h:32:99: warning: right-hand operand of comma expression has no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/EditImputeCont.Rcheck/00install.out' for details.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.3Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.4Mb
Running examples in 'eqn2svg-Ex.R' failed
The error most likely occurred in:

> ### Name: eqn2svg
> ### Title: Convert a LaTeX math formula to an SVG object
> ### Aliases: eqn2svg
> 
> ### ** Examples
> 
> # Take LaTeX code for the Heaviside
> # Function and convert that to SVG
> heaviside <-
+   eqn2svg(
+     eqn = l_time_domain[25],
+     preview = FALSE
+   )
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in file(con, "r") : cannot open the connection
Calls: eqn2svg -> readLines -> file
Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(eqn2svg)
  > 
  > test_check("eqn2svg")
  -- 1. Error: SVG conversion works (@test-eqn2svg.R#3)  -------------------------
  cannot open the connection
  Backtrace:
   1. eqn2svg::eqn2svg(eqn = l_time_domain[25], preview = FALSE)
   2. base::readLines(url, warn = FALSE)
   3. base::file(con, "r")
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: SVG conversion works (@test-eqn2svg.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/ESTER.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.7Mb
File 'fastmatch/libs/i386/fastmatch.dll':
  Found non-API call to R: 'match5'
File 'fastmatch/libs/x64/fastmatch.dll':
  Found non-API call to R: 'match5'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/FastRWeb.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/fdANOVA.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.9Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
    libs   1.7Mb
Packages suggested but not available for checking: 'doMC', 'RSvgDevice'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   1.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/float.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R   6.3Mb
Package required and available but unsuitable version: 'aws'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   5.5Mb
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(freetypeharfbuzz)
  > 
  > test_check("freetypeharfbuzz")
  -- 1. Failure: string metrics are computed for various edge cases (@test-string-
  `metrics` not equal to c(width = w, height = h, ascent = a, descent = d).
  2/4 mismatches (average diff: 1e-04)
  [2] 1.28 - 1.28 == 1e-04
  [3] 1.28 - 1.28 == 1e-04
  
  == testthat results  ===========================================================
  [ OK: 27 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: string metrics are computed for various edge cases (@test-string-info.R#52) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
Package suggested but not available for checking: 'dggrids'
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    2.1Mb
    libs   1.4Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    data  16.2Mb
Found the following significant warnings:
  FunctionalNetworks.c:223:17: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/FunctionalNetworks.Rcheck/00install.out' for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.5Mb
    libs      1.5Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb
finterp.data.frame: no visible global function definition for
  'as.formula'
finterp.data.frame: no visible global function definition for 'terms'
finterp.data.frame: no visible global function definition for
  'model.matrix'
finterp.data.frame: no visible global function definition for
  'model.frame'
finterp.default: no visible global function definition for 'terms'
finterp.default: no visible global function definition for
  'model.matrix'
finterp.default: no visible global function definition for
  'model.frame'
gamlss.nl: no visible global function definition for 'nlm'
nl: no visible global function definition for 'is'
nlgamlss: no visible global function definition for 'NO'
nlgamlss: no visible global function definition for 'as.gamlss.family'
nlgamlss: no visible global function definition for 'nlm'
nlgamlss: no visible global function definition for 'cov2cor'
summary.nlgamlss: no visible global function definition for 'coef'
summary.nlgamlss: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  NO as.formula as.gamlss.family coef cov2cor is model.frame
  model.matrix nlm pnorm terms
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "as.formula", "coef", "cov2cor", "model.frame",
             "model.matrix", "nlm", "pnorm", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      4.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.8Mb
installed size is 84.5Mb
  sub-directories of 1Mb or more:
    L8NY18   2.2Mb
    gdal     3.8Mb
    libs    72.1Mb
    proj     5.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   3.0Mb
    libs      1.4Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R  10.2Mb
Warnings in file 'R/utils.R':
  unable to translate '<U+00E9>' to native encoding
  unable to translate '<U+00F6>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+2019>' to native encoding
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/gensphere.Rcheck/00install.out' for details.
Found the following significant warnings:
  runMCMCfunc.cpp:40:42: warning: left operand of comma operator has no effect [-Wunused-value]
  runMCMCfunc.cpp:41:45: warning: left operand of comma operator has no effect [-Wunused-value]
  runMCMCfunc.cpp:55:44: warning: left operand of comma operator has no effect [-Wunused-value]
  runMCMCfunc.cpp:56:47: warning: left operand of comma operator has no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/geoCount.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.2Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R         8.9Mb
    extdata   1.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    data   3.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   1.8Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    doc         1.1Mb
    libs       21.2Mb
    test_data   1.2Mb
plot.glmulti: no visible global function definition for 'windows'
glmulti,character-character-ANY-ANY: no visible global function
  definition for 'regsubsets'
Undefined global functions or variables:
  regsubsets windows
Consider adding
  importFrom("grDevices", "windows")
to your NAMESPACE file.
Package suggested but not available for checking: 'cplexAPI'
Found the following significant warnings:
  Warning: namespace 'lme4' is not available and has been replaced
See 'd:/Rcompile/CRANpkg/local/4.0/GMMAT.Rcheck/00install.out' for details.
File 'gnmf/libs/i386/gnmf.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'FactorMatrix.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'FactorMatrix.o'
File 'gnmf/libs/x64/gnmf.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'FactorMatrix.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'FactorMatrix.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/GPareto.Rcheck/00install.out' for details.
Running 'bug1.R' [1s]
  Running 'reg-tests.R' [1s]
  Comparing 'reg-tests.Rout' to 'reg-tests.Rout.save' ...58c58
< Formal class 'gpc.poly' [package "gpclib"] with 1 slot
---
> Formal class 'gpc.poly' [package "gpclib"] with 1 slots
68c68
< Formal class 'gpc.poly' [package "gpclib"] with 1 slot
---
> Formal class 'gpc.poly' [package "gpclib"] with 1 slots
83c83
< Formal class 'gpc.poly' [package "gpclib"] with 1 slot
---
> Formal class 'gpc.poly' [package "gpclib"] with 1 slots
Running the tests in 'tests/bug1.R' failed.
Complete output:
  > suppressMessages(library(gpclib))
  > to_numeric <- selectMethod(coerce, c("gpc.poly", "numeric"))
  > load("bug1_data.RData")
  > plot(p)  ## loads a polygon, looks fine
  > plot(as(vec, "gpc.poly"))  ## looks fine
  > clip <- to_numeric(p); str(clip)
   num [1:17] 1 7 0 570545 7890092 ...
  > 
  > ## Crashes R 2.14 and 2.15 (32-bit) on Windows
  > vec <- .Call("Rgpc_polygon_clip", vec, clip, 3, PACKAGE="gpclib")
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.7/gpuR.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'dse1'
normalweight: no visible binding for global variable 'NW_above'
normalweight: no visible binding for global variable 'NW_below'
obese: no visible global function definition for 'data'
obese: no visible binding for global variable 'OB_above'
obese: no visible binding for global variable 'OB_below'
overweight: no visible global function definition for 'data'
overweight: no visible binding for global variable 'OW_above'
overweight: no visible binding for global variable 'OW_below'
Undefined global functions or variables:
  NW_above NW_below OB_above OB_below OW_above OW_below data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    CWrappers_1.10.2   2.5Mb
    CWrappers_1.10.3   2.4Mb
    libs               6.7Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs   4.0Mb
Undocumented S4 classes:
  'otherornull'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc           3.7Mb
    htmlwidgets   4.0Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
    libs   1.5Mb
PlotOptPower: no visible global function definition for 'bmp'
PlotOptPower: no visible global function definition for
  'filled.contour'
PlotOptPower: no visible global function definition for 'title'
PlotOptPower: no visible global function definition for 'grey.colors'
PlotOptPower: no visible global function definition for 'axis'
PlotOptPower: no visible global function definition for 'polygon'
PlotOptPower: no visible global function definition for 'legend'
PlotOptPower: no visible global function definition for 'mtext'
PlotOptPower: no visible global function definition for 'dev.off'
PlotOptPower: no visible global function definition for
  'terrain.colors'
ShowOptDesign: no visible global function definition for 'head'
diffVariantError: no visible global function definition for 'pbinom'
predictPoolNCP: no visible global function definition for 'data'
probDetEqual3: no visible global function definition for 'dbinom'
probDetEqual3: no visible global function definition for 'pbinom'
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/HRM.Rcheck/00install.out' for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.5Mb
    libs   1.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Error(s) in re-building vignettes:
--- re-building 'DecisionNetworks.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: nnet
--- finished re-building 'DecisionNetworks.Rmd'

--- re-building 'GettingStartedWithHydeNet.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building 'GettingStartedWithHydeNet.Rmd'

--- re-building 'HydeNetPlots.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 158-167 (HydeNetPlots.Rmd) 
Error: processing vignette 'HydeNetPlots.Rmd' failed with diagnostics:
Blackjack rules URL does not exist.  Find a new link
--- failed re-building 'HydeNetPlots.Rmd'

--- re-building 'WorkingWithHydeNetObjects.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building 'WorkingWithHydeNetObjects.Rmd'

SUMMARY: processing the following file failed:
  'HydeNetPlots.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   1.4Mb
    libs   2.4Mb
Running examples in 'icrf-Ex.R' failed
The error most likely occurred in:

> ### Name: plot
> ### Title: icrf IMSE rate plot
> ### Aliases: plot plot.icrf
> 
> ### ** Examples
> 
> # rats data example
> # Note that this is a toy example. Use a larger ntree and nfold in practice.
> data(rat2)
> set.seed(1)
> samp <- sample(1:dim(rat2)[1], 200)
> rats.train <- rat2[samp, ]
> rats.test <- rat2[-samp, ]
> L = ifelse(rats.train$tumor, 0, rats.train$survtime)
> R = ifelse(rats.train$tumor, rats.train$survtime, Inf)
> # Note that this is a toy example. Use a larger ntree and nfold in practice.
> set.seed(2)
> ## Don't show: 
> # 1. formula (currentstatus)
>  rats.icrf.small <-
+    icrf(~ dose.lvl + weight + male + cage.no, data = rat2,
+         data.type = "currentstatus", currentstatus.label = c("survtime", "tumor"),
+         returnBest = TRUE, ntree=2, nfold=1)
Error in icrf.default(m, L, R, ...) : 
  NA/NaN/Inf in foreign function call (arg 50)
Calls: icrf -> icrf.formula -> icrf.default
Execution halted
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   7.4Mb
Found the following significant warnings:
  uuid/gen_uuid.c:321:11: warning: ordered comparison of pointer with integer zero [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0/igraph.Rcheck/00install.out' for details.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  13.4Mb
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       1.1Mb
    extdata   1.1Mb
    include   3.0Mb
    libs     15.7Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
ClearBottomMenuPlot: no visible global function definition for 'rect'
InteractiveIGraph : mousedown: no visible global function definition
  for 'grconvertX'
InteractiveIGraph : mousedown: no visible global function definition
  for 'grconvertY'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'grconvertX'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'grconvertY'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'polygon'
InteractiveIGraph : mouseup: no visible global function definition for
  'grconvertX'
InteractiveIGraph : mouseup: no visible global function definition for
  'grconvertY'
InteractiveIGraph : keybd: no visible global function definition for
  'readClipboard'
InteractiveIGraph : keybd: no visible global function definition for
  'par'
PlotRegionGeneral: no visible global function definition for 'polygon'
plot.InteractiveIGraph: no visible global function definition for
  'plot'
plot.InteractiveIGraph: no visible global function definition for 'par'
plot.Menu: no visible global function definition for 'par'
plot.Menu: no visible binding for global variable 'rect'
plot.MenuItem: no visible binding for global variable 'strwidth'
plot.MenuItem: no visible binding for global variable 'strheight'
plot.MenuItem: no visible binding for global variable 'rect'
plot.MenuItem: no visible binding for global variable 'text'
plot.MenuLine: no visible binding for global variable 'rect'
Undefined global functions or variables:
  grconvertX grconvertY par plot polygon readClipboard rect strheight
  strwidth text
Consider adding
  importFrom("graphics", "grconvertX", "grconvertY", "par", "plot",
             "polygon", "rect", "strheight", "strwidth", "text")
  importFrom("utils", "readClipboard")
to your NAMESPACE file.
Interpol: no visible global function definition for 'splinefun'
Undefined global functions or variables:
  splinefun
Consider adding
  importFrom("stats", "splinefun")
to your NAMESPACE file.
File 'iotools/libs/i386/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'
File 'iotools/libs/x64/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Running examples in 'iotools-Ex.R' failed
The error most likely occurred in:

> ### Name: idstrsplit
> ### Title: Create an iterator for splitting binary or character input into
> ###   a dataframe
> ### Aliases: idstrsplit
> ### Keywords: iterator
> 
> ### ** Examples
> 
> col_names <- names(iris)
> write.csv(iris, file="iris.csv", row.names=FALSE)
> it <- idstrsplit("iris.csv", col_types=c(rep("numeric", 4), "character"), 
+                  sep=",")
> # Get the elements
> iris_read <- it$nextElem()[-1,]
> # or with the iterators package
> # nextElem(it)
> names(iris_read) <- col_names
> print(head(iris_read))
  Sepal.Length Sepal.Width Petal.Length Petal.Width  Species
2          5.1         3.5          1.4         0.2 "setosa"
3          4.9         3.0          1.4         0.2 "setosa"
4          4.7         3.2          1.3         0.2 "setosa"
5          4.6         3.1          1.5         0.2 "setosa"
6          5.0         3.6          1.4         0.2 "setosa"
7          5.4         3.9          1.7         0.4 "setosa"
> unlink("iris.csv")
> 
> 
> 
> cleanEx()
Error: connections left open:
	iris.csv (file)
Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data      1.3Mb
    extdata   7.5Mb
Running examples in 'iRF-Ex.R' failed
The error most likely occurred in:

> ### Name: readForest
> ### Title: Pass data through a fitted forest, record node characteristics
> ###   [works for binary classification with continuous variables]
> ### Aliases: readForest
> 
> ### ** Examples
> 
>   n = 50; p = 10
>   X = array(rnorm(n*p), c(n, p))
>   Y = (X[,1]>0.35 & X[,2]>0.35)|(X[,5]>0.35 & X[,7]>0.35)
>   Y = as.factor(as.numeric(Y>0))
> 
>   train.id = 1:(n/2)
>   test.id = setdiff(1:n, train.id)
>   
>   rf <- randomForest(x=X, y=Y, keep.forest=TRUE, track.nodes=TRUE,
+     ntree=100)
>   rforest <- readForest(rfobj=rf, x=X, n.core=2)
>   head(rforest$tree_info)
NULL
> 
>  # count number of leaf nodes with at least 5 observations
>   sum(rforest$tree.info$size.node > 5)
[1] 293
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11132 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11132 (sockconn)
Execution halted
Running examples in 'iRF-Ex.R' failed
The error most likely occurred in:

> ### Name: readForest
> ### Title: Pass data through a fitted forest, record node characteristics
> ###   [works for binary classification with continuous variables]
> ### Aliases: readForest
> 
> ### ** Examples
> 
>   n = 50; p = 10
>   X = array(rnorm(n*p), c(n, p))
>   Y = (X[,1]>0.35 & X[,2]>0.35)|(X[,5]>0.35 & X[,7]>0.35)
>   Y = as.factor(as.numeric(Y>0))
> 
>   train.id = 1:(n/2)
>   test.id = setdiff(1:n, train.id)
>   
>   rf <- randomForest(x=X, y=Y, keep.forest=TRUE, track.nodes=TRUE,
+     ntree=100)
>   rforest <- readForest(rfobj=rf, x=X, n.core=2)
>   head(rforest$tree_info)
NULL
> 
>  # count number of leaf nodes with at least 5 observations
>   sum(rforest$tree.info$size.node > 5)
[1] 284
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11031 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11031 (sockconn)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/jackalope.Rcheck/00install.out' for details.
Package unavailable to check Rd xrefs: 'doMC'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   3.9Mb
comp.npci: no visible global function definition for 'qnorm'
epband.fun: no visible global function definition for 'data'
epband.fun: no visible binding for global variable
  'critical.value.nair.90'
epband.fun: no visible binding for global variable
  'critical.value.nair.95'
epband.fun: no visible binding for global variable
  'critical.value.nair.99'
hall.wellner.fun: no visible global function definition for 'data'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.90'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.95'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.99'
lrt.confints: no visible global function definition for 'qchisq'
rothman.fun: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  critical.value.hall.90 critical.value.hall.95 critical.value.hall.99
  critical.value.nair.90 critical.value.nair.95 critical.value.nair.99
  data qchisq qnorm
Consider adding
  importFrom("stats", "qchisq", "qnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.6Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   8.4Mb
installed size is 79.1Mb
  sub-directories of 1Mb or more:
    gdal   3.8Mb
    libs  68.9Mb
    proj   5.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.4Mb
    libs   2.3Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
Package suggested but not available for checking: 'rsyslog'
Package unavailable to check Rd xrefs: 'rsyslog'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      2.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
    libs   1.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/lmds.Rcheck/00install.out' for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        2.4Mb
    libs       2.1Mb
    testdata   1.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      1.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.1Mb
    libs   1.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   1.6Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:

======== End of example output (where/before crash/hang up occured ?) ========
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
    proj   5.0Mb
SelectedInput:
  function(...)
SelectedInput.formula:
  function(..., data, control, metrics, stat, cutoff)

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    TS_files     5.8Mb
    base_files   6.3Mb
installed size is 41.2Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs  34.2Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc           1.2Mb
    htmlwidgets   1.4Mb
    libs          7.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   2.5Mb
Found the following significant warnings:
  Warning: unable to find a consistent ordering of superclasses for class "dsparseModelMatrix": order chosen is inconsistent with the superclasses of "sparseModelMatrix"
See 'd:/Rcompile/CRANpkg/local/4.0/MatrixModels.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.6Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.2Mb
Depends: includes the non-default packages:
  'MASS', 'boot', 'RColorBrewer', 'scatterplot3d', 'tcltk', 'tcltk2',
  'tkrplot', 'rpanel', 'rgl'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      1.5Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.1Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
Package suggested but not available for checking: 'unix'
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.1Mb
Packages suggested but not available for checking: 'doMC', 'doSMP'
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   1.7Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.1Mb
    libs   4.1Mb
    misc   1.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
cdf.pval: no visible global function definition for 'median'
cdf.pval: no visible binding for global variable 'ecdf'
find_hits: no visible global function definition for 'na.omit'
mad.scores: no visible global function definition for 'as.formula'
mad.scores: no visible binding for global variable 'median'
mad.scores: no visible binding for global variable 'mad'
rm.outliers: no visible global function definition for 'as.formula'
rm.outliers: no visible binding for global variable 'median'
rm.outliers: no visible binding for global variable 'mad'
Undefined global functions or variables:
  as.formula ecdf mad median na.omit
Consider adding
  importFrom("stats", "as.formula", "ecdf", "mad", "median", "na.omit")
to your NAMESPACE file.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
listGenoToTable: no visible binding for global variable 'dummy'
Undefined global functions or variables:
  dummy
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
    help   1.4Mb
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    libs   2.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Error(s) in re-building vignettes:
--- re-building 'Brief-Overview.Rmd' using rmarkdown
--- finished re-building 'Brief-Overview.Rmd'

--- re-building 'Example1.Rmd' using rmarkdown
pandoc.exe: Could not fetch https://www4.stat.ncsu.edu/~boos/Monte.Carlo.se/table9_1.jpg
HttpExceptionRequest Request {
  host                 = "www4.stat.ncsu.edu"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/~boos/Monte.Carlo.se/table9_1.jpg"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure getAddrInfo: does not exist (error 11001))
Error: processing vignette 'Example1.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
--- failed re-building 'Example1.Rmd'

--- re-building 'Example2.Rmd' using rmarkdown
--- finished re-building 'Example2.Rmd'

--- re-building 'Example3.Rmd' using rmarkdown
--- finished re-building 'Example3.Rmd'

SUMMARY: processing the following file failed:
  'Example1.Rmd'

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Morpho.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   1.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   1.6Mb
    libs   1.4Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    R             1.1Mb
    libs         13.9Mb
    mathematica   1.5Mb
File 'MRwarping/libs/i386/MRwarping.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'interfaceRC_warp.o'
File 'MRwarping/libs/x64/MRwarping.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'interfaceRC_warp.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.1Mb
    libs  20.9Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Error(s) in re-building vignettes:
--- re-building 'muHVT.Rmd' using rmarkdown
Warning: unable to access index for repository http://cran.us.r-project.org/src/contrib:
  cannot open URL 'http://cran.us.r-project.org/src/contrib/PACKAGES'
Warning: package 'R.utils' is not available (for R Under development)
Warning: unable to access index for repository http://cran.us.r-project.org/bin/windows/contrib/4.0:
  cannot open URL 'http://cran.us.r-project.org/bin/windows/contrib/4.0/PACKAGES'
Quitting from lines 18-121 (muHVT.Rmd) 
Error: processing vignette 'muHVT.Rmd' failed with diagnostics:
there is no package called 'R.utils'
--- failed re-building 'muHVT.Rmd'

SUMMARY: processing the following file failed:
  'muHVT.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.5Mb
    libs   1.5Mb
Running 'spelling.R' [0s]
  Running 'testthat.R' [118s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(nandb)
  > 
  > test_check("nandb")
  -- 1. Failure: median and smooth filters work (@test-filters.R#7)  -------------
  round(mean(median_filter(m, na_rm = TRUE), na.rm = TRUE), 3) not equal to 3.812.
  1/1 mismatches
  [1] 3.81 - 3.81 == 0.001
  
  == testthat results  ===========================================================
  [ OK: 153 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: median and smooth filters work (@test-filters.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.9Mb
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("nat.utils")
  Loading required package: nat.utils
  -- 1. Failure: common_path works (@test-fsutils.r#79)  -------------------------
  common_path(c("/a", "/b"), normalise = T) not equal to np("/").
  1/1 mismatches
  x[1]: "d:/"
  y[1]: "D:/"
  
  == testthat results  ===========================================================
  [ OK: 73 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: common_path works (@test-fsutils.r#79) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
File 'NeatMap/libs/i386/NeatMap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'nMDS_R.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'nMDS_R.o'
File 'NeatMap/libs/x64/NeatMap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'nMDS_R.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'nMDS_R.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  generateData.cpp:105:18: warning: passing NULL to non-pointer argument 1 of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion-null]
See 'd:/Rcompile/CRANpkg/local/4.0/NestedCategBayesImpute.Rcheck/00install.out' for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   2.3Mb
Running examples in 'nFactors-Ex.R' failed
The error most likely occurred in:

> ### Name: eigenComputes
> ### Title: Computes Eigenvalues According to the Data Type
> ### Aliases: eigenComputes
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> # .......................................................
> # Different data types
> # Vector of eigenvalues
>   data(dFactors)
>   x1 <- dFactors$Cliff1$eigenvalues
>   eigenComputes(x1)
 [1]  2.842  1.080  0.640  0.171  0.015 -0.008 -0.008 -0.126 -0.040 -0.066
[11] -0.111 -0.116
>   
> # Data from a data.frame
>   x2 <- data.frame(matrix(20*rnorm(100), ncol=5))
>   eigenComputes(x2, cor=TRUE,  use="everything")
[1] 1.5562290 1.3713228 1.1323986 0.6806224 0.2594272
>   eigenComputes(x2, cor=FALSE, use="everything")
[1] 527.95290 485.38169 365.44540 209.02148  84.80241
>   eigenComputes(x2, cor=TRUE,  use="everything", method="spearman")
[1] 1.486597 1.448541 1.249002 0.625795 0.190065
>   eigenComputes(x2, cor=TRUE,  use="everything", method="kendall")
[1] 1.3682956 1.3334477 1.2159607 0.7120364 0.3702597
> 
> # From a covariance matrix
>   x3 <- cov(x2)
>   eigenComputes(x3, cor=TRUE,  use="everything")
Error in switch(classType, data.frame = "data", matrix = "correlation",  : 
  EXPR must be a length 1 vector
Calls: eigenComputes -> eigenFrom
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    CppCode   2.6Mb
    R         6.2Mb
    include   5.6Mb
    libs      1.8Mb
    tests     1.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/nonlinearTseries.Rcheck/00install.out' for details.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    7.4Mb
    libs   2.7Mb
File 'nws/R/zzz.R':
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.

blendOptions: warning in assign(names[i], new[[i]], env = options):
  partial argument match of 'env' to 'envir'
docall: warning in get(as.character(fun), env = .GlobalEnv, mode =
  "function"): partial argument match of 'env' to 'envir'
logMsg: no visible global function definition for 'flush.console'
nwsPkgInfo: no visible global function definition for
  'packageDescription'
initialize,nwsServer: no visible global function definition for
  'make.socket'
initialize,nwsServer: no visible global function definition for
  'close.socket'
Undefined global functions or variables:
  close.socket flush.console make.socket packageDescription
Consider adding
  importFrom("utils", "close.socket", "flush.console", "make.socket",
             "packageDescription")
to your NAMESPACE file.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
File 'obliclus/libs/i386/obliclus.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'random_cluster_C.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'random_cluster_C.o'
File 'obliclus/libs/x64/obliclus.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'random_cluster_C.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'random_cluster_C.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    doc    2.3Mb
    help   2.7Mb
    libs   2.0Mb
mapvar: no visible global function definition for 'data'
mapvar: no visible binding for global variable 'state.fips'
mapvar: no visible global function definition for 'rgb'
mapvar: no visible global function definition for 'rect'
mapvar: no visible global function definition for 'text'
rowScrape: no visible global function definition for 'tail'
rowScrape: no visible global function definition for 'head'
scrapeTable: no visible binding for global variable 'tail'
Undefined global functions or variables:
  data head rect rgb state.fips tail text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "rect", "text")
  importFrom("utils", "data", "head", "tail")
to your NAMESPACE file.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
MLparameters: no visible global function definition for 'optim'
comp.freq: no visible global function definition for 'x11'
comp.freq: no visible global function definition for 'par'
comp.freq: no visible global function definition for 'plot'
Undefined global functions or variables:
  optim par plot x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "optim")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.7/OpenCL.Rcheck/00install.out' for details.
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    libs   20.0Mb
    share   9.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.4Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    R        2.5Mb
    libs     7.6Mb
    models   4.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/openssl.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/optBiomarker.Rcheck/00install.out' for details.
Package required but not available: 'ROracle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
File 'OriGen/libs/i386/OriGen.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'OriGen.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'OriGen.o'
File 'OriGen/libs/x64/OriGen.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'OriGen.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'OriGen.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
Package suggested but not available for checking: 'Rcplex'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   1.8Mb
Running 'test-pkgdepends.R' [52s]
  Running 'test-pkginstall.R' [0s]
  Running 'testthat.R' [19s]
Running the tests in 'tests/test-pkgdepends.R' failed.
Complete output:
  > 
  > do <- function() {
  +   old <- Sys.getenv("R_PKG_CACHE_DIR", NA_character_)
  +   if (is.na(old)) {
  +     on.exit(Sys.unsetenv("R_PKG_CACHE_DIR"), add = TRUE)
  +   } else {
  +     on.exit(Sys.setenv("R_PKG_CACHE_DIR" = old), add = TRUE)
  +   }
  +   Sys.setenv("R_PKG_CACHE_DIR" = tempfile())
  + 
  +   if (file.exists("pkgdepends")) {
  +     library(testthat)
  +     library(pak)
  +     test <- function() {
  +       package <- "pak"
  +       env_test <- asNamespace("testthat")$env_test
  +       env_test$in_test <- TRUE
  +       env_test$package <- package
  +       on.exit({
  +         env_test$in_test <- FALSE
  +         env_test$package <- NULL
  +       }, add = TRUE)
  +       test_path <- "pkgdepends"
  +       asNamespace("testthat")$test_package_dir(
  +         package = package, test_path = test_path,
  +         filter = NULL, reporter = "check")
  +     }
  +     test()
  +   }
  + }
  > 
  > do()
  -- 1. Error: dependencies are honoured (@test-resolution.R#291)  ---------------
  Wrong entry types: `filesize (double, expected integer)`
  Backtrace:
   1. asNamespace("pkgcache")$synchronise(do("cran::dplyr", FALSE))
  
  == testthat results  ===========================================================
  [ OK: 675 | SKIPPED: 32 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: dependencies are honoured (@test-resolution.R#291) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [73s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(panelr)
  Loading required package: lme4
  Loading required package: Matrix
  
  Attaching package: 'panelr'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("panelr")
  -- 1. Error: (unknown) (@test_wbm.R#283)  --------------------------------------
  could not find function "arma"
  Backtrace:
   1. panelr::wbm_stan(...)
   2. brms::make_stancode(...)
   4. brms:::validate_formula.default(...)
   6. brms:::validate_formula.brmsformula(bf(formula), ...)
   7. brms:::validate_autocor(autocor)
   8. brms:::parse_ac(autocor)
   9. base::lapply(out, eval2)
  
  == testthat results  ===========================================================
  [ OK: 271 | SKIPPED: 0 | WARNINGS: 60 | FAILED: 1 ]
  1. Error: (unknown) (@test_wbm.R#283) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   1.2Mb
    doc    2.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/PathSelectMP.Rcheck/00install.out' for details.
Not exits: C:/Program Files/netCDF 4.3.2
Not exits: C:/Program Files/netCDF 4.3.2/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcp100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcr100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/zlib.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5_hl.dll
Not exits: C:/Program Files/netCDF 4.3.2/bin/netcdf.dll
===== WARNING =====
- netCDF 4.3.2 may not install at compile time.
- Environment variables may not be correct at compile and run time.
- pbdNCDF4 binary may not link with netCDF.
- Please consider to rebuild from source.
===================
get.sysenv: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
  shortPathName
Consider adding
  importFrom("utils", "shortPathName")
to your NAMESPACE file.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    lib    5.6Mb
    libs   4.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.3Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  13.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs   13.3Mb
    share  11.9Mb
Malformed Title field: should not end in a period.
'LinkingTo' for 'ggplot2' is unused as it has no 'include' directory
Running examples in 'penDvine-Ex.R' failed
The error most likely occurred in:

> ### Name: penDvine-package
> ### Title: The package 'penDvine' offers routines for estimating densities
> ###   and copula distribution of D-vines.
> ### Aliases: penDvine-package
> 
> ### ** Examples
> 
> #This examples describes the estimation of a D-vine to winddata,
> #available in this package. After the margins are prepared, we estimate a
> #D-vine using B-splines with 9 (K+1) marginal knots and penalizing second (m=2)
> #order differences (pen=1) of the basis coefficients.
> 
> data(Winddata)
> ex.data<-Winddata[c(1:100),c(1:4)] #examplary subdata for fast calculation
> wind.example<-Dvine(ex.data,K=7,pen=1,lambda=100,order.Dvine=FALSE,base="B-spline",m=2,cores=2)
>   
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11137 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11137 (sockconn)
Execution halted
Found the following significant warnings:
  permTest.c:20:3: warning: statement with no effect [-Wunused-value]
  permTest.c:62:3: warning: statement with no effect [-Wunused-value]
  permTest.c:90:3: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/permDep.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/phateR.Rcheck/00install.out' for details.
Running examples in 'phenocamapi-Ex.R' failed
The error most likely occurred in:

> ### Name: download_midday_images
> ### Title: Downloading the midday images for PhenoCam sites given a time
> ###   range
> ### Aliases: download_midday_images
> 
> ### ** Examples
> 
> 
> download_dir <- download_midday_images('dukehw',
+  y = 2018,
+  months = 2,
+  days=1,
+  download_dir= tempdir())
Warning in get_midday_list(site, direct = FALSE) :
  midday list file was not found on the Phenocam server!
Error in basename(filepaths) : a character vector argument expected
Calls: download_midday_images -> parse_phenocam_filenames -> gsub -> basename
Execution halted
Running 'testthat.R' [82s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(phenocamapi)
  Loading required package: data.table
  Loading required package: rjson
  Loading required package: RCurl
  > library(data.table)
  > 
  > test_check("phenocamapi")
  trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
  Content type 'application/octet-stream' length 202940 bytes (198 KB)
  ==================================================
  downloaded 198 KB
  
  Error in file(con, "r") : cannot open the connection
  -- 1. Error: (unknown) (@testphenocamapi.R#18)  --------------------------------
  a character vector argument expected
  Backtrace:
   1. base::basename(duke_middays[1])
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 1 ]
  1. Error: (unknown) (@testphenocamapi.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'getting_started_phenocam_api.Rmd' using rmarkdown
trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
Content type 'application/octet-stream' length 202940 bytes (198 KB)
==================================================
downloaded 198 KB

trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/2013/05/dukehw_2013_05_31_150331.jpg'
Content type 'image/jpeg' length 470270 bytes (459 KB)
==================================================
downloaded 459 KB

Quitting from lines 282-298 (getting_started_phenocam_api.Rmd) 
Error: processing vignette 'getting_started_phenocam_api.Rmd' failed with diagnostics:
a character vector argument expected
--- failed re-building 'getting_started_phenocam_api.Rmd'

--- re-building 'phenocam_data_fusion.Rmd' using rmarkdown
Loading required package: rjson
Loading required package: RCurl
trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
Content type 'application/octet-stream' length 202940 bytes (198 KB)
==================================================
downloaded 198 KB

trying URL 'http://phenocam.sr.unh.edu/data/archive/oregonMP/ROI/oregonMP_EN_1000_3day.csv'
Content type 'application/octet-stream' length 269042 bytes (262 KB)
==================================================
downloaded 262 KB

--- finished re-building 'phenocam_data_fusion.Rmd'

SUMMARY: processing the following file failed:
  'getting_started_phenocam_api.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.0Mb
    libs      1.5Mb
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(phrasemachine)
  phrasemachine: Simple Phrase Extraction
  Version 1.1.2 created on 2017-05-29.
  copyright (c) 2016, Matthew J. Denny, Abram Handler, Brendan O'Connor.
  Type help('phrasemachine') or
  vignette('getting_started_with_phrasemachine') to get started.
  Development website: https://github.com/slanglab/phrasemachine
  > 
  > test_check("phrasemachine")
  -- 1. Error: See if tagging five documents works, and if coarsening works (@test
  unused argument (alist())
  Backtrace:
   1. documents[1:5, ]
  
  -- 2. Error: See if extractor works (@test_extract_phrases.R#7)  ---------------
  unused argument (alist())
  Backtrace:
   1. documents[1:5, ]
  
  Currently tagging document 1 of 1 
  Extracting phrases from document 1 of 1 
  == testthat results  ===========================================================
  [ OK: 10 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: See if tagging five documents works, and if coarsening works (@test_POS_tag_documents.R#7) 
  2. Error: See if extractor works (@test_extract_phrases.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'getting_started_with_phrasemachine.Rmd' using rmarkdown
Quitting from lines 82-91 (getting_started_with_phrasemachine.Rmd) 
Error: processing vignette 'getting_started_with_phrasemachine.Rmd' failed with diagnostics:
unused argument (alist())
--- failed re-building 'getting_started_with_phrasemachine.Rmd'

SUMMARY: processing the following file failed:
  'getting_started_with_phrasemachine.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.8Mb
Warnings in file 'R/HT_IVIVE_InputModule.R':
  unable to translate '	<U+03BC>m' to native encoding
  unable to translate '<U+03BC>mol/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/h/mg Protein' to native encoding
  unable to translate '<U+03BC>L/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/h/mg Protein' to native encoding
  unable to translate '<U+03BC>L/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/h/mg Protein' to native encoding

Warnings in file 'R/IVIVEGadget.R':
  unable to translate '<U+03BC>L/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/h/mg Protein' to native encoding
  unable to translate '<U+03BC>mol/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/h/mg Protein' to native encoding
  unable to translate '<U+03BC>L/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/h/mg Protein' to native encoding

Warnings in file 'R/performIVIVEModule.R':
  unable to translate '<U+03BC>mol/min/10^6 hepatocytes' to native encoding
  unable to translate '<U+03BC>mol/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/h/mg Protein' to native encoding
  unable to translate '<U+03BC>L/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/h/mg Protein' to native encoding
  unable to translate '<U+03BC>L/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/h/mg Protein' to native encoding
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/pollimetry.Rcheck/00install.out' for details.
Found the following significant warnings:
  StandardizeString.cpp:13:25: warning: passing NULL to non-pointer argument 1 of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 16; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion-null]
See 'd:/Rcompile/CRANpkg/local/4.0/PPRL.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'preputils.Rmd' using rmarkdown
Error: processing vignette 'preputils.Rmd' failed with diagnostics:
Scanner error: while parsing a quoted scalar at line 3, column 7 found unknown escape character at line 10, column 4

--- failed re-building 'preputils.Rmd'

SUMMARY: processing the following file failed:
  'preputils.Rmd'

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(preText)
  preText: Diagnostics to Assess the Effects of Text Preprocessing Decisions
  Version 0.6.3 created on 2018-01-12.
  copyright (c) 2017, Matthew J. Denny, Penn State University
                      Arthur Spirling, NYU
  Type vignette('getting_started_with_preText') to get started.
  Development website: https://github.com/matthewjdenny/preText
  > 
  > test_check("preText")
  -- 1. Error: Small example works (@test_factorial_preprocessing.R#6)  ----------
  unused argument (alist())
  Backtrace:
   1. documents[1:10, ]
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Small example works (@test_factorial_preprocessing.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'getting_started_with_preText.Rmd' using rmarkdown
Quitting from lines 60-69 (getting_started_with_preText.Rmd) 
Error: processing vignette 'getting_started_with_preText.Rmd' failed with diagnostics:
unused argument (alist())
--- failed re-building 'getting_started_with_preText.Rmd'

SUMMARY: processing the following file failed:
  'getting_started_with_preText.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   2.7Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    doc           9.2Mb
    htmlwidgets   2.5Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    extdata   7.4Mb
    libs      1.6Mb
Package suggested but not available for checking: 'qtbase'
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
    proj   5.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   1.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.3Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    gui          1.1Mb
    staticdocs   3.2Mb
Running 'test_asis.R' [4s]
  Running 'test_bayesqgcomp.R' [4s]
  Running 'test_boot_ints.R' [5s]
  Running 'test_boot_vs_noboot.R' [35s]
  Running 'test_bootchooser.R' [50s]
  Running 'test_cox_msmtest.R' [6s]
  Running 'test_zi.R' [4s]
Running the tests in 'tests/test_zi.R' failed.
Complete output:
  > cat("# zi test\n")
  # zi test
  > library(qgcomp)
  > n=100
  > dat <- data.frame(y=rbinom(n, 1, 0.5)*rpois(n, 1.2), x1=runif(n), x2=runif(n), z=runif(n))
  > 
  > # should not cause error
  > ee = qgcomp.zi.noboot(f=y ~ z + x1 + x2 | z, expnms = c('x1', 'x2'), data=dat, q=2, dist="negbin")
  > qgcomp.zi.noboot(f=y ~ z + x1 + x2 | x1 + x2 + z, expnms = c('x1', 'x2'), data=dat, q=2, dist="negbin")
  Error in solve.default(as.matrix(fit$hessian)) : 
    system is computationally singular: reciprocal condition number = 3.65185e-33
  Calls: qgcomp.zi.noboot -> zeroinfl -> solve -> solve.default
  Execution halted
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    data  10.8Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.6Mb
    doc       2.9Mb
Package required but not available: 'qtbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   1.3Mb
    libs   2.5Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   2.1Mb
File 'QUIC/libs/i386/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.o'
File 'QUIC/libs/x64/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
File 'qVarSel/libs/i386/qVarSel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'qVarSelH.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'qVarSelH.o'
File 'qVarSel/libs/x64/qVarSel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'qVarSelH.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'qVarSelH.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    Output   2.2Mb
    bin      9.3Mb
Packages suggested but not available for checking: 'rcom', 'RDCOMClient'
'library' or 'require' calls in package code:
  'RDCOMClient' 'rcom'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
PPT.AddBlankSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'write.table'
PPT.AddDataFrame: no visible global function definition for 'write.csv'
PPT.AddGraphicstoSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.cur'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.list'
PPT.AddGraphicstoSlide: no visible global function definition for
  'savePlot'
PPT.AddTextSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleOnlySlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleSlide: no visible global function definition for
  'comIsValidHandle'
PPT.ApplyTemplate: no visible global function definition for
  'comIsValidHandle'
PPT.Close: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'comCreateObject'
PPT.Init: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'COMCreate'
PPT.Present: no visible global function definition for
  'comIsValidHandle'
PPT.SaveAs: no visible global function definition for
  'comIsValidHandle'
PPT.getAbsolutePath : PPT.filePath: no visible global function
  definition for 'readWindowsShortcut'
Undefined global functions or variables:
  COMCreate comCreateObject comIsValidHandle dev.cur dev.list
  readWindowsShortcut savePlot write.csv write.table
Consider adding
  importFrom("grDevices", "dev.cur", "dev.list", "savePlot")
  importFrom("utils", "write.csv", "write.table")
to your NAMESPACE file.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    5.9Mb
    libs   1.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   6.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.2Mb
    libs   3.0Mb
.disableThreads: no visible global function definition for
  'stopCluster'
.enableThreads: no visible global function definition for 'detectCores'
.enableThreads: no visible global function definition for
  'makePSOCKcluster'
.enableThreads: no visible global function definition for
  'clusterExport'
.enableThreads: no visible global function definition for 'clusterCall'
.forwardSelection: no visible binding for global variable 'var'
.forwardSelection: no visible global function definition for 'glm'
.forwardSelection: no visible global function definition for 'formula'
.forwardSelection: no visible global function definition for 'binomial'
.forwardSelection: no visible global function definition for 'lm'
.forwardSelection: no visible global function definition for 'predict'
.predict.internal: no visible global function definition for 'predict'
randomGLM: no visible binding for global variable 'cor'
randomGLM: no visible binding for global variable 'sd'
randomGLM: no visible global function definition for 'var'
thinRandomGLM: no visible global function definition for 'glm'
thinRandomGLM: no visible global function definition for 'binomial'
thinRandomGLM: no visible global function definition for 'lm'
Undefined global functions or variables:
  binomial clusterCall clusterExport cor detectCores formula glm lm
  makePSOCKcluster predict sd stopCluster var
Consider adding
  importFrom("stats", "binomial", "cor", "formula", "glm", "lm",
             "predict", "sd", "var")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/randstr.Rcheck/00install.out' for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   2.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    libs   2.4Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    etc    1.9Mb
    po     1.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   3.8Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/4.0/Rblpapi.Rcheck/00install.out' for details.
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    cont  23.3Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.0Mb
    po    2.2Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    corpora   7.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.7/Rcplex.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    include   6.2Mb
    libs      1.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
    libs      1.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    include   1.6Mb
    lib       3.9Mb
    libs      2.9Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      1.8Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    include   1.8Mb
    lib       8.9Mb
    libs      1.0Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    include   6.3Mb
    libs      2.0Mb
Warnings in file 'R/crAddins.R':
  unable to translate '<U+25B2>' to native encoding
  unable to translate '<U+25BC>' to native encoding
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Found the following significant warnings:
  skein_block64.c:226:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/4.0/RDieHarder.Rcheck/00install.out' for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   2.6Mb
Error(s) in re-building vignettes:
--- re-building 'readabs_vignette.Rmd' using rmarkdown
Quitting from lines 64-67 (readabs_vignette.Rmd) 
Error: processing vignette 'readabs_vignette.Rmd' failed with diagnostics:
cannot open URL 'https://ausstats.abs.gov.au/servlet/TSSearchServlet?catno=6345.0&pg=1'
--- failed re-building 'readabs_vignette.Rmd'

SUMMARY: processing the following file failed:
  'readabs_vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
bestmods: no visible global function definition for 'abline'
bestmods: no visible global function definition for 'axis'
bestmods: no visible global function definition for 'lines'
cic: no visible global function definition for 'lsfit'
cic: no visible global function definition for 'var'
cvic: no visible global function definition for 'lsfit'
cvic: no visible global function definition for 'lm'
eic: no visible global function definition for 'lsfit'
eic: no visible global function definition for 'lm'
ic.min: no visible global function definition for 'lsfit'
scoremods: no visible global function definition for 'lsfit'
scoremods: no visible global function definition for 'var'
xy: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  abline axis lines lm lsfit rnorm var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "lm", "lsfit", "rnorm", "var")
to your NAMESPACE file.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Package which this enhances but not available for checking: 'Rcplex'
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs   1.7Mb
CA: no visible global function definition for 'readClipboard'
LL: no visible global function definition for 'readClipboard'
US: no visible global function definition for 'readClipboard'
delete: no visible global function definition for 'menu'
doc_temp: no visible global function definition for 'menu'
html5: no visible global function definition for 'na.omit'
install_pandoc: no visible global function definition for
  'download.file'
latexlist: no visible global function definition for 'readClipboard'
new_report: no visible global function definition for 'tail'
new_report: no visible global function definition for 'head'
new_report: no visible global function definition for 'menu'
presentation: no visible global function definition for 'head'
presentation: no visible global function definition for 'tail'
presentation: no visible global function definition for 'menu'
repo2github: no visible global function definition for 'download.file'
repo2github: no visible global function definition for 'unzip'
reveal.js: no visible global function definition for 'na.omit'
strWrap: no visible global function definition for 'readClipboard'
update_bib: no visible global function definition for 'tail'
update_bib: no visible global function definition for 'menu'
Undefined global functions or variables:
  download.file head menu na.omit readClipboard tail unzip
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "download.file", "head", "menu", "readClipboard",
             "tail", "unzip")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/reticulate.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
installed size is 80.3Mb
  sub-directories of 1Mb or more:
    gdal       3.9Mb
    libs      68.7Mb
    pictures   1.3Mb
    proj       5.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.7Mb
Found a 'configure.in' file: 'configure.ac' has long been preferred.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc     3.7Mb
    fonts   1.5Mb
    libs    2.0Mb
Packages suggested but not available for checking: 'pmg', 'SVGAnnotation'
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extra   9.3Mb
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  10.6Mb
    libs   5.0Mb
File 'RGtk2/libs/i386/RGtk2.dll':
  Found non-API calls to R: 'R_new_custom_connection',
    'Rf_EncodeInteger', 'Rf_EncodeLogical', 'Rf_EncodeReal',
    'Rf_formatInteger', 'Rf_formatLogical', 'Rf_formatReal'
File 'RGtk2/libs/x64/RGtk2.dll':
  Found non-API calls to R: 'R_new_custom_connection',
    'Rf_EncodeInteger', 'Rf_EncodeLogical', 'Rf_EncodeReal',
    'Rf_formatInteger', 'Rf_formatLogical', 'Rf_formatReal'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    lib    3.5Mb
    libs   4.8Mb
File 'RInside/libs/i386/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/i386/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.0/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/4.0/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'rJava/libs/i386/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'
File 'rJava/libs/x64/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Rmagic.Rcheck/00install.out' for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    rmd   8.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   2.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RNAseqNet.Rcheck/00install.out' for details.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      5.6Mb
Found the following significant warnings:
  Warning: unable to find a consistent ordering of superclasses for class "GPDORobEstimate": order chosen is inconsistent with the superclasses of "GPDkStepEstimate"
  Warning: unable to find a consistent ordering of superclasses for class "GEVORobEstimate": order chosen is inconsistent with the superclasses of "GEVkStepEstimate"
See 'd:/Rcompile/CRANpkg/local/4.0/RobExtremes.Rcheck/00install.out' for details.
'LinkingTo' for 'mgcv' is unused as it has no 'include' directory
Package required but not available: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.7/ROracle.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    libs    1.7Mb
    tests   1.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      2.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Rquake.Rcheck/00install.out' for details.
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    libs  27.8Mb
Found the following significant warnings:
   #warning Please include winsock2.h before windows.h
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/4.0/Rserve.Rcheck/00install.out' for details.
Rserve: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
  shortPathName
Consider adding
  importFrom("utils", "shortPathName")
to your NAMESPACE file.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.0/Rserve/libs/i386/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'd:/Rcompile/CRANpkg/lib/4.0/Rserve/libs/x64/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/i386/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### Name: SolrList-class
> ### Title: SolrList
> ### Aliases: class:SolrList SolrList-class length,SolrList-method
> ###   names,SolrList-method [<-,SolrList,ANY,ANY,ANY-method
> ###   [[,SolrList,ANY-method [,SolrList-method [[,SolrList-method
> ###   [[<-,SolrList-method unique,SolrList-method searchDocs
> ###   searchDocs,Solr SolrList coerce,Solr,SolrList-method
> ###   coerce,SolrList,DocCollection-method show,SolrList-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  3.98 0.19 4.15 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RSpectra.Rcheck/00install.out' for details.
installed size is 24.4Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    4.4Mb
    libs  17.8Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rstap.Rcheck/00install.out' for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.2Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
Running examples in 'RSVGTipsDevice-Ex.R' failed
The error most likely occurred in:

> ### Name: RSVGTipsDevice
> ### Title: A SVG Graphics Driver with dynamic tips
> ### Aliases: RSVGTipsDevice
> ### Keywords: device package
> 
> ### ** Examples
> 
> library("RSVGTipsDevice")
> sessionInfo()
R Under development (unstable) (2019-07-05 r76784)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2008 x64 (build 6003) Service Pack 2

Matrix products: default

locale:
[1] LC_COLLATE=C                 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=C                LC_NUMERIC=C                
[5] LC_TIME=C                   

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RSVGTipsDevice_1.0-7

loaded via a namespace (and not attached):
[1] compiler_3.7.0
> devSVGTips("svgplot1.svg", toolTipMode=1,
+     title="SVG example plot 1: Shapes and Points, Tooltips are Title + 1 Line")
> plot(c(0,10),c(0,10), type="n", xlab="x", ylab="y",
+     main="Example SVG plot with title + 1 line tips (mode=1)")
> setSVGShapeToolTip(title="A rectangle", desc="that is yellow")
> rect(1,1,4,6, col='yellow')
> setSVGShapeToolTip(title="1st circle with title only")
> points(5.5,7.5,cex=20,pch=19,col='red')
> setSVGShapeToolTip(title="A triangle", desc="big and green")
> polygon(c(3,6,8), c(3,6,3), col='green')
> # no tooltips on these points
> points(2:8, 8:2, cex=3, pch=19, col='black')
> # tooltips on each these points
> invisible(sapply(1:7, function(x)
+ {setSVGShapeToolTip(title=paste("point", x))
+  points(x+1, 8-x, cex=3, pch=1, col='black')}))
> setSVGShapeToolTip(title="Text", desc="can have a tool tip too!")
> text(x=4, y=9, lab="Poke me!", col="blue")
> dev.off()
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    Lib  11.5Mb
Math.Sym: no visible binding for global variable 'transtab'
jythonStart: no visible global function definition for '.jinit'
jythonStart: no visible global function definition for '.jnew'
jythonStart: no visible binding for global variable '.Jython'
sympy: no visible binding for global variable '.Jython'
sympy: no visible global function definition for '.jstrVal'
sympyStart: no visible binding for global variable '.Jython'
Undefined global functions or variables:
  .Jython .jinit .jnew .jstrVal transtab
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.8Mb
    projects   2.7Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs   4.9Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   1.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   2.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Package suggested but not available for checking: 'gpuR'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs      8.4Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
File 'RWinEdt/R/zzz.R':
  .onAttach calls:
    writeLines(edtFile, con = send2RedtLoc)
    writeLines(edtFile, con = send2RedtLoc)

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
Package suggested but not available for checking: 'SnakeCharmR'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Error(s) in re-building vignettes:
--- re-building 'R-versus-CPP.Rmd' using rmarkdown
Quitting from lines 63-72 (R-versus-CPP.Rmd) 
Error: processing vignette 'R-versus-CPP.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'R-versus-CPP.Rmd'

SUMMARY: processing the following file failed:
  'R-versus-CPP.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.3Mb
    libs   1.9Mb
prime.factor: no visible global function definition for 'data'
prime.factor: no visible binding for global variable 'primlist'
Undefined global functions or variables:
  data primlist
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
Running examples in 'scriptexec-Ex.R' failed
The error most likely occurred in:

> ### Name: execute
> ### Title: Executes a script and returns the output. The stdout and stderr
> ###   are captured and returned. In case of errors, the exit code will
> ###   return in the status field.
> ### Aliases: execute
> 
> ### ** Examples
> 
> library('scriptexec')
> library('testthat')
> 
> # execute script text
> output <- scriptexec::execute('echo command1\necho command2')
> expect_equal(output$status, 0)
> expect_equal(grepl('command1', output$output), TRUE)
Error: grepl("command1", output$output) not equal to TRUE.
1 element mismatch
Execution halted
Error(s) in re-building vignettes:
--- re-building 'scriptexec.Rmd' using rmarkdown
Quitting from lines 24-62 (scriptexec.Rmd) 
Error: processing vignette 'scriptexec.Rmd' failed with diagnostics:
grepl("command1", output$output) not equal to TRUE.
1 element mismatch
--- failed re-building 'scriptexec.Rmd'

SUMMARY: processing the following file failed:
  'scriptexec.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   3.5Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R   7.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   3.0Mb
Package which this enhances but not available for checking: 'doMC'
Running examples in 'seeclickfixr-Ex.R' failed
The error most likely occurred in:

> ### Name: list_places
> ### Title: Query sub-city neighborhoods in which issues can be reported.
> ### Aliases: list_places
> 
> ### ** Examples
> 
> list_places("Boston, MA",limit = 5)
Error in function (type, msg, asError = TRUE)  : 
  Unknown SSL protocol error in connection to seeclickfix.com:443 
Calls: list_places -> <Anonymous> -> curlPerform -> <Anonymous> -> fun
Execution halted
Running 'spelling.R' [0s]
  Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sen2r)
  Welcome to sen2r. To use the package from a GUI, launch
   > sen2r()
  Documentation: http://sen2r.ranghetti.info
  
  IMPORTANT: sen2r depends on some external tools;
  before using it, it is strongly recommended to run function
   > check_sen2r_deps()
  to check them and install the missing ones.
  > 
  > test_check("sen2r")
  Error : GET https://scihub.copernicus.eu/apihub/
  -- 1. Error: st_crs2, input WKT (@test-t34_st_crs2.R#14)  ----------------------
  there is no package called 'rgdal'
  Backtrace:
   1. sen2r:::st_as_text_2(st_crs(32609))
   2. utils::packageVersion("rgdal")
  
  -- 2. Error: st_crs2, input spatial file path (@test-t34_st_crs2.R#34)  --------
  Cannot create RasterLayer object from this file; perhaps you need to install rgdal first
  Backtrace:
   1. testthat::expect_equal(...)
   6. raster::raster(raster_path)
   7. raster:::.local(x, ...)
   8. raster:::.rasterObjectFromFile(...)
  
  == testthat results  ===========================================================
  [ OK: 53 | SKIPPED: 18 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: st_crs2, input WKT (@test-t34_st_crs2.R#14) 
  2. Error: st_crs2, input spatial file path (@test-t34_st_crs2.R#34) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   3.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
    libs   1.5Mb
capture: no visible binding for global variable 'resultText'
restore.session: no visible binding for global variable
  '.save.session.packages'
restore.session: no visible binding for global variable
  '.save.session.search'
save.session: no visible global function definition for 'dev.list'
save.session: no visible binding for '<<-' assignment to
  '.save.session.search'
save.session: no visible binding for '<<-' assignment to
  '.save.session.packages'
Undefined global functions or variables:
  .save.session.packages .save.session.search dev.list resultText
Consider adding
  importFrom("grDevices", "dev.list")
to your NAMESPACE file.
Package suggested but not available for checking: 'loomR'
Package unavailable to check Rd xrefs: 'loomR'
installed size is 95.1Mb
  sub-directories of 1Mb or more:
    doc     12.0Mb
    gdal     3.9Mb
    libs    70.1Mb
    proj     5.0Mb
    sqlite   1.5Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    www   7.3Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    www   8.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   2.8Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   4.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   2.5Mb
Found the following significant warnings:
  slfm_MDN.cpp:26:40: warning: left operand of comma operator has no effect [-Wunused-value]
  slfm_MNN.cpp:26:40: warning: left operand of comma operator has no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/slfm.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.6Mb
Warnings in file 'R/replace_special_characters_internal.R':
  unable to translate '<U+00C4>' to native encoding
  unable to translate '<U+00D6>' to native encoding
  unable to translate '<U+00DC>' to native encoding
  unable to translate '<U+00E4>' to native encoding
  unable to translate '<U+00F6>' to native encoding
  unable to translate '<U+00FC>' to native encoding
  unable to translate '<U+00DF>' to native encoding
  unable to translate '<U+00C6>' to native encoding
  unable to translate '<U+00E6>' to native encoding
  unable to translate '<U+00D8>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+00C5>' to native encoding
  unable to translate '<U+00E5>' to native encoding
  unable to translate '<U+00C6>' to native encoding
  unable to translate '<U+00E6>' to native encoding
  unable to translate '<U+00D8>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+00C6>' to native encoding
  unable to translate '<U+00E6>' to native encoding
  unable to translate '<U+00D8>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+00C5>' to native encoding
  unable to translate '<U+00E5>' to native encoding
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      1.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.6Mb
    libs   2.1Mb
Error(s) in re-building vignettes:
--- re-building 'SongEvo.Rmd' using rmarkdown
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

The following objects are masked from 'package:base':

    format.pval, units

! Package pdftex.def Error: File `D:/RCompile/CRANpkg/local/4.0/SongEvo.Rcheck/
vign_test/SongEvo/vignettes/SongEvo_files/figure-latex/Examine\%20population\%2
0size\%20over\%20time-1.pdf' not found.

Error: processing vignette 'SongEvo.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.0/SongEvo.Rcheck/vign_test/SongEvo/vignettes/SongEvo.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SongEvo.log for more info.
--- failed re-building 'SongEvo.Rmd'

SUMMARY: processing the following file failed:
  'SongEvo.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
Running 'lint.R' [1s]
  Running 'spelling.R' [1s]
  Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library("testthat")
  > library("spacyr")
  > 
  > test_check("spacyr")
  -- 1. Error: spacy_parse handles numbers/tibbles correctly (@test-2-spacy_parse.
  lexical error: invalid char in json text.
                                         NA
                       (right here) ------^
  Backtrace:
   1. global::skip_if_no_python_or_no_spacy()
   2. spacyr::find_spacy_env()
   4. reticulate::conda_list(conda = "auto")
   5. jsonlite::fromJSON(conda_envs)
   6. jsonlite:::parse_and_simplify(...)
   7. jsonlite:::parseJSON(txt, bigint_as_char)
   8. jsonlite:::parse_string(txt, bigint_as_char)
  
  == testthat results  ===========================================================
  [ OK: 1 | SKIPPED: 50 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: spacy_parse handles numbers/tibbles correctly (@test-2-spacy_parse.R#165) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/spatstat.Knet.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/spatstat.local.Rcheck/00install.out' for details.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    R      5.3Mb
    doc    4.9Mb
    help   5.3Mb
    libs   1.2Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
    libs   2.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   1.6Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   2.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   2.0Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
stkde: no visible global function definition for 'npudensbw'
stkde: no visible global function definition for 'npudens'
stkde: no visible global function definition for 'quantile'
stkde: no visible global function definition for 'heat.colors'
stkde: no visible global function definition for 'par'
stkde: no visible global function definition for 'image'
stkde: no visible global function definition for 'contour'
stkde.base: no visible global function definition for 'npudensbw'
stkde.base: no visible global function definition for 'npudens'
stkde.sig: no visible global function definition for 'SpatialPoints'
stkde.sig: no visible global function definition for 'spsample'
stkde.sig: no visible global function definition for 'bbox'
stkde.sig: no visible global function definition for 'quantile'
stkde.sig: no visible global function definition for 'heat.colors'
stkde.sig: no visible global function definition for 'par'
stkde.sig: no visible global function definition for 'image'
stkde.sig: no visible global function definition for 'contour'
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    include   9.4Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    doc  10.3Mb
    nc    4.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.0Mb
Error(s) in re-building vignettes:
--- re-building 'Details.Rmd' using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

The following object is masked from 'package:dplyr':

    combine

Linking to GEOS 3.6.1, GDAL 2.2.3, PROJ 4.9.3
Warning: Removed 1 rows containing missing values (geom_path).
Quitting from lines 904-907 (Details.Rmd) 
Error: processing vignette 'Details.Rmd' failed with diagnostics:
there is no package called 'ggmap'
--- failed re-building 'Details.Rmd'

--- re-building 'Overview.Rmd' using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

To enable 
caching of data, set `options(tigris_use_cache = TRUE)` in your R script or .Rprofile.

Attaching package: 'tigris'

The following object is masked from 'package:graphics':

    plot

Loading required package: sp
rgeos version: 0.5-2, (SVN revision 621)
 GEOS runtime version: 3.6.1-CAPI-1.10.1 
 Linking to sp version: 1.4-0 
 Polygon checking: TRUE 

Linking to GEOS 3.6.1, GDAL 2.2.3, PROJ 4.9.3
Loading required package: viridisLite
Warning: Removed 1 rows containing missing values (geom_path).
--- finished re-building 'Overview.Rmd'

SUMMARY: processing the following file failed:
  'Details.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R          2.0Mb
    datasets   2.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.6Mb
Package suggested but not available for checking: 'BSgenome.Ptroglodytes.UCSC.panTro5'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/stringi.Rcheck/00install.out' for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    libs   1.7Mb
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   3.2Mb
    doc    3.3Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
dlgMessage.tcltkGUI: no visible global function definition for 'alarm'
dlgMessage.tcltkGUI: no visible global function definition for
  'bringToTop'
Undefined global functions or variables:
  alarm bringToTop
Consider adding
  importFrom("grDevices", "bringToTop")
  importFrom("utils", "alarm")
to your NAMESPACE file.
Found the following significant warnings:
  lineariadmm.c:189:17: warning: value computed is not used [-Wunused-value]
  lineariadmm.c:190:17: warning: value computed is not used [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/svmadmm.Rcheck/00install.out' for details.
File 'svmpath/libs/i386/svmpath.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'mi10unix.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'mi10unix.o'
File 'svmpath/libs/x64/svmpath.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'mi10unix.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'mi10unix.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    java  11.5Mb
Package suggested but not available for checking: 'duckdb'
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.9Mb
    libs   1.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.8Mb
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs      13.3Mb
    tessdata  14.0Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    2.9Mb
    libs   1.9Mb
Running 'testthat.R' [19s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(textrecipes)
  Loading required package: recipes
  Loading required package: dplyr
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  
  Attaching package: 'recipes'
  
  The following object is masked from 'package:stats':
  
      step
  
  > 
  > test_check("textrecipes")
  -- 1. Failure: step_tfidf works as intended (@test-tfidf.R#44)  ----------------
  as.matrix(rec_answer) not equal to as.matrix(manual_answer).
  29/68 mismatches (average diff: 0.123)
  [4]  0.201 - 0.0866 == 0.115
  [7]  0.201 - 0.0866 == 0.115
  [10] 0.268 - 0.1155 == 0.153
  [16] 0.201 - 0.0866 == 0.115
  [17] 0.106 - 0.0000 == 0.106
  [18] 0.141 - 0.0000 == 0.141
  [19] 0.106 - 0.0000 == 0.106
  [23] 0.201 - 0.0866 == 0.115
  [27] 0.201 - 0.0866 == 0.115
  ...
  
  == testthat results  ===========================================================
  [ OK: 88 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 1 ]
  1. Failure: step_tfidf works as intended (@test-tfidf.R#44) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.1Mb
Running 'testthat.R' [21s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidytext)
  > 
  > test_check("tidytext")
  -- 3. Error: (unknown) (@test-corpus-tidiers.R#33)  ----------------------------
  Internal error: Trace data is not square.
  Backtrace:
    1. testthat::test_check("tidytext")
    2. testthat:::test_package_dir(...)
    3. testthat::test_dir(...)
    4. testthat:::test_files(...)
   10. base::lapply(...)
   11. testthat:::FUN(X[[i]], ...)
   17. testthat::source_file(...)
   18. testthat:::test_code(NULL, exprs, env)
   27. [ base::eval(...) ] with 1 more call
   29. testthat::test_that(...)
       ...
   40. testthat:::o_apply(...)
   41. base::lapply(objects, function(x) x[[method]](...))
   42. testthat:::FUN(X[[i]], ...)
   43. x[[method]](...)
   47. testthat:::failure_summary(result, self$n_fail)
   50. testthat:::format.expectation(x)
   51. testthat:::format_with_trace(x)
   53. rlang:::format.rlang_trace(...)
   54. rlang:::trace_format_branch(x, max_frames, dir, srcrefs)
   55. rlang:::branch_uncollapse_pipe(trace)
  
  == testthat results  ===========================================================
  [ OK: 274 | SKIPPED: 1 | WARNINGS: 2 | FAILED: 3 ]
  1. Error: Can tidy corpus from quanteda using accessor functions (@test-corpus-tidiers.R#38) 
  2. Error: Can tidy corpus from quanteda using accessor functions (@test-corpus-tidiers.R#33) 
  3. Error: (unknown) (@test-corpus-tidiers.R#33) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.9Mb
Packages suggested but not available for checking:
  'Rcampdf', 'Rpoppler', 'tm.lexicon.GeneralInquirer'
Package unavailable to check Rd xrefs: 'Rpoppler'
Running examples in 'tosca-Ex.R' failed
The error most likely occurred in:

> ### Name: as.textmeta.corpus
> ### Title: Transform corpus to textmeta
> ### Aliases: as.textmeta.corpus
> ### Keywords: manip
> 
> ### ** Examples
> 
> texts <- c("Give a Man a Fish, and You Feed Him for a Day.
+  Teach a Man To Fish, and You Feed Him for a Lifetime",
+  "So Long, and Thanks for All the Fish",
+  "A very able manipulative mathematician, Fisher enjoys a real mastery
+  in evaluating complicated multiple integrals.")
> 
> corp <- quanteda::corpus(x = texts)
> obj <- as.textmeta.corpus(corp, addMetadata = FALSE)
NOTE: No ID-column "id", set to ascending numbers
NOTE: No date-column "date", set to NA
NOTE: No title-column "title", set to NA
success
number of observations in text: 3 

NAs in text:
 NA.abs NA.rel
      0      0
---------------------------------------------------------------------- 

meta: 3 observations of 3 variables

NAs in meta:
      abs rel
id      0   0
date    3   1
title   3   1
---------------------------------------------------------------------- 

NAs in date: 3 (1)
> 
> quanteda::docvars(corp, "title") <- c("Fishing", "Don't panic!", "Sir Ronald")
> quanteda::docvars(corp, "date") <- c("1885-01-02", "1979-03-04", "1951-05-06")
> quanteda::docvars(corp, "id") <- c("A", "B", "C")
> quanteda::docvars(corp, "additionalVariable") <- 1:3
> 
> obj <- as.textmeta.corpus(corp)
Error in matrix(rep(tmp, each = length(tmpid)), nrow = length(tmpid)) : 
  'data' must be of a vector type, was 'NULL'
Calls: as.textmeta.corpus -> matrix
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
File 'tpr/libs/i386/tpr.dll':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'utils.o'
File 'tpr/libs/x64/tpr.dll':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'utils.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    4.3Mb
    libs   1.5Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs  11.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc     6.4Mb
    ubinc   2.0Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc         6.9Mb
    dummydata   1.4Mb
    libs        4.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.6Mb
    libs   2.3Mb
Running examples in 'upwaver-Ex.R' failed
The error most likely occurred in:

> ### Name: storypoints_and_status
> ### Title: Calculate storypoints ans status of the Cards of a specific
> ###   Board
> ### Aliases: storypoints_and_status
> 
> ### ** Examples
> 
> upwaver::storypoints_and_status("4597", 14351, "807a0c3451c04602b4dbfdc0338a65f7")
No encoding supplied: defaulting to UTF-8.
Error in cards[[i]] : subscript out of bounds
Calls: <Anonymous>
Execution halted
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(upwaver)
  > 
  > test_check("upwaver")
  -- 1. Failure: list_cards() works (@test-upwaver.R#53)  ------------------------
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 1 - 4 == -3
  
  -- 2. Error: storypoints() works (@test-upwaver.R#71)  -------------------------
  subscript out of bounds
  Backtrace:
   1. upwaver::storypoints_and_status("4597", 14351, "807a0c3451c04602b4dbfdc0338a65f7")
  
  == testthat results  ===========================================================
  [ OK: 20 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: list_cards() works (@test-upwaver.R#53) 
  2. Error: storypoints() works (@test-upwaver.R#71) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'upwaver.Rmd' using rmarkdown
No encoding supplied: defaulting to UTF-8.
No encoding supplied: defaulting to UTF-8.
No encoding supplied: defaulting to UTF-8.
No encoding supplied: defaulting to UTF-8.
Quitting from lines 106-109 (upwaver.Rmd) 
Error: processing vignette 'upwaver.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building 'upwaver.Rmd'

SUMMARY: processing the following file failed:
  'upwaver.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   6.4Mb
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  23.3Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
installed size is 79.1Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    gdal      3.8Mb
    libs     68.8Mb
    proj      5.0Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    doc    1.2Mb
    help   2.9Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   8.2Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc           4.3Mb
    docjs         1.4Mb
    htmlwidgets   3.9Mb
Error(s) in re-building vignettes:
--- re-building 'vignette_apartments.Rmd' using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Welcome to DALEX (version: 1.0.1).
Find examples and detailed introduction at: https://pbiecek.github.io/ema/
Additional features will be available after installation of: iBreakDown, ggpubr.
Use 'install_dependencies()' to get all suggested dependencies

Attaching package: 'DALEX'

The following object is masked from 'package:dplyr':

    explain

randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.

Attaching package: 'randomForest'

The following object is masked from 'package:ggplot2':

    margin

The following object is masked from 'package:dplyr':

    combine


Attaching package: 'ingredients'

The following object is masked from 'package:DALEX':

    feature_importance

Quitting from lines 81-82 (vignette_apartments.Rmd) 
Error: processing vignette 'vignette_apartments.Rmd' failed with diagnostics:
could not find function "theme_drwhy_colors"
--- failed re-building 'vignette_apartments.Rmd'

SUMMARY: processing the following file failed:
  'vignette_apartments.Rmd'

Error: Vignette re-building failed.
Execution halted
File 'waffect/libs/i386/waffect.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'waffect.o'
File 'waffect/libs/x64/waffect.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'waffect.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   6.3Mb
Error(s) in re-building vignettes:
--- re-building 'wCorrArguments.Rmd' using rmarkdown
Loading required package: knitr
Loading required package: wCorr
wCorr v1.9.1

Loading required package: lattice
Loading required package: captioner
! Package pdftex.def Error: File `D:/RCompile/CRANpkg/local/4.0/wCorr.Rcheck/vi
gn_test/wCorr/vignettes/wCorrArguments_files/figure-latex/ML\%20RMSE\%20plot-1.
pdf' not found.

Error: processing vignette 'wCorrArguments.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.0/wCorr.Rcheck/vign_test/wCorr/vignettes/wCorrArguments.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See wCorrArguments.log for more info.
--- failed re-building 'wCorrArguments.Rmd'

--- re-building 'wCorrFormulas.Rmd' using rmarkdown
Loading required package: wCorr
wCorr v1.9.1

Loading required package: lattice
Loading required package: captioner
! Package pdftex.def Error: File `D:/RCompile/CRANpkg/local/4.0/wCorr.Rcheck/vi
gn_test/wCorr/vignettes/wCorrFormulas_files/figure-latex/bias\%20Versus\%20rho-
1.pdf' not found.

Error: processing vignette 'wCorrFormulas.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.0/wCorr.Rcheck/vign_test/wCorr/vignettes/wCorrFormulas.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See wCorrFormulas.log for more info.
--- failed re-building 'wCorrFormulas.Rmd'

SUMMARY: processing the following files failed:
  'wCorrArguments.Rmd' 'wCorrFormulas.Rmd'

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(webddx)
  > 
  > test_check("webddx")
  -- 1. Error: query_fz works for a simple query (@testfz_normal.R#7)  -----------
  HTTP error 410.
  Backtrace:
   1. webddx::query_fz(...)
   2. jsonlite::fromJSON(query_url)
   3. jsonlite:::parse_and_simplify(...)
   4. jsonlite:::parseJSON(txt, bigint_as_char)
   5. jsonlite:::parse_con(txt, bigint_as_char)
   7. base::open.connection(con, "rb")
  
  == testthat results  ===========================================================
  [ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: query_fz works for a simple query (@testfz_normal.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    client   8.9Mb
    doc      1.0Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc   11.9Mb
    libs   1.6Mb
Bundesliga.Mannschaft: no visible global function definition for 'data'
Bundesliga.Mannschaft: no visible binding for global variable
  'Bundesliga'
Bundesliga.Tabelle: no visible global function definition for 'data'
Bundesliga.Tabelle: no visible binding for global variable 'Bundesliga'
Bundesliga.XML: no visible global function definition for 'data'
Bundesliga.XML: no visible binding for global variable 'Bundesliga'
sens.spec: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
.__A__.1 : <anonymous>: no visible binding for global variable '.hwnd'
Undefined global functions or variables:
  .hwnd
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    bn   7.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/4.0/x13binary.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    java  19.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/xml2.Rcheck/00install.out' for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    exampleData   1.4Mb
    libs          4.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    include   3.4Mb
    libs      1.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.3Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/adaptiveGPCA.Rcheck/00install.out' for details.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    extdata  11.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs     4.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   2.3Mb
Package vignette with placeholder title 'Vignette Title':
  'antaresViz.Rmd'
installed size is 73.7Mb
  sub-directories of 1Mb or more:
    gdal   3.8Mb
    libs  69.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   1.1Mb
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    R      3.2Mb
    libs  24.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      2.1Mb
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    bin   22.9Mb
    misc   2.1Mb
Found the following significant warnings:
  wmm.c:428:2: warning: initialization of 'struct audio_instance * (*)(struct SEXPREC *, float,  int)' from incompatible pointer type 'wmm_instance_t * (*)(struct SEXPREC *, float,  int)' {aka 'struct wmm_instance * (*)(struct SEXPREC *, float,  int)'} [-Wincompatible-pointer-types]
  wmm.c:429:2: warning: initialization of 'struct audio_instance * (*)(struct SEXPREC *, float,  int,  int)' from incompatible pointer type 'wmm_instance_t * (*)(struct SEXPREC *, float,  int,  int)' {aka 'struct wmm_instance * (*)(struct SEXPREC *, float,  int,  int)'} [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/audio.Rcheck/00install.out' for details.
Running examples in 'AWR.Kinesis-Ex.R' failed
The error occurred in:


R Under development (unstable) (2020-01-27 r77730) -- "Unsuffered Consequences"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> pkgname <- "AWR.Kinesis"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> library('AWR.Kinesis')
> 
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
> cleanEx()
Error: connections left open:
	stdin (file)
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   3.3Mb
    libs   2.3Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Package suggested but not available for checking: 'mzR'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BALD.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.1Mb
    libs   2.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.3Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/bayesCL.Rcheck/00install.out' for details.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs   2.7Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   4.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   4.2Mb
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    libs  25.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BcDiag.Rcheck/00install.out' for details.
installed size is 132.5Mb
  sub-directories of 1Mb or more:
    include  131.6Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   3.1Mb
Found the following significant warnings:
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/biganalytics.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   2.5Mb
    libs      2.2Mb
Found the following significant warnings:
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/bigmemory.Rcheck/00install.out' for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      3.3Mb
Found the following significant warnings:
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/bigtabulate.Rcheck/00install.out' for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   2.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   8.2Mb
Package suggested but not available for checking: 'maxent'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/bioRad.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.0Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BonEV.Rcheck/00install.out' for details.
installed size is 62.5Mb
  sub-directories of 1Mb or more:
    include   8.6Mb
    lib      53.5Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Brundle.Rcheck/00install.out' for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.7Mb
Found the following significant warnings:
  w32-backend.c:24:5: warning: initialization of 'char **' from incompatible pointer type 'const char **' [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Cairo.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   2.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    extdata   1.1Mb
    libs      2.2Mb
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   2.4Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.7Mb
    libs   2.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ceterisParibus.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   2.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Found the following significant warnings:
  VCLDefines.c:265:2: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/clv.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   3.2Mb
    libs      2.0Mb
Package suggested but not available for checking: 'xcms'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/cplexAPI.Rcheck/00install.out' for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   6.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/CSFA.Rcheck/00install.out' for details.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   4.2Mb
Found the following significant warnings:
  ./src/common/Random.c:105:5: warning: 'memcpy' pointer overflow between offset 0 and size [4294967292, 2147483647] [-Warray-bounds]
  ./src/common/Random.c:105:5: warning: 'memcpy' pointer overflow between offset 0 and size [-4, 9223372036854775807] [-Warray-bounds]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/cubature.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   5.5Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   7.1Mb
File 'curl/libs/i386/curl.dll':
  Found non-API call to R: 'R_new_custom_connection'
File 'curl/libs/x64/curl.dll':
  Found non-API call to R: 'R_new_custom_connection'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    doc    1.2Mb
    help   1.0Mb
    libs   2.4Mb
Package required but not available: 'flowDensity'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'DALEXtra-Ex.R' failed
The error most likely occurred in:

> ### Name: explain_scikitlearn
> ### Title: Wrapper for Python Scikit-Learn Models
> ### Aliases: explain_scikitlearn
> 
> ### ** Examples
> 
> library("DALEXtra")
> if(DALEXtra:::is_conda()) {
+    # Explainer build (Keep in mind that 18th column is target)
+    titanic_test <- read.csv(system.file("extdata", "titanic_test.csv", package = "DALEXtra"))
+    # Keep in mind that when pickle is being built and loaded,
+    # not only Python version but libraries versions has to match aswell
+    explainer <- explain_scikitlearn(system.file("extdata", "scikitlearn.pkl", package = "DALEXtra"),
+    yml = system.file("extdata", "testing_environment.yml", package = "DALEXtra"),
+    data = titanic_test[,1:17], y = titanic_test$survived)
+    plot(model_performance(explainer))
+ 
+    # Predictions with newdata
+    predict(explainer, titanic_test[1:10,1:17])
+ 
+ } else {
+   print('Conda is required.')
+ }
There already exists environment named the same as it is specified in .yml file - myenv. It will be used
Warning in system2(command = python, args = paste0("\"", config_script,  :
  running command '"C:/Users/CRAN/AppData/Local/r-miniconda/envs/myenv/python.exe" "D:/RCompile/CRANpkg/lib/4.0gcc8/reticulate/config/config.py"' had status 2
Warning: Error in python_config(python_version, required_module, python_version, : Error 2 occurred running C:/Users/CRAN/AppData/Local/r-miniconda/envs/myenv/python.exe 

Error: Yours environment has to match environment where pickle file was created. It also includes encoding, python version, and libraries version. Specifying .yml file or path to virtual environment may help. For more information look warnings() and then ?explain_scikitlearn
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   2.4Mb
Found the following significant warnings:
  DTDataFile.cpp:134:19: warning: 'void* memcpy(void*, const void*, size_t)' forming offset [5, 8] is out of the bounds [0, 4] of object 'offset' with type 'off_t' {aka 'long int'} [-Warray-bounds]
  DTDataFile.cpp:499:11: warning: 'void* memcpy(void*, const void*, size_t)' forming offset [5, 8] is out of the bounds [0, 4] of object 'startOfVariable' with type 'off_t' {aka 'long int'} [-Warray-bounds]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/DataGraph.Rcheck/00install.out' for details.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   5.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   2.1Mb
Running examples in 'DCD-Ex.R' failed
The error most likely occurred in:

> ### Name: DCD
> ### Title: Differential Community Detection for Paired Biological Networks,
> ###   for e.g. case vs control
> ### Aliases: DCD
> 
> ### ** Examples
> 
> 
> DCD_output <- DCD()
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
> ## Not run: 
> ##D library(igraph)
> ##D g_A <- sample_grg(200, 0.15, torus=FALSE, coords = FALSE)
> ##D g_B <- permute(g_A,c(sample(20),21:200))
> ##D ground_truth <- c(rep(1,20),rep(0,180))
> ##D DCD_output2 <- DCD(g_A = g_A, g_B = g_B, method = "Spectral", mink = 7,
> ##D                    ground_truth = ground_truth, plot_flag = 1, color = "red",
> ##D                    iter = 1, cores = 1 )
> ##D   
> ## End(Not run)
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11674 (sockconn)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/DeducerSpatial.Rcheck/00install.out' for details.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.8Mb
    help   1.4Mb
    libs   2.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.7Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Found the following significant warnings:
  clipper.cpp:721:34: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct ClipperLib::TEdge'; use assignment or value-initialization instead [-Wclass-memaccess]
  dbfopen.c:1346:6: warning: 'strncpy' output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:1328:6: warning: 'strncpy' output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:879:9: warning: 'strncpy' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopen.c:1693:9: warning: 'strncpy' output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
  dbfopen.c:2065:9: warning: 'strncpy' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/dggridR.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   4.4Mb
Running examples in 'DiffNet-Ex.R' failed
The error most likely occurred in:

> ### Name: diffnet
> ### Title: Detection of Statistically Significant Changes in Paired
> ###   Biological Networks
> ### Aliases: diffnet
> 
> ### ** Examples
> 
> library("DiffNet")
> # this step is optional, it helps speed up calculations, run in parallel on 2 processors
> library(doParallel)
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> registerDoParallel(2)
> # Run the differential network analysis tehcnique on sample data
> p <- diffnet()
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11684 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11684 (sockconn)
Execution halted
Running examples in 'DiffNet-Ex.R' failed
The error most likely occurred in:

> ### Name: diffnet
> ### Title: Detection of Statistically Significant Changes in Paired
> ###   Biological Networks
> ### Aliases: diffnet
> 
> ### ** Examples
> 
> library("DiffNet")
> # this step is optional, it helps speed up calculations, run in parallel on 2 processors
> library(doParallel)
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> registerDoParallel(2)
> # Run the differential network analysis tehcnique on sample data
> p <- diffnet()
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11824 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11824 (sockconn)
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    5.1Mb
    libs   2.0Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    5.6Mb
    libs   2.0Mb
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    include  15.9Mb
    libs      1.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   2.1Mb
    libs   2.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   3.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.6Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs   5.4Mb
Found the following significant warnings:
  lpkit.h:32:99: warning: right-hand operand of comma expression has no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/EditImputeCont.Rcheck/00install.out' for details.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
Running examples in 'empiricalFDR.DESeq2-Ex.R' failed
The error most likely occurred in:

> ### Name: empiricalFDR.DESeq2-package
> ### Title: Simulation-Based False Discovery Rate in RNA-Seq
> ### Aliases: empiricalFDR.DESeq2-package empiricalFDR.DESeq2
> 
> ### ** Examples
> 
> 
> dds = makeExampleDESeqDataSet(betaSD=1, n=100)
> dds = DESeq(dds)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
> sims = simulateCounts(dds)
simulating...
================================================================================converting counts to integer mode
> sims = DESeq(sims)
using pre-existing size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
> res = results(dds)
Error in .wrap_in_length_one_list_like_object(value, name, x) : 
  failed to coerce 'list(value)' to a DESeqResults object of length 1
Calls: results ... .append_list_element -> .wrap_in_length_one_list_like_object
Execution halted
Running 'testthat.R' [75s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > test_check("EventDetectR")
  Loading required package: EventDetectR
  -- 1. Error: neural network prediction works (@test-eventClassification.R#96)  -
  requires numeric/complex matrix/vector arguments
  Backtrace:
   1. EventDetectR:::predict.NeuralNetwork(m, newDataReal)
   3. neuralnet:::predict.nn(object$modelList[[i]], test_input)
  
  [1] "EDS is working on index: 500"
  == testthat results  ===========================================================
  [ OK: 24 | SKIPPED: 2 | WARNINGS: 4 | FAILED: 1 ]
  1. Error: neural network prediction works (@test-eventClassification.R#96) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   2.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      2.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/FastRWeb.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   2.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.6Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.4Mb
Running examples in 'fedreporter-Ex.R' failed
The error most likely occurred in:

> ### Name: fe_projects_search
> ### Title: Search Federal RePORTER Projects
> ### Aliases: fe_projects_search
> 
> ### ** Examples
> 
> res = fe_projects_search(
+ project_number = "USFS*",
+ fiscal_year = 2012)
GET command is:
Response [https://api.federalreporter.nih.gov/v1/Projects/search?query=projectNumber%3AUSFS*%24fy%3A2012&offset=1&limit=50]
  Date: 2020-02-24 19:49
  Status: 500
  Content-Type: <unknown>
<EMPTY BODY>
Error in fe_projects_search(project_number = "USFS*", fiscal_year = 2012) : 
  Internal Server Error (HTTP 500).
Calls: fe_projects_search -> <Anonymous>
Execution halted
Found the following significant warnings:
  fgsg.h:96:61: warning: passing argument 8 of 'dpotrs_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:202:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:347:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:460:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:516:61: warning: passing argument 8 of 'dpotrs_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:636:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:717:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:852:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:996:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/FGSG.Rcheck/00install.out' for details.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
    libs   2.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   2.5Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Package required but not available: 'flowWorkspace'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
Found the following significant warnings:
  RngStream.c:275:7: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/freeknotsplines.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   3.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.0Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    2.1Mb
    libs   2.0Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/fs.Rcheck/00install.out' for details.
Found the following significant warnings:
  FunctionalNetworks.c:223:17: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/FunctionalNetworks.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.5Mb
    libs      2.0Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      5.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.2Mb
installed size is 85.2Mb
  sub-directories of 1Mb or more:
    L8NY18   2.2Mb
    gdal     3.8Mb
    libs    72.9Mb
    proj     5.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   3.0Mb
    libs      1.8Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.1Mb
Running examples in 'GENLIB-Ex.R' failed
The error most likely occurred in:

> ### Name: gen.find.Min.Distance.MRCA
> ### Title: Finds the minimum distances between pairs of individuals given a
> ###   set of ancestors.
> ### Aliases: gen.find.Min.Distance.MRCA
> ### Keywords: manip
> 
> ### ** Examples
> 
> data(geneaJi) 
> genJi<-gen.genealogy(geneaJi) 
> matMRCA<-gen.findMRCA(genJi, individuals=c(1,29), NbProcess = 1)
[1] "warning"
converting NULL pointer to R NULL> gen.find.Min.Distance.MRCA(matMRCA)
Error in gen.find.Min.Distance.MRCA(matMRCA) : 
  genMatrix must be a matrix output from gen.findMRCA
Execution halted
Found the following significant warnings:
  runMCMCfunc.cpp:40:42: warning: left operand of comma operator has no effect [-Wunused-value]
  runMCMCfunc.cpp:41:45: warning: left operand of comma operator has no effect [-Wunused-value]
  runMCMCfunc.cpp:55:44: warning: left operand of comma operator has no effect [-Wunused-value]
  runMCMCfunc.cpp:56:47: warning: left operand of comma operator has no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/geoCount.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.3Mb
Found the following significant warnings:
  Sequence.cpp:387:17: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  Sequence.cpp:388:17: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  Sequence.cpp:387:10: warning: 'char* __builtin_strcpy(char*, const char*)' source argument is the same as destination [-Wrestrict]
  Sequence.cpp:388:10: warning: 'char* __builtin_strcpy(char*, const char*)' source argument is the same as destination [-Wrestrict]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/gkmSVM.Rcheck/00install.out' for details.
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  20.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    doc         1.1Mb
    libs       21.7Mb
    test_data   1.2Mb
Found the following significant warnings:
  kmppini.cpp:241:14: warning: 'void* memcpy(void*, const void*, size_t)' forming offset [5, 8] is out of the bounds [0, 4] of object 'sed' with type 'std::size_t' {aka 'unsigned int'} [-Warray-bounds]
  kmppini.cpp:275:14: warning: 'void* memcpy(void*, const void*, size_t)' forming offset [5, 8] is out of the bounds [0, 4] of object 'sed' with type 'std::size_t' {aka 'unsigned int'} [-Warray-bounds]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/GMKMcharlie.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: namespace 'lme4' is not available and has been replaced
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/GMMAT.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/gpuR.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Found the following significant warnings:
  readstat/readstat_convert.c:18:42: warning: passing argument 2 of 'libiconv' from incompatible pointer type [-Wincompatible-pointer-types]
  src/spss/readstat_sav_parse.rl:89:17: warning: passing argument 2 of 'libiconv' from incompatible pointer type [-Wincompatible-pointer-types]
  src/spss/readstat_sav_parse.rl:197:17: warning: passing argument 2 of 'libiconv' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/haven.Rcheck/00install.out' for details.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs   4.4Mb
Found the following significant warnings:
  Warning: replacing previous import 'GenomicRanges::.__C__GenomicRanges_OR_GenomicRangesList' by 'rtracklayer::.__C__GenomicRanges_OR_GenomicRangesList' when loading 'HiCfeat'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/HiCfeat.Rcheck/00install.out' for details.
Found the following significant warnings:
  gener.c:39:13: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  gener.c:39:26: warning: 'sprintf' may write a terminating nul past the end of the destination [-Wformat-overflow=]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/hier.part.Rcheck/00install.out' for details.
'library' or 'require' call to 'gtools' which was already attached by Depends.
  Please remove these calls from your code.
all.regs: no visible global function definition for 'glm'
all.regs: no visible global function definition for 'logLik'
combos: no visible global function definition for 'menu'
current.model: no visible global function definition for 'formula'
current.model: no visible global function definition for 'glm'
current.model: no visible global function definition for 'logLik'
current.model: no visible global function definition for 'lm'
rand.hp: no visible global function definition for 'runif'
rand.hp: no visible global function definition for 'sd'
Undefined global functions or variables:
  formula glm lm logLik menu runif sd
Consider adding
  importFrom("stats", "formula", "glm", "lm", "logLik", "runif", "sd")
  importFrom("utils", "menu")
to your NAMESPACE file.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
    libs   2.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.4Mb
Error(s) in re-building vignettes:
--- re-building 'Using_Hot_Deck_Data.Rnw' using Sweave
Loading required package: mice

Attaching package: 'mice'

The following objects are masked from 'package:base':

    cbind, rbind

Warning in hot.deck(isq99, sdCutoff = 3, IDvars = c("IDORIGIN", "YEAR")) :
  52 observations with no observed data.  These observations were removed

Warning in hot.deck(isq99, sdCutoff = 3, IDvars = c("IDORIGIN", "YEAR")) :
  45 of 4661 imputations with # donors < 5, consider increasing sdCutoff or using method='p.draw'

Loading required package: survival
* miceadds 3.8-9 (2020-02-17 11:03:15)
Warning: Number of logged events: 1

Error: processing vignette 'Using_Hot_Deck_Data.Rnw' failed with diagnostics:
 chunk 10 (label = conv) 
Error in Math.data.frame(structure(list(term = structure(1:12, .Label = c("(Intercept)",  : 
  non-numeric variable(s) in data frame: term

--- failed re-building 'Using_Hot_Deck_Data.Rnw'

SUMMARY: processing the following file failed:
  'Using_Hot_Deck_Data.Rnw'

Error: Vignette re-building failed.
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.5Mb
    libs   1.6Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   1.8Mb
    libs          3.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   3.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.6Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   1.4Mb
    libs   2.9Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   7.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.9Mb
Found the following significant warnings:
  uuid/gen_uuid.c:321:11: warning: ordered comparison of pointer with integer zero [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/igraph.Rcheck/00install.out' for details.
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  14.2Mb
Running 'testthat.R' [166s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(igraph)
  
  Attaching package: 'igraph'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  The following objects are masked from 'package:stats':
  
      decompose, spectrum
  
  The following object is masked from 'package:base':
  
      union
  
  > 
  > suppressWarnings(RNGversion("3.5.0"))
  > test_check("igraph")
  -- 1. Failure:  (@test_layout.fr.R#13)  ----------------------------------------
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 10.8 - 10.8 == 7.97e-05
  
  -- 2. Failure:  (@test_layout.fr.R#22)  ----------------------------------------
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 941 - 1004 == -62.5
  
  -- 3. Failure: SIR works (@test_sir.R#15)  ---------------------------------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "bc42d0cbe0bb3321e83979c0432f9cea"
  y[1]: "b73a8ad03b832b3543f2f03d07330398"
  
  == testthat results  =======================================================
  [ OK: 3308 | SKIPPED: 4 | WARNINGS: 1376 | FAILED: 3 ]
  1. Failure:  (@test_layout.fr.R#13) 
  2. Failure:  (@test_layout.fr.R#22) 
  3. Failure: SIR works (@test_sir.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
installed size is 23.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       1.1Mb
    extdata   1.0Mb
    include   3.0Mb
    libs     16.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.6Mb
Error(s) in re-building vignettes:
--- re-building 'intePareto.Rmd' using rmarkdown
Loading required package: intePareto
get RNA counts
Cache found
get chip counts
use DESeq2 to calculate log2FoldChange of RNA-Seq
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
Quitting from lines 118-126 (intePareto.Rmd) 
Error: processing vignette 'intePareto.Rmd' failed with diagnostics:
failed to coerce 'list(value)' to a DESeqResults object of length 1
--- failed re-building 'intePareto.Rmd'

SUMMARY: processing the following file failed:
  'intePareto.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   2.3Mb
Running examples in 'iRF-Ex.R' failed
The error most likely occurred in:

> ### Name: readForest
> ### Title: Pass data through a fitted forest, record node characteristics
> ###   [works for binary classification with continuous variables]
> ### Aliases: readForest
> 
> ### ** Examples
> 
>   n = 50; p = 10
>   X = array(rnorm(n*p), c(n, p))
>   Y = (X[,1]>0.35 & X[,2]>0.35)|(X[,5]>0.35 & X[,7]>0.35)
>   Y = as.factor(as.numeric(Y>0))
> 
>   train.id = 1:(n/2)
>   test.id = setdiff(1:n, train.id)
>   
>   rf <- randomForest(x=X, y=Y, keep.forest=TRUE, track.nodes=TRUE,
+     ntree=100)
>   rforest <- readForest(rfobj=rf, x=X, n.core=2)
>   head(rforest$tree_info)
NULL
> 
>  # count number of leaf nodes with at least 5 observations
>   sum(rforest$tree.info$size.node > 5)
[1] 284
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11783 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11783 (sockconn)
Execution halted
Running examples in 'iRF-Ex.R' failed
The error most likely occurred in:

> ### Name: readForest
> ### Title: Pass data through a fitted forest, record node characteristics
> ###   [works for binary classification with continuous variables]
> ### Aliases: readForest
> 
> ### ** Examples
> 
>   n = 50; p = 10
>   X = array(rnorm(n*p), c(n, p))
>   Y = (X[,1]>0.35 & X[,2]>0.35)|(X[,5]>0.35 & X[,7]>0.35)
>   Y = as.factor(as.numeric(Y>0))
> 
>   train.id = 1:(n/2)
>   test.id = setdiff(1:n, train.id)
>   
>   rf <- randomForest(x=X, y=Y, keep.forest=TRUE, track.nodes=TRUE,
+     ntree=100)
>   rforest <- readForest(rfobj=rf, x=X, n.core=2)
>   head(rforest$tree_info)
NULL
> 
>  # count number of leaf nodes with at least 5 observations
>   sum(rforest$tree.info$size.node > 5)
[1] 284
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11958 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11958 (sockconn)
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.1Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs           4.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   2.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   3.4Mb
Found the following significant warnings:
  model_simul.cpp:838:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  model_simul.cpp:719:19: warning: '.bin' directive writing 4 bytes into a region of size between 3 and 11 [-Wformat-overflow=]
  model_simul.cpp:720:22: warning: '.bin' directive writing 4 bytes into a region of size between 0 and 8 [-Wformat-overflow=]
  model_simul.cpp:721:19: warning: '.bin' directive writing 4 bytes into a region of size between 3 and 11 [-Wformat-overflow=]
  model_simul.cpp:722:19: warning: '.bin' directive writing 4 bytes into a region of size between 3 and 11 [-Wformat-overflow=]
  model_simul.cpp:723:19: warning: '.bin' directive writing 4 bytes into a region of size between 3 and 11 [-Wformat-overflow=]
  model_simul.cpp:724:19: warning: '.bin' directive writing 4 bytes into a region of size between 3 and 11 [-Wformat-overflow=]
  printReadWrite.cpp:54:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:74:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:84:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:138:38: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:139:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:140:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:141:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:152:91: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/landsepi.Rcheck/00install.out' for details.
installed size is 79.7Mb
  sub-directories of 1Mb or more:
    gdal   3.8Mb
    libs  69.5Mb
    proj   5.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.4Mb
    libs   2.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      3.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
    libs   2.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.5Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        2.4Mb
    libs       2.6Mb
    testdata   1.6Mb
Found the following significant warnings:
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/container/detail/copy_move_algo.hpp:182:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'value_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/container/detail/copy_move_algo.hpp:896:16: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/container/detail/copy_move_algo.hpp:196:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/lolog.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Running 'testthat.R' [37s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(loose.rock)
  > 
  > test_check("loose.rock")
  -- 1. Error: coding genes retrieves some genes (@test-coding.genes.R#4)  -------
  cannot open the connection
  Backtrace:
   1. loose.rock::coding.genes(verbose = FALSE)
   4. utils::read.table(...)
   6. base::open.connection(file, "rt")
  
  == testthat results  ===========================================================
  [ OK: 146 | SKIPPED: 2 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: coding genes retrieves some genes (@test-coding.genes.R#4) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  In ix.me(ix, n.obs, n.vars) :
    closing unused connection 4 (https://ftp.ncbi.nih.gov/pub/CCDS/current_human/CCDS.current.txt)
  Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      2.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   3.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.1Mb
    libs   2.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   2.1Mb
Found the following significant warnings:
  liblwgeom/lwgeom_topo.c:4305:36: warning: too many arguments for format [-Wformat-extra-args]
  liblwgeom/lwgeom_topo.c:4357:38: warning: too many arguments for format [-Wformat-extra-args]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/lwgeom.Rcheck/00install.out' for details.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
    proj   5.0Mb
Found the following significant warnings:
  lxb.c:62:21: warning: '%d' directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/lxb.Rcheck/00install.out' for details.
installed size is 41.8Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs  34.8Mb
Found the following significant warnings:
  Manifolds/SmartSpace.cpp:147:25: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ManifoldOptim.Rcheck/00install.out' for details.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc           1.2Mb
    htmlwidgets   1.4Mb
    libs          8.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   2.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.2Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   3.2Mb
Found the following significant warnings:
  Warning: unable to find a consistent ordering of superclasses for class "dsparseModelMatrix": order chosen is inconsistent with the superclasses of "sparseModelMatrix"
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/MatrixModels.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   3.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      2.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.6Mb
Running 'testthat.R' [30s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > suppressPackageStartupMessages(library(metacoder))
  > 
  > test_check("metacoder")
  -- 1. Error: Converting to phyloseq (@test--parsers_and_writers.R#202)  --------
  package or namespace load failed for 'phyloseq' in library.dynam(lib, package, package.lib):
   DLL 'Rhdf5lib' not found: maybe not installed for this architecture?
  Backtrace:
   1. base::library(phyloseq)
   2. base::tryCatch(...)
   3. base:::tryCatchList(expr, classes, parentenv, handlers)
   4. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   5. value[[3L]](cond)
  
  == testthat results  ===========================================================
  [ OK: 95 | SKIPPED: 1 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: Converting to phyloseq (@test--parsers_and_writers.R#202) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.1Mb
    libs   4.5Mb
    misc   1.1Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/mixKernel.Rcheck/00install.out' for details.
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    libs   2.5Mb
Found the following significant warnings:
  ./bson/bson-macros.h:180:19: warning: ISO C does not support '__FUNCTION__' predefined identifier [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/mongolite.Rcheck/00install.out' for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   1.6Mb
    libs   1.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   3.2Mb
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.1Mb
    libs  21.2Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Found the following significant warnings:
  eclat/tract/src/tract.c:1399:41: warning: too many arguments for format [-Wformat-extra-args]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/multinet.Rcheck/00install.out' for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.5Mb
    libs   2.0Mb
Found the following significant warnings:
  generateData.cpp:105:18: warning: passing NULL to non-pointer argument 1 of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion-null]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/NestedCategBayesImpute.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   2.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   2.6Mb
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    CppCode   2.7Mb
    R         6.2Mb
    include   5.6Mb
    libs      2.4Mb
    tests     1.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   2.2Mb
Running examples in 'NSO1212-Ex.R' failed
The error most likely occurred in:

> ### Name: all_tables
> ### Title: Brief Information about All Tables on the API opendata.1212.mn
> ### Aliases: all_tables
> 
> ### ** Examples
> 
> all.tables <- all_tables()
Error in open.connection(con, "rb") : HTTP error 500.
Calls: all_tables ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
Execution halted
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc    7.4Mb
    libs   3.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    doc    2.3Mb
    help   2.7Mb
    libs   2.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.4Mb
Running examples in 'opencastR-Ex.R' failed
The error most likely occurred in:

> ### Name: oc_event_publication
> ### Title: Query Opencast for a specific events single publication
> ### Aliases: oc_event_publication
> 
> ### ** Examples
> 
> Sys.setenv(OPENCAST_HOST = "https://legacy.opencast.org")
> Sys.setenv(OPENCAST_USERNAME = "admin")
> Sys.setenv(OPENCAST_PASSWORD = "opencast")
> 
> events <- oc_list_events()
> publications <- oc_event_list_publications(events$content$identifier[1])
> 
> oc_event_publication(events$content$identifier[1],
+                      publications$content$id[1])
Error in if (publicationId == "") { : argument is of length zero
Calls: oc_event_publication
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/OpenCL.Rcheck/00install.out' for details.
installed size is 29.6Mb
  sub-directories of 1Mb or more:
    libs   19.8Mb
    share   9.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.0Mb
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    R        2.5Mb
    libs     7.9Mb
    models   4.7Mb
Running 'testthat.R' [43s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(OpenMx)
  > 
  > test_check("OpenMx")
  -- 1. Failure: (unknown) (@test-wls-binary.R#43)  ------------------------------
  `mxRun(wlsTest4)` did not throw an error.
  
  == testthat results  ===========================================================
  [ OK: 567 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: (unknown) (@test-wls-binary.R#43) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      2.3Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.6Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   2.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    doc    1.3Mb
    libs   2.0Mb
Running 'test-pkgdepends.R' [46s]
  Running 'test-pkginstall.R' [0s]
  Running 'testthat.R' [17s]
Running the tests in 'tests/test-pkgdepends.R' failed.
Complete output:
  > 
  > do <- function() {
  +   old <- Sys.getenv("R_PKG_CACHE_DIR", NA_character_)
  +   if (is.na(old)) {
  +     on.exit(Sys.unsetenv("R_PKG_CACHE_DIR"), add = TRUE)
  +   } else {
  +     on.exit(Sys.setenv("R_PKG_CACHE_DIR" = old), add = TRUE)
  +   }
  +   Sys.setenv("R_PKG_CACHE_DIR" = tempfile())
  + 
  +   if (file.exists("pkgdepends")) {
  +     library(testthat)
  +     library(pak)
  +     test <- function() {
  +       package <- "pak"
  +       env_test <- asNamespace("testthat")$env_test
  +       env_test$in_test <- TRUE
  +       env_test$package <- package
  +       on.exit({
  +         env_test$in_test <- FALSE
  +         env_test$package <- NULL
  +       }, add = TRUE)
  +       test_path <- "pkgdepends"
  +       asNamespace("testthat")$test_package_dir(
  +         package = package, test_path = test_path,
  +         filter = NULL, reporter = "check")
  +     }
  +     test()
  +   }
  + }
  > 
  > do()
  -- 1. Error: dependencies are honoured (@test-resolution.R#291)  ---------------
  Wrong entry types: `filesize (double, expected integer)`
  Backtrace:
   1. asNamespace("pkgcache")$synchronise(do("cran::dplyr", FALSE))
  
  == testthat results  ===========================================================
  [ OK: 675 | SKIPPED: 32 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: dependencies are honoured (@test-resolution.R#291) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [51s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(panelr)
  Loading required package: lme4
  Loading required package: Matrix
  
  Attaching package: 'panelr'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("panelr")
  -- 1. Error: (unknown) (@test_wbm.R#283)  --------------------------------------
  could not find function "arma"
  Backtrace:
   1. panelr::wbm_stan(...)
   2. brms::make_stancode(...)
   4. brms:::validate_formula.default(...)
   6. brms:::validate_formula.brmsformula(bf(formula), ...)
   7. brms:::validate_autocor(autocor)
   8. brms:::parse_ac(autocor)
   9. base::lapply(out, eval2)
  
  == testthat results  ===========================================================
  [ OK: 271 | SKIPPED: 0 | WARNINGS: 60 | FAILED: 1 ]
  1. Error: (unknown) (@test_wbm.R#283) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  putty/windows/winstore.c:665:38: warning: passing argument 6 of 'RegQueryValueExA' from incompatible pointer type [-Wincompatible-pointer-types]
  putty/windows/winstore.c:673:42: warning: passing argument 6 of 'RegQueryValueExA' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/pbdRPC.Rcheck/00install.out' for details.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    lib    5.6Mb
    libs   4.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.9Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.9Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  13.1Mb
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    libs   13.8Mb
    share  11.9Mb
Running examples in 'penDvine-Ex.R' failed
The error most likely occurred in:

> ### Name: penDvine-package
> ### Title: The package 'penDvine' offers routines for estimating densities
> ###   and copula distribution of D-vines.
> ### Aliases: penDvine-package
> 
> ### ** Examples
> 
> #This examples describes the estimation of a D-vine to winddata,
> #available in this package. After the margins are prepared, we estimate a
> #D-vine using B-splines with 9 (K+1) marginal knots and penalizing second (m=2)
> #order differences (pen=1) of the basis coefficients.
> 
> data(Winddata)
> ex.data<-Winddata[c(1:100),c(1:4)] #examplary subdata for fast calculation
> wind.example<-Dvine(ex.data,K=7,pen=1,lambda=100,order.Dvine=FALSE,base="B-spline",m=2,cores=2)
>   
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11966 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11966 (sockconn)
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs        2.0Mb
    xvg-files   3.2Mb
Found the following significant warnings:
  permTest.c:20:3: warning: statement with no effect [-Wunused-value]
  permTest.c:62:3: warning: statement with no effect [-Wunused-value]
  permTest.c:90:3: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/permDep.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   2.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/phateR.Rcheck/00install.out' for details.
Running 'testthat.R' [34s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(phenocamapi)
  Loading required package: data.table
  Loading required package: rjson
  Loading required package: RCurl
  > library(data.table)
  > 
  > test_check("phenocamapi")
  trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
  Content type 'application/octet-stream' length 202442 bytes (197 KB)
  ==================================================
  downloaded 197 KB
  
  -- 1. Failure: test getting awb data (@testphenocamapi.R#42)  ------------------
  `wb` not equal to "LIKELY_NO".
  target is NULL, current is character
  
  == testthat results  ===========================================================
  [ OK: 5 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: test getting awb data (@testphenocamapi.R#42) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'getting_started_phenocam_api.Rmd' using rmarkdown
trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
Content type 'application/octet-stream' length 202442 bytes (197 KB)
==================================================
downloaded 197 KB

trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/2013/05/dukehw_2013_05_31_150331.jpg'
Content type 'image/jpeg' length 470270 bytes (459 KB)
==================================================
downloaded 459 KB

Quitting from lines 282-298 (getting_started_phenocam_api.Rmd) 
Error: processing vignette 'getting_started_phenocam_api.Rmd' failed with diagnostics:
a character vector argument expected
--- failed re-building 'getting_started_phenocam_api.Rmd'

--- re-building 'phenocam_data_fusion.Rmd' using rmarkdown
Loading required package: rjson
Loading required package: RCurl
trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
Content type 'application/octet-stream' length 202442 bytes (197 KB)
==================================================
downloaded 197 KB

trying URL 'http://phenocam.sr.unh.edu/data/archive/oregonMP/ROI/oregonMP_EN_1000_3day.csv'
Content type 'application/octet-stream' length 268525 bytes (262 KB)
==================================================
downloaded 262 KB

--- finished re-building 'phenocam_data_fusion.Rmd'

SUMMARY: processing the following file failed:
  'getting_started_phenocam_api.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.0Mb
    libs      2.0Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/phyloseqGraphTest.Rcheck/00install.out' for details.
Warning in inla.print.version() :
  INLA_18.07.12: 32bit binaries are no longer supported!

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
Running 'spelling.R' [0s]
  Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(piggyback)
  > Sys.setenv(piggyback_cache_duration=0)
  > test_check("piggyback")
  -- 1. Error: Attempt to delete non-existent file (@test-errors.R#148)  ---------
  
  GitHub API error (404): 404 Not Found
  Message: Not Found
  Read more at https://developer.github.com/v3/repos/releases/#delete-a-release-asset
  
  URL not found: https://api.github.com/repos/cboettig/piggyback-tests/releases/assets/18180503
  Backtrace:
    1. testthat::expect_message(...)
    6. piggyback::pb_delete(...)
    7. base::lapply(...)
    8. piggyback:::FUN(X[[i]], ...)
    9. gh::gh(...)
   10. gh:::gh_process_response(raw)
   11. gh:::gh_error(response)
   12. throw(cond)
  
  == testthat results  ===========================================================
  [ OK: 6 | SKIPPED: 18 | WARNINGS: 11 | FAILED: 1 ]
  1. Error: Attempt to delete non-existent file (@test-errors.R#148) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    1.1Mb
    libs   2.3Mb
Found the following significant warnings:
  StandardizeString.cpp:13:25: warning: passing NULL to non-pointer argument 1 of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 16; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion-null]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/PPRL.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.2Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    extdata   7.4Mb
    libs      2.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   2.1Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
    proj   5.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   2.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    gui          1.1Mb
    staticdocs   3.3Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.0Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.6Mb
    doc       2.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.3Mb
    libs   3.6Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   2.6Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    Output   2.2Mb
    bin     12.3Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    5.9Mb
    libs   2.1Mb
Running examples in 'randNames-Ex.R' failed
The error most likely occurred in:

> ### Name: rand_names
> ### Title: Random name generator
> ### Aliases: rand_names
> 
> ### ** Examples
> 
> data <- rand_names(5)
No encoding supplied: defaulting to UTF-8.
Error: lexical error: invalid char in json text.
                                       <!DOCTYPE html> <!--[if lt IE 7
                     (right here) ------^
Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(randNames)
  > 
  > test_check("randNames")
  -- 1. Error: Random names work (@test_rand_names.R#4)  -------------------------
  lexical error: invalid char in json text.
                                         <!DOCTYPE html> <!--[if lt IE 7
                       (right here) ------^
  Backtrace:
   1. testthat::expect_is(rand_names(1), "data.frame")
   4. randNames::rand_names(1)
   5. jsonlite::fromJSON(...)
   6. jsonlite:::parse_and_simplify(...)
   7. jsonlite:::parseJSON(txt, bigint_as_char)
   8. jsonlite:::parse_string(txt, bigint_as_char)
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Random names work (@test_rand_names.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.2Mb
    libs   3.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   2.0Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   2.8Mb
Found the following significant warnings:
  avc_binwr.c:166:9: warning: 'strncpy' output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:173:9: warning: 'strncpy' output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:180:9: warning: 'strncpy' output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:187:9: warning: 'strncpy' output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:1453:29: warning: '%4.4d' directive writing between 4 and 10 bytes into a region of size 5 [-Wformat-overflow=]
  avc_binwr.c:1553:28: warning: '%s' directive writing up to 39 bytes into a region of size between 38 and 77 [-Wformat-overflow=]
  avc_e00write.c:386:30: warning: 'sprintf' may write a terminating nul past the end of the destination [-Wformat-overflow=]
  avc_e00write.c:387:30: warning: '-ID' directive writing 3 bytes into a region of size between 1 and 40 [-Wformat-overflow=]
  avc_e00write.c:401:61: warning: '%s' directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:397:61: warning: '%s' directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:409:39: warning: '%s' directive writing up to 39 bytes into a region of size 33 [-Wformat-overflow=]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RArcInfo.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    libs   2.9Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   4.3Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rblpapi.Rcheck/00install.out' for details.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RcmdrPlugin.BiclustGUI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rcplex.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    include   6.2Mb
    libs      2.3Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
    libs      2.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib       3.9Mb
    libs      3.4Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      2.3Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib      13.2Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    include   6.3Mb
    libs      2.5Mb
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(RcppXsimd)
  > 
  > test_check("RcppXsimd")
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rcrypt)
  > 
  > test_check("rcrypt")
  gpg: decryption failed: bad key
  -- 1. Error: Decryption with passphrase passthrough and armor works (@test-decry
  cannot open the connection
  Backtrace:
   1. base::readLines("file2-decrypt.txt")
   2. base::file(con, "r")
  
  == testthat results  ===========================================================
  [ OK: 18 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 1 ]
  1. Error: Decryption with passphrase passthrough and armor works (@test-decrypt.r#69) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  skein_block64.c:226:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RDieHarder.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
Found the following significant warnings:
  Rreadsdpa.c:608:15: warning: 'strncpy' output may be truncated copying 3999 bytes from a string of length 3999 [-Wstringop-truncation]
  Rreadsdpa.c:1041:13: warning: 'strncpy' output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  Rreadsdpa.c:1042:13: warning: 'strncpy' output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:164:4: warning: 'strncpy' output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:165:4: warning: 'strncpy' output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rdsdp.Rcheck/00install.out' for details.
Found the following significant warnings:
  compile.cc:292:69: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class re2::Prog::Inst'; use assignment or value-initialization instead [-Wclass-memaccess]
  regexp.cc:343:33: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class re2::Regexp' with no trivial copy-assignment [-Wclass-memaccess]
  regexp.cc:344:32: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class re2::Regexp' with no trivial copy-assignment [-Wclass-memaccess]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/re2r.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.2Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs   2.3Mb
Running 'testthat.R' [154s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(renv)
  
  Attaching package: 'renv'
  
  The following object is masked from 'package:stats':
  
      update
  
  The following objects are masked from 'package:utils':
  
      history, upgrade
  
  The following objects are masked from 'package:base':
  
      load, remove
  
  > 
  > renv:::renv_tests_init()
  > renv:::renv_tests_diagnostics()
  The following R libraries are set:
  
  	- D:/temp/RtmpqkDMFW/renv-library-1dd7067276fe
  	- D:/temp/RtmpqkDMFW/renv-system-library
  
  The following repositories are set:
  
  	CRAN: file:///D:\temp\RtmpqkDMFW\renv-repos-1dd7066fa578c
  
  The following renv root directory is being used:
  
  	- D:\temp\RtmpqkDMFW\renv-root-1dd70389a573b
  
  The following renv cache directory is being used:
  
  	- D:\temp\RtmpqkDMFW\renv-root-1dd70389a573b/cache/v5/R-4.0-r77730/x86_64-w64-mingw32
  
  The following packages are available in the test repositories:
  
  	bread, breakfast, brunch, egg, halloween, oatmeal, packrat,
  	toast
  
  	R_LIBS      : <NA>
  	R_LIBS_SITE : "'no_such_dir'"
  	R_LIBS_USER : "'no_such_dir'"
  
  > 
  > test_check("renv")
  [4/4] -- 1. Error: we can retrieve files using file URIs (@test-retrieve.R#282)  -----
  (converted from warning) cannot open file 'D:/temp/RtmpqkDMFW/renv-test-1dd70c0656a/target': No such file or directory
  Backtrace:
   1. testthat::expect_equal(readLines(target), "Hello, world!")
   4. base::readLines(target)
  
  == testthat results  ===========================================================
  [ OK: 304 | SKIPPED: 53 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: we can retrieve files using file URIs (@test-retrieve.R#282) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.1Mb
Running 'testthat.R' [183s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(restatapi)
  restatapi: - config file with the API version 1 loaded from GitHub (the 'current' API version number is 1).
             - 2 from the 32 cores are used for parallel computing.
             - 'libcurl' will be used for file download.
             - the Table of contents (TOC) was not pre-loaded into the deafult cache ('.restatapi_env').
  > 
  > test_check("restatapi")
  -- 1. Failure: test of the get_eurostat_raw/bulk/data functions (@test-all.R#84)
  `rt1 <- get_eurostat_raw(id, verbose = FALSE)` did not produce any messages.
  
  -- 2. Error: test of the get_eurostat_raw/bulk/data functions (@test-all.R#85)  
  'target' and 'current' must both be data.tables
  Backtrace:
   1. testthat::expect_equal(rt1, NULL)
   3. testthat:::compare.default(act$val, exp$val, ...)
   5. data.table:::all.equal.data.table(x, y, ...)
  
  == testthat results  ===========================================================
  [ OK: 67 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: test of the get_eurostat_raw/bulk/data functions (@test-all.R#84) 
  2. Error: test of the get_eurostat_raw/bulk/data functions (@test-all.R#85) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is 80.8Mb
  sub-directories of 1Mb or more:
    gdal       3.9Mb
    libs      69.2Mb
    pictures   1.3Mb
    proj       5.0Mb
Found the following significant warnings:
  IP2Location.c:339:35: warning: passing argument 3 of 'inet_pton' from incompatible pointer type [-Wincompatible-pointer-types]
  IP2Location.c:893:39: warning: passing argument 3 of 'inet_pton' from incompatible pointer type [-Wincompatible-pointer-types]
  IP2Location.c:900:41: warning: passing argument 3 of 'inet_pton' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/rgeolocate.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      2.2Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc     3.7Mb
    fonts   1.5Mb
    libs    1.4Mb
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  10.6Mb
    libs   5.1Mb
Found the following significant warnings:
  fakemaster.c:82:57: warning: embedded '\0' in format [-Wformat-contains-nul]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rhpc.Rcheck/00install.out' for details.
Found the following significant warnings:
  RInside.cpp:169:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 260 equals destination size [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RInside.Rcheck/00install.out' for details.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    lib    6.3Mb
    libs   8.0Mb
Found the following significant warnings:
  Rinit.c:251:21: warning: assignment to 'blah1' {aka 'int (*)(const char *, char *, int,  int)'} from incompatible pointer type 'int (*)(const char *, unsigned char *, int,  int)' [-Wincompatible-pointer-types]
  Rinit.c:257:21: warning: assignment to 'blah5' {aka 'int (*)(const char *)'} from incompatible pointer type 'int (*)(char *)' [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/rJava.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.0gcc8/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/4.0gcc8/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'rJava/libs/i386/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'
File 'rJava/libs/x64/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rmagic.Rcheck/00install.out' for details.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   2.8Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doxygen   1.4Mb
    libs      2.7Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      6.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   2.6Mb
Found the following significant warnings:
  Warning: unable to find a consistent ordering of superclasses for class "GPDORobEstimate": order chosen is inconsistent with the superclasses of "GPDkStepEstimate"
  Warning: unable to find a consistent ordering of superclasses for class "GEVORobEstimate": order chosen is inconsistent with the superclasses of "GEVkStepEstimate"
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RobExtremes.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ROracle.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    libs    2.2Mb
    tests   1.3Mb
Found the following significant warnings:
  bgc_hmm.c:241:15: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  bgc_hmm.c:242:13: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  bgc_hmm.c:241:31: warning: ', ' directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
  rph_tfbs.c:371:11: warning: 'strncpy' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:351:11: warning: 'strncpy' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:819:5: warning: 'strncpy' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/rphast.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      2.7Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.5Mb
Found the following significant warnings:
  fe-protocol2.c:1615:2: warning: 'strncpy' specified bound 32 equals destination size [-Wstringop-truncation]
  fe-protocol2.c:1616:2: warning: 'strncpy' specified bound 64 equals destination size [-Wstringop-truncation]
  fe-protocol2.c:1620:3: warning: 'strncpy' specified bound 64 equals destination size [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RPostgreSQL.Rcheck/00install.out' for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Error(s) in re-building vignettes:
--- re-building 'rpredictit-vignette.Rmd' using rmarkdown
Quitting from lines 54-56 (rpredictit-vignette.Rmd) 
Error: processing vignette 'rpredictit-vignette.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building 'rpredictit-vignette.Rmd'

SUMMARY: processing the following file failed:
  'rpredictit-vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 27.4Mb
  sub-directories of 1Mb or more:
    libs  26.8Mb
Found the following significant warnings:
  cli.c:232:44: warning: passing argument 4 of 'setsockopt' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RSclient.Rcheck/00install.out' for details.
Found the following significant warnings:
  RSserver.c:64:44: warning: passing argument 4 of 'setsockopt' from incompatible pointer type [-Wincompatible-pointer-types]
   #warning Please include winsock2.h before windows.h
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rserve.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.0gcc8/Rserve/libs/i386/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'd:/Rcompile/CRANpkg/lib/4.0gcc8/Rserve/libs/x64/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/i386/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  kr_io.cpp:891:9: warning: 'char* strcat(char*, const char*)' accessing 631 or more bytes at offsets 6607 and 7237 may overlap 1 byte at offset 7237 [-Wrestrict]
  kr_io.cpp:868:9: warning: 'char* strcat(char*, const char*)' accessing 631 or more bytes at offsets 6607 and 7237 may overlap 1 byte at offset 7237 [-Wrestrict]
  kr_io.cpp:891:9: warning: 'char* strcat(char*, const char*)' accessing 631 or more bytes at offsets 6719 and 7349 may overlap 1 byte at offset 7349 [-Wrestrict]
  kr_io.cpp:868:9: warning: 'char* strcat(char*, const char*)' accessing 631 or more bytes at offsets 6719 and 7349 may overlap 1 byte at offset 7349 [-Wrestrict]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RSNNS.Rcheck/00install.out' for details.
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### Name: SolrList-class
> ### Title: SolrList
> ### Aliases: class:SolrList SolrList-class length,SolrList-method
> ###   names,SolrList-method [<-,SolrList,ANY,ANY,ANY-method
> ###   [[,SolrList,ANY-method [,SolrList-method [[,SolrList-method
> ###   [[<-,SolrList-method unique,SolrList-method searchDocs
> ###   searchDocs,Solr SolrList coerce,Solr,SolrList-method
> ###   coerce,SolrList,DocCollection-method show,SolrList-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  3.75 0.14 3.92 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    4.4Mb
    libs  17.5Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/rstap.Rcheck/00install.out' for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.6Mb
Running examples in 'RSVGTipsDevice-Ex.R' failed
The error most likely occurred in:

> ### Name: RSVGTipsDevice
> ### Title: A SVG Graphics Driver with dynamic tips
> ### Aliases: RSVGTipsDevice
> ### Keywords: device package
> 
> ### ** Examples
> 
> library("RSVGTipsDevice")
> sessionInfo()
R Under development (unstable) (2020-01-27 r77730)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2008 x64 (build 6003) Service Pack 2

Matrix products: default

locale:
[1] LC_COLLATE=C                 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=C                LC_NUMERIC=C                
[5] LC_TIME=C                   

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RSVGTipsDevice_1.0-7

loaded via a namespace (and not attached):
[1] compiler_4.0.0
> devSVGTips("svgplot1.svg", toolTipMode=1,
+     title="SVG example plot 1: Shapes and Points, Tooltips are Title + 1 Line")
> plot(c(0,10),c(0,10), type="n", xlab="x", ylab="y",
+     main="Example SVG plot with title + 1 line tips (mode=1)")
> setSVGShapeToolTip(title="A rectangle", desc="that is yellow")
> rect(1,1,4,6, col='yellow')
> setSVGShapeToolTip(title="1st circle with title only")
> points(5.5,7.5,cex=20,pch=19,col='red')
> setSVGShapeToolTip(title="A triangle", desc="big and green")
> polygon(c(3,6,8), c(3,6,3), col='green')
> # no tooltips on these points
> points(2:8, 8:2, cex=3, pch=19, col='black')
> # tooltips on each these points
> invisible(sapply(1:7, function(x)
+ {setSVGShapeToolTip(title=paste("point", x))
+  points(x+1, 8-x, cex=3, pch=1, col='black')}))
> setSVGShapeToolTip(title="Text", desc="can have a tool tip too!")
> text(x=4, y=9, lab="Poke me!", col="blue")
> dev.off()
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Running 'test-all.R' [34s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("rtext")
  Loading required package: rtext
  Loading required package: stringb
  -- 1. Error: rtext tokenize_data_lines (@test_rtext.R#116)  --------------------
  arguments must have same length
  Backtrace:
   1. testthat::expect_true(...)
   4. dings$tokenize_data_lines()
   5. self$tokenize_data_regex(...)
   6. self$tokenize_data_sequences(...)
   8. stats::aggregate.data.frame(...)
  
  == testthat results  ===========================================================
  [ OK: 281 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: rtext tokenize_data_lines (@test_rtext.R#116) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       2.3Mb
    projects   2.7Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs   5.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   2.2Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   2.8Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs      8.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.3Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.3Mb
    libs   2.6Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         1.5Mb
    extdata   1.3Mb
    libs      2.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   2.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   4.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   2.0Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   3.5Mb
Running 'spelling.R' [0s]
  Running 'testthat.R' [16s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sen2r)
  Welcome to sen2r. To use the package from a GUI, launch
   > sen2r()
  Documentation: http://sen2r.ranghetti.info
  
  IMPORTANT: sen2r depends on some external tools;
  before using it, it is strongly recommended to run function
   > check_sen2r_deps()
  to check them and install the missing ones.
  > 
  > test_check("sen2r")
  Error : GET https://scihub.copernicus.eu/apihub/
  -- 1. Error: st_crs2, input WKT (@test-t34_st_crs2.R#14)  ----------------------
  there is no package called 'rgdal'
  Backtrace:
   1. sen2r:::st_as_text_2(st_crs(32609))
   2. utils::packageVersion("rgdal")
  
  -- 2. Error: st_crs2, input spatial file path (@test-t34_st_crs2.R#34)  --------
  Cannot create RasterLayer object from this file; perhaps you need to install rgdal first
  Backtrace:
   1. testthat::expect_equal(...)
   6. raster::raster(raster_path)
   7. raster:::.local(x, ...)
   8. raster:::.rasterObjectFromFile(...)
  
  == testthat results  ===========================================================
  [ OK: 53 | SKIPPED: 18 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: st_crs2, input WKT (@test-t34_st_crs2.R#14) 
  2. Error: st_crs2, input spatial file path (@test-t34_st_crs2.R#34) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.6Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   3.6Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
    libs   2.0Mb
installed size is 95.7Mb
  sub-directories of 1Mb or more:
    doc     12.0Mb
    gdal     3.9Mb
    libs    70.7Mb
    proj     5.0Mb
    sqlite   1.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/SigTree.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   3.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   4.5Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   3.1Mb
Found the following significant warnings:
  slfm_MDN.cpp:26:40: warning: left operand of comma operator has no effect [-Wunused-value]
  slfm_MNN.cpp:26:40: warning: left operand of comma operator has no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/slfm.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/smapr.Rcheck/00install.out' for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   3.1Mb
Running 'testthat.R' [87s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(smooth)
  Loading required package: greybox
  Package "greybox", v0.5.8 loaded.
  This is package "smooth", v2.5.5
  > 
  > test_check("smooth")
  -- 1. Failure: Select exogenous variables for GUMX on N1457 (@test_ges.R#40)  --
  suppressWarnings(testModel$xreg) is not null.
  
  == testthat results  ===========================================================
  [ OK: 72 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Select exogenous variables for GUMX on N1457 (@test_ges.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.6Mb
    libs   2.8Mb
Error(s) in re-building vignettes:
--- re-building 'SongEvo.Rmd' using rmarkdown
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

The following objects are masked from 'package:base':

    format.pval, units

! Package pdftex.def Error: File `D:/RCompile/CRANpkg/local/4.0gcc8/SongEvo.Rch
eck/vign_test/SongEvo/vignettes/SongEvo_files/figure-latex/Examine\%20populatio
n\%20size\%20over\%20time-1.pdf' not found.

Error: processing vignette 'SongEvo.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.0gcc8/SongEvo.Rcheck/vign_test/SongEvo/vignettes/SongEvo.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SongEvo.log for more info.
--- failed re-building 'SongEvo.Rmd'

SUMMARY: processing the following file failed:
  'SongEvo.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'SciencesPo'
Running 'lint.R' [1s]
  Running 'spelling.R' [0s]
  Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library("testthat")
  > library("spacyr")
  > 
  > test_check("spacyr")
  -- 1. Error: spacy_parse handles numbers/tibbles correctly (@test-2-spacy_parse.
  lexical error: invalid char in json text.
                                         NA
                       (right here) ------^
  Backtrace:
   1. global::skip_if_no_python_or_no_spacy()
   2. spacyr::find_spacy_env()
   4. reticulate::conda_list(conda = "auto")
   5. jsonlite::fromJSON(conda_envs)
   6. jsonlite:::parse_and_simplify(...)
   7. jsonlite:::parseJSON(txt, bigint_as_char)
   8. jsonlite:::parse_string(txt, bigint_as_char)
  
  == testthat results  ===========================================================
  [ OK: 1 | SKIPPED: 50 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: spacy_parse handles numbers/tibbles correctly (@test-2-spacy_parse.R#165) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    libs   2.8Mb
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   2.1Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   5.2Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    R      5.3Mb
    doc    4.9Mb
    help   5.3Mb
    libs   1.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
    libs   3.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   2.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.1Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   3.1Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   2.5Mb
Found the following significant warnings:
  dbfopenSSN.c:1119:6: warning: 'strncpy' output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:1100:6: warning: 'strncpy' output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:663:2: warning: 'strncpy' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopenSSN.c:1511:2: warning: 'strncpy' output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/SSN.Rcheck/00install.out' for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.5Mb
Found the following significant warnings:
  MaxChi.c:468:20: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  Phylpro.c:457:24: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/stepwise.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   2.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.2Mb
installed size is 35.6Mb
  sub-directories of 1Mb or more:
    libs  34.8Mb
Found the following significant warnings:
  computeQ.cpp:75:15: warning: catching polymorphic type 'class std::runtime_error' by value [-Wcatch-value=]
  computeQ.cpp:134:15: warning: catching polymorphic type 'class std::runtime_error' by value [-Wcatch-value=]
  computeQ.cpp:142:17: warning: catching polymorphic type 'class std::runtime_error' by value [-Wcatch-value=]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/strum.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   2.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/superbiclust.Rcheck/00install.out' for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    libs   2.2Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
Running examples in 'survival-Ex.R' failed
The error most likely occurred in:

> ### Name: mgus
> ### Title: Monoclonal gammopathy data
> ### Aliases: mgus mgus1
> ### Keywords: datasets survival
> 
> ### ** Examples
> 
> # Create the competing risk curves for time to first of death or PCM
> sfit <- survfit(Surv(start, stop, event) ~ sex, mgus1, id=id,
+                 subset=(enum==1))
Error in if (flag["teleport"] > 0) { : 
  missing value where TRUE/FALSE needed
Calls: survfit -> survfit.formula -> survfitCI -> survcheck2
Execution halted
Found the following significant warnings:
  lineariadmm.c:189:17: warning: value computed is not used [-Wunused-value]
  lineariadmm.c:190:17: warning: value computed is not used [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/svmadmm.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.9Mb
    libs   2.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   3.2Mb
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs      13.9Mb
    tessdata  14.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   2.2Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    2.9Mb
    libs   2.5Mb
Running 'testthat.R' [15s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(textrecipes)
  Loading required package: recipes
  Loading required package: dplyr
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  
  Attaching package: 'recipes'
  
  The following object is masked from 'package:stats':
  
      step
  
  > 
  > test_check("textrecipes")
  -- 1. Failure: step_tfidf works as intended (@test-tfidf.R#44)  ----------------
  as.matrix(rec_answer) not equal to as.matrix(manual_answer).
  29/68 mismatches (average diff: 0.123)
  [4]  0.201 - 0.0866 == 0.115
  [7]  0.201 - 0.0866 == 0.115
  [10] 0.268 - 0.1155 == 0.153
  [16] 0.201 - 0.0866 == 0.115
  [17] 0.106 - 0.0000 == 0.106
  [18] 0.141 - 0.0000 == 0.141
  [19] 0.106 - 0.0000 == 0.106
  [23] 0.201 - 0.0866 == 0.115
  [27] 0.201 - 0.0866 == 0.115
  ...
  
  == testthat results  ===========================================================
  [ OK: 88 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 1 ]
  1. Failure: step_tfidf works as intended (@test-tfidf.R#44) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.9Mb
    libs      2.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc          1.0Mb
    libs         2.2Mb
    references   1.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/theseus.Rcheck/00install.out' for details.
Running 'testthat.R' [18s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidygeocoder)
  > 
  > test_check("tidygeocoder")
  -- 3. Error: (unknown) (@test-geocode.R#2)  ------------------------------------
  Internal error: Trace data is not square.
  Backtrace:
    1. testthat::test_check("tidygeocoder")
    2. testthat:::test_package_dir(...)
    3. testthat::test_dir(...)
    4. testthat:::test_files(...)
   10. base::lapply(...)
   11. testthat:::FUN(X[[i]], ...)
   17. testthat::source_file(...)
   18. testthat:::test_code(NULL, exprs, env)
   27. [ base::eval(...) ] with 1 more call
   29. testthat::test_that(...)
       ...
   40. testthat:::o_apply(...)
   41. base::lapply(objects, function(x) x[[method]](...))
   42. testthat:::FUN(X[[i]], ...)
   43. x[[method]](...)
   47. testthat:::failure_summary(result, self$n_fail)
   50. testthat:::format.expectation(x)
   51. testthat:::format_with_trace(x)
   53. rlang:::format.rlang_trace(...)
   54. rlang:::trace_format_branch(x, max_frames, dir, srcrefs)
   55. rlang:::branch_uncollapse_pipe(trace)
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Error: geocode default colnames (@test-geocode.R#3) 
  2. Error: geocode default colnames (@test-geocode.R#2) 
  3. Error: (unknown) (@test-geocode.R#2) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 23.2Mb
  sub-directories of 1Mb or more:
    examples  19.5Mb
    include    3.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/treeDA.Rcheck/00install.out' for details.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    4.3Mb
    libs   2.0Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs  11.4Mb
Found the following significant warnings:
  libqhull/rboxlib.c:351:5: warning: 'strncat' output may be truncated copying between 0 and 199 bytes from a string of length 199 [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/TukeyRegion.Rcheck/00install.out' for details.
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    doc         6.9Mb
    dummydata   1.4Mb
    libs        4.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.6Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.6Mb
    libs   2.9Mb
Found the following significant warnings:
  gen_uuid.c:309:11: warning: ordered comparison of pointer with integer zero [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/uuid.Rcheck/00install.out' for details.
File 'uuid/libs/i386/uuid.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'gen_uuid.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'gen_uuid.o'
File 'uuid/libs/x64/uuid.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'gen_uuid.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'gen_uuid.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 25.0Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  23.2Mb
Found the following significant warnings:
  include/rapidjson/document.h:1952:24: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'rapidjson::GenericValue<rapidjson::UTF8<> >::Member' {aka 'struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::MemoryPoolAllocator<> >'} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'class rapidjson::GenericValue<rapidjson::UTF8<> >' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  include/rapidjson/document.h:1952:24: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>::Member' {aka 'struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::CrtAllocator>'} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'class rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/validatejsonr.Rcheck/00install.out' for details.
installed size is 79.7Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    gdal      3.8Mb
    libs     69.4Mb
    proj      5.0Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   8.7Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc           4.3Mb
    docjs         1.3Mb
    htmlwidgets   3.9Mb
Error(s) in re-building vignettes:
--- re-building 'vignette_apartments.Rmd' using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Welcome to DALEX (version: 1.0).
Find examples and detailed introduction at: https://pbiecek.github.io/ema/
Additional features will be available after installation of: iBreakDown, ggpubr.
Use 'install_dependencies()' to get all suggested dependencies

Attaching package: 'DALEX'

The following object is masked from 'package:dplyr':

    explain

randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.

Attaching package: 'randomForest'

The following object is masked from 'package:ggplot2':

    margin

The following object is masked from 'package:dplyr':

    combine


Attaching package: 'ingredients'

The following object is masked from 'package:DALEX':

    feature_importance

Quitting from lines 81-82 (vignette_apartments.Rmd) 
Error: processing vignette 'vignette_apartments.Rmd' failed with diagnostics:
could not find function "theme_drwhy_colors"
--- failed re-building 'vignette_apartments.Rmd'

SUMMARY: processing the following file failed:
  'vignette_apartments.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Error(s) in re-building vignettes:
--- re-building 'wCorrArguments.Rmd' using rmarkdown
Loading required package: knitr
Loading required package: wCorr
wCorr v1.9.1

Loading required package: lattice
Loading required package: captioner
! Package pdftex.def Error: File `D:/RCompile/CRANpkg/local/4.0gcc8/wCorr.Rchec
k/vign_test/wCorr/vignettes/wCorrArguments_files/figure-latex/ML\%20RMSE\%20plo
t-1.pdf' not found.

Error: processing vignette 'wCorrArguments.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.0gcc8/wCorr.Rcheck/vign_test/wCorr/vignettes/wCorrArguments.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See wCorrArguments.log for more info.
--- failed re-building 'wCorrArguments.Rmd'

--- re-building 'wCorrFormulas.Rmd' using rmarkdown
Loading required package: wCorr
wCorr v1.9.1

Loading required package: lattice
Loading required package: captioner
! Package pdftex.def Error: File `D:/RCompile/CRANpkg/local/4.0gcc8/wCorr.Rchec
k/vign_test/wCorr/vignettes/wCorrFormulas_files/figure-latex/bias\%20Versus\%20
rho-1.pdf' not found.

Error: processing vignette 'wCorrFormulas.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.0gcc8/wCorr.Rcheck/vign_test/wCorr/vignettes/wCorrFormulas.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See wCorrFormulas.log for more info.
--- failed re-building 'wCorrFormulas.Rmd'

SUMMARY: processing the following files failed:
  'wCorrArguments.Rmd' 'wCorrFormulas.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    doc   11.9Mb
    libs   2.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   2.2Mb
Found the following significant warnings:
  tabix/razf.c:188:2: warning: 'strncpy' output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/WhopGenome.Rcheck/00install.out' for details.
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/x13binary.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Found the following significant warnings:
  RSDTD.c:298:23: warning: passing argument 2 of 'xmlHashScan' from incompatible pointer type [-Wincompatible-pointer-types]
  RSDTD.c:372:23: warning: passing argument 2 of 'xmlHashScan' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/XML.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    include   3.4Mb
    libs      2.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    libs   2.4Mb
Documented arguments not in \usage in documentation object 'summary':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘annual-maps.Rmd’ using rmarkdown
Some values in the specified facet_geo column 'BUYER_STATE' do not
  match the 'code' column of the specified grid and will be removed:
  AE, GU, MP, PR, PW, VI
--- finished re-building ‘annual-maps.Rmd’

--- re-building ‘county-analysis.Rmd’ using rmarkdown
Joining, by = c("year", "countyfips")
Quitting from lines 121-137 (county-analysis.Rmd) 
Error: processing vignette 'county-analysis.Rmd' failed with diagnostics:
Can't join on 'year' x 'year' because of incompatible types (character / integer)
--- failed re-building ‘county-analysis.Rmd’

--- re-building ‘per-capita-pharmacies.Rmd’ using rmarkdown
--- finished re-building ‘per-capita-pharmacies.Rmd’

SUMMARY: processing the following file failed:
  ‘county-analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
Dependence on R version ‘3.4.2’ not with patchlevel 0
Found the following significant warnings:
  pa.c:247:2: warning: initialization of ‘struct audio_instance * (*)(struct SEXPREC *, float,  int)’ from incompatible pointer type ‘void * (*)(struct SEXPREC *, float,  int)’ [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Blasso.cpp:451:53: warning: ‘*<unknown>.Blasso::icept’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/bayesCL.Rcheck/00install.out’ for details.
Dependence on R version ‘3.4.1’ not with patchlevel 0
Package suggested but not available for checking: ‘pcadapt’
Running ‘test-all.R’ [22s/71s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check('bold')
  Loading required package: bold
  ── 1. Failure: bold_identify_parents: catch wrong type param inputs (@test-bold_
  `bold_identify_parents(ww[[1]][1, ], tax_rank = 5)` threw an error with unexpected message.
  Expected match: "tax_rank must be of class character"
  Actual message: "Recv failure: Connection reset by peer"
  Backtrace:
    1. testthat::expect_error(...)
    7. bold:::bold_identify_parents.data.frame(ww[[1]][1, ], tax_rank = 5)
    9. bold:::bold_identify_parents.list(...)
   11. base::lapply(...)
   12. bold:::FUN(X[[i]], ...)
   13. bold::bold_tax_name(w, ...)
   14. base::lapply(...)
   15. bold:::FUN(X[[i]], ...)
   16. bold:::get_response(...)
   17. cli$get(query = args, ...)
   18. private$make_request(rr)
   19. crul:::crul_fetch(opts)
   20. curl::curl_fetch_memory(x$url$url, handle = x$url$handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 43 | SKIPPED: 29 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: bold_identify_parents: catch wrong type param inputs (@test-bold_identify_parents.R#52) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘cobalt-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bal.tab.mimids
> ### Title: Balance Statistics for MatchThem Objects
> ### Aliases: bal.tab.mimids bal.tab.wimids
> ### Keywords: tables
> 
> ### ** Examples
> 
> library(MatchThem)
Loading required package: MatchIt

Attaching package: ‘MatchIt’

The following object is masked from ‘package:cobalt’:

    lalonde

Loading required package: WeightIt
> library(mice)

Attaching package: ‘mice’

The following objects are masked from ‘package:MatchThem’:

    complete, pool

The following objects are masked from ‘package:base’:

    cbind, rbind

> data("lalonde_mis", package = "cobalt")
> 
> #Imputing the missing data
> imp <- mice(lalonde_mis, m = 5)

 iter imp variable
  1   1  married  re74  re75
  1   2  married  re74  re75
  1   3  married  re74  re75
  1   4  married  re74  re75
  1   5  married  re74  re75
  2   1  married  re74  re75
  2   2  married  re74  re75
  2   3  married  re74  re75
  2   4  married  re74  re75
  2   5  married  re74  re75
  3   1  married  re74  re75
  3   2  married  re74  re75
  3   3  married  re74  re75
  3   4  married  re74  re75
  3   5  married  re74  re75
  4   1  married  re74  re75
  4   2  married  re74  re75
  4   3  married  re74  re75
  4   4  married  re74  re75
  4   5  married  re74  re75
  5   1  married  re74  re75
  5   2  married  re74  re75
  5   3  married  re74  re75
  5   4  married  re74  re75
  5   5  married  re74  re75
> 
> #Matching using within-imputation propensity scores
> mt.out1 <- matchthem(treat ~ age + educ + race + 
+                        married + nodegree + re74 + re75, 
+                        data = imp, approach = "within")
Error in mice::is.mids(object) : 
  argument "object" is missing, with no default
Calls: matchthem ... complete.mids -> <Anonymous> -> complete.mids -> <Anonymous>
Execution halted
Running examples in ‘cptec-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: condicoes_tempo
> ### Title: Data frame containing "tempo" descriptions
> ### Aliases: condicoes_tempo
> ### Keywords: brazil forecast weather
> 
> ### ** Examples
> 
> condicoes_tempo()
Error in open.connection(x, "rb") : 
  Timeout was reached: [servicos.cptec.inpe.br] Resolving timed out after 10000 milliseconds
Calls: condicoes_tempo -> <Anonymous> -> read_html.default
Execution halted
Package suggested but not available for checking: ‘profdpm’
Found the following significant warnings:
  clipper.cpp:721:34: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct ClipperLib::TEdge’; use assignment or value-initialization instead [-Wclass-memaccess]
  dbfopen.c:1346:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:1328:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:879:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopen.c:1693:9: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
  dbfopen.c:2065:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/dggridR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/dpglasso.Rcheck/00install.out’ for details.
Rd file 'mosaicPermDialog.Rd':
  \usage lines wider than 90 characters:
                                                             displayPermCommand=TRUE, extendedOptions=TRUE)
     setMosaicPalette(palettename,reverse=FALSE)                                                     

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Killed
Rd file 'POICalc.Rd':
  \examples lines wider than 100 characters:
        irisPOI@wordsInQuery <- c('high.Sepal.Length', 'high.Sepal.Width', 'high.Petal.Length', 'high.Petal.Width',
                                  'low.Sepal.Length', 'low.Sepal.Width', 'low.Petal.Length', 'low.Petal.Width')

Rd file 'POIcoords_-.Rd':
  \examples lines wider than 100 characters:
        irisPOI@wordsInQuery <- c('high.Sepal.Length', 'high.Sepal.Width', 'high.Petal.Length', 'high.Petal.Width',
                                  'low.Sepal.Length', 'low.Sepal.Width', 'low.Petal.Length', 'low.Petal.Width')

Rd file 'plotPOI.Rd':
  \examples lines wider than 100 characters:
          graphPOI@docs <- matrix(c(seq(1:nrow(graphPOI@objeto)), seq(1:nrow(graphPOI@objeto))), ncol = 2)
        graphPOI@objeto <- graphPOI@objeto <- rbind(c(0,.05), c(.05,0), c(0,-.05), c(-.05,0) ,round(circulo(0,0,.3,PLOT = FALSE),2))
         1 - (max(USArrests[,4]) - USArrests[,4]) / (max(max(USArrests[,4]) - USArrests[,4])),                                               ... [TRUNCATED]
        usaPOI@wordsInQuery <- c(paste('High', names(USArrests[,c(1,2,4)])), paste('Low', names(USArrests[,c(1,2,4)])))

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  RngStream.c:275:7: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/freeknotsplines.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_41_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gglasso.Rcheck/00install.out’ for details.
Warning: no function found corresponding to methods exports from ‘gpclib’ for: ‘coerce’, ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
read.polyfile: no visible global function definition for ‘as’
write.polyfile: no visible global function definition for ‘is’
write.polyfile: no visible global function definition for ‘as’
[,gpc.poly: no visible global function definition for ‘new’
append.poly,gpc.poly-gpc.poly: no visible global function definition
  for ‘new’
coerce,data.frame-gpc.poly: no visible global function definition for
  ‘as’
coerce,list-gpc.poly: no visible global function definition for ‘as’
coerce,matrix-gpc.poly: no visible global function definition for ‘new’
coerce,numeric-gpc.poly: no visible global function definition for
  ‘new’
coerce,numeric-gpc.poly.nohole: no visible global function definition
  for ‘new’
intersect,gpc.poly-gpc.poly: no visible global function definition for
  ‘as’
intersect,gpc.poly-gpc.poly: no visible global function definition for
  ‘new’
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  ‘as’
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  ‘new’
tristrip,gpc.poly: no visible global function definition for ‘as’
union,gpc.poly-gpc.poly: no visible global function definition for ‘as’
union,gpc.poly-gpc.poly: no visible global function definition for
  ‘new’
Undefined global functions or variables:
  as is new
Consider adding
  importFrom("methods", "as", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Rd file 'N2.cohen.kappa.Rd':
  \examples lines wider than 100 characters:
       N2.cohen.kappa(c(0.2, 0.25, 0.55), k1=0.6, k0=0.4)                                                            

These lines will be truncated in the PDF manual.
Dependence on R version ‘3.4.4’ not with patchlevel 0
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:182:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘value_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:896:16: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:196:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lolog.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘MLTA_Gollini_2019.Rmd’ using rmarkdown
Loading required package: MASS
Loading required package: ergm
Loading required package: network
network: Classes for Relational Data
Version 1.16.0 created on 2019-11-30.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
                    Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Martina Morris, University of Washington
                    Skye Bender-deMoll, University of Washington
 For citation information, type citation("network").
 Type help("network-package") to get started.


ergm: version 3.10.4, created on 2019-06-10
Copyright (c) 2019, Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Carter T. Butts, University of California -- Irvine
                    Steven M. Goodreau, University of Washington
                    Pavel N. Krivitsky, University of Wollongong
                    Martina Morris, University of Washington
                    with contributions from
                    Li Wang
                    Kirk Li, University of Washington
                    Skye Bender-deMoll, University of Washington
                    Chad Klumb
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("ergm").

NOTE: Versions before 3.6.1 had a bug in the implementation of the bd()
constriant which distorted the sampled distribution somewhat. In
addition, Sampson's Monks datasets had mislabeled vertices. See the
NEWS and the documentation for more details.

NOTE: Some common term arguments pertaining to vertex attribute and
level selection have changed in 3.10.0. See terms help for more
details. Use 'options(ergm.term=list(version="3.9.4"))' to use old
behavior.

Killed
SelectedInput:
  function(...)
SelectedInput.formula:
  function(..., data, control, metrics, stat, cutoff)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  Manifolds/SmartSpace.cpp:147:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ManifoldOptim.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [10m/11m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(matrixTests)
  > 
  > test_check("matrixTests")
  Killed
Dependence on R version ‘3.4.3’ not with patchlevel 0
Documented arguments not in \usage in documentation object 'miss_summary':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
calc.stress: no visible global function definition for ‘sd’
opscale: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Documented arguments not in \usage in documentation object 'opscale':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Rd file 'dmes.Rd':
  \examples lines wider than 100 characters:
     > #cf. Efron, B. & Tibshirani (1993). An Introduction to the Bootstrap. New York/London: Chapman&Hall.
     > #Ruscio, J. & Mullen, T. (2012). Confidence Intervals for the Probability of Superiority Effect Size Measure and the Area Under a Rec ... [TRUNCATED]

Rd file 'orddom_f.Rd':
  \examples lines wider than 100 characters:
     orddom_f(con_pre,ex_pre,alpha=0.025,decimalpt=",",description="EXP 01: Between groups at time 01")   
     orddom_f(con_post,ex_post,alpha=0.025,decimalpt=",",description="EXP 01: Between groups at time 02") 
     orddom_f(ex_pre,ex_post,alpha=0.025,paired=TRUE,decimalpt=",",description="EXP 01: Within exp 01 to 02") 
     orddom_f(con_pre,con_post,alpha=0.025,paired=TRUE,decimalpt=",",description="EXP 01: Within con 01 to 02") 

These lines will be truncated in the PDF manual.
Rd file 'CalGIF.Rd':
  \examples lines wider than 100 characters:
     ###calculate the global influence factor (GIF) by using the random walk with restart (RWR) algorithm###
     #Each element is the GIF score and whose name correspond to gene symbol in the gene expression data. 
     #Each element is the GIF score and whose name correspond to gene symbol in the gene expression data. 

Rd file 'PAGI.Main.Rd':
  \examples lines wider than 100 characters:
     #Its columns include "Gene number in the (sorted) pathway", "gene symbol from the gene express data",
     #"location of the gene in the sorted gene list", "the T-score of gene between two biological states",
     #Its columns include "Gene number in the (sorted) pathway", "gene symbol from the gene express data",
     #"location of the gene in the sorted gene list", "the T-score of gene between two biological states",

These lines will be truncated in the PDF manual.
Running ‘testthat.R’ [53s/56s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(panelr)
  Loading required package: lme4
  Loading required package: Matrix
  
  Attaching package: 'panelr'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("panelr")
  ── 1. Error: (unknown) (@test_wbm.R#283)  ──────────────────────────────────────
  could not find function "arma"
  Backtrace:
   1. panelr::wbm_stan(...)
   2. brms::make_stancode(...)
   4. brms:::validate_formula.default(...)
   6. brms:::validate_formula.brmsformula(bf(formula), ...)
   7. brms:::validate_autocor(autocor)
   8. brms:::parse_ac(autocor)
   9. base::lapply(out, eval2)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 271 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 1 ]
  1. Error: (unknown) (@test_wbm.R#283) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [9s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(phrasemachine)
  phrasemachine: Simple Phrase Extraction
  Version 1.1.2 created on 2017-05-29.
  copyright (c) 2016, Matthew J. Denny, Abram Handler, Brendan O'Connor.
  Type help('phrasemachine') or
  vignette('getting_started_with_phrasemachine') to get started.
  Development website: https://github.com/slanglab/phrasemachine
  > 
  > test_check("phrasemachine")
  ── 1. Error: See if tagging five documents works, and if coarsening works (@test
  unused argument (alist())
  Backtrace:
   1. documents[1:5, ]
  
  ── 2. Error: See if extractor works (@test_extract_phrases.R#7)  ───────────────
  unused argument (alist())
  Backtrace:
   1. documents[1:5, ]
  
  Currently tagging document 1 of 1 
  Extracting phrases from document 1 of 1 
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 10 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: See if tagging five documents works, and if coarsening works (@test_POS_tag_documents.R#7) 
  2. Error: See if extractor works (@test_extract_phrases.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Rd file 'envelopeArea_and_Perimeter.Rd':
  \examples lines wider than 100 characters:
     cat("envelope area = ", envelopeStats["area"], " perimeter = ", envelopeStats["perimeter"],"\n")        
     cat("circle area = ", pi * r^2, " = ", sum(pi * r^2), "\ncircle perimenter = ",  2 * pi * r, " = ",  2 * pi * sum(r), "\n")

Rd file 'generateEnvelope.Rd':
  \examples lines wider than 100 characters:
     cat("envelope area = ", envelopeStats["area"], " perimeter = ", envelopeStats["perimeter"],"\n")        
     cat("circle area = ", pi * r^2, " = ", sum(pi * r^2), "\ncircle perimenter = ",  2 * pi * r, " = ",  2 * pi * sum(r), "\n")
     grid.polygon(envelopeXY[,1], envelopeXY[,2], gp=gpar(fill="pink", col="transparent", lwd=5), default.units="npc")

Rd file 'tangentLine.Rd':
  \examples lines wider than 100 characters:
                     tangent <- tangentLine(centers[1,], centers[2,], r0, r[2], k=k)  # compute coefficients for the tangent line, if NA, th ... [TRUNCATED]
                             grid.abline(-tangent["c"] / tangent["b"], -tangent["a"] / tangent["b"], gp=gpar(col="blue", lwd=ii), units="npc ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Rd file 'ppoistweedie.Rd':
  \examples lines wider than 100 characters:
     layout.show(1)                                                                                                                          ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘ABE.Rmd’ using rmarkdown
--- finished re-building ‘ABE.Rmd’

--- re-building ‘DP.Rmd’ using rmarkdown
--- finished re-building ‘DP.Rmd’

--- re-building ‘NI.Rmd’ using rmarkdown
--- finished re-building ‘NI.Rmd’

--- re-building ‘PA.Rmd’ using rmarkdown
--- finished re-building ‘PA.Rmd’

--- re-building ‘RSABE.Rmd’ using rmarkdown
Killed
--- re-building ‘vignette.Rmd’ using rmarkdown
--- finished re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘RSABE.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(preText)
  preText: Diagnostics to Assess the Effects of Text Preprocessing Decisions
  Version 0.6.3 created on 2018-01-12.
  copyright (c) 2017, Matthew J. Denny, Penn State University
                      Arthur Spirling, NYU
  Type vignette('getting_started_with_preText') to get started.
  Development website: https://github.com/matthewjdenny/preText
  > 
  > test_check("preText")
  ── 1. Error: Small example works (@test_factorial_preprocessing.R#6)  ──────────
  unused argument (alist())
  Backtrace:
   1. documents[1:10, ]
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Small example works (@test_factorial_preprocessing.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘prettymapr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mergebbox
> ### Title: Combine bounding boxes
> ### Aliases: mergebbox
> 
> ### ** Examples
> 
> box1 <- searchbbox("wolfville, ns")
Using default API key for pickpoint.io. If batch geocoding, please get your own (free) API key at https://app.pickpoint.io/sign-up
Error: $ operator is invalid for atomic vectors
Execution halted
Unexported objects imported by ':::' calls:
  ‘pch:::pch.fit’ ‘pch:::predF.pch’ ‘pch:::sim.pch’
  See the note in ?`:::` about the use of this operator.
Rd file 'predict.randomGLM.Rd':
  \examples lines wider than 100 characters:
     RGLM = randomGLM(xTrain, yTrain, nCandidateCovariates=ncol(xTrain), nBags=30, keepModels = TRUE, nThreads = 1)

Rd file 'randomGLM.Rd':
  \usage lines wider than 90 characters:
       # Multi-level classification options - only apply to classification with multi-level response
  \examples lines wider than 100 characters:
     RGLM = randomGLM(xTrain, yTrain, xTest, classify=FALSE, nCandidateCovariates=ncol(xTrain), nBags=10, 

Rd file 'thinRandomGLM.Rd':
  \examples lines wider than 100 characters:
     RGLM = randomGLM(xTrain, yTrain, nCandidateCovariates=ncol(xTrain), nBags=30, keepModels = TRUE, nThreads = 1)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  avc_binwr.c:166:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:173:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:180:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:187:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:1453:29: warning: ‘%4.4d’ directive writing between 4 and 10 bytes into a region of size 5 [-Wformat-overflow=]
  avc_binwr.c:1553:28: warning: ‘%s’ directive writing up to 39 bytes into a region of size between 38 and 77 [-Wformat-overflow=]
  avc_e00write.c:386:30: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  avc_e00write.c:387:30: warning: ‘-ID’ directive writing 3 bytes into a region of size between 1 and 40 [-Wformat-overflow=]
  avc_e00write.c:401:61: warning: ‘%s’ directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:397:61: warning: ‘%s’ directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:409:39: warning: ‘%s’ directive writing up to 39 bytes into a region of size 33 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RArcInfo.Rcheck/00install.out’ for details.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rblpapi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rreadsdpa.c:608:15: warning: ‘strncpy’ output may be truncated copying 3999 bytes from a string of length 3999 [-Wstringop-truncation]
  Rreadsdpa.c:1041:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  Rreadsdpa.c:1042:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:164:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:165:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rdsdp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  compile.cc:292:69: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class re2::Prog::Inst’; use assignment or value-initialization instead [-Wclass-memaccess]
  regexp.cc:343:33: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
  regexp.cc:344:32: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/re2r.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘rosm.Rmd’ using rmarkdown
Using default API key for pickpoint.io. If batch geocoding, please get your own (free) API key at https://app.pickpoint.io/sign-up
Quitting from lines 35-38 (rosm.Rmd) 
Error: processing vignette 'rosm.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building ‘rosm.Rmd’

SUMMARY: processing the following file failed:
  ‘rosm.Rmd’

Error: Vignette re-building failed.
Execution halted
Rd file 'C.FRNN.FRST.Rd':
  \examples lines wider than 100 characters:
                     type.relation = c("tolerance", "eq.1"), t.implicator = "lukasiewicz")                                                   ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  bgc_hmm.c:241:31: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
  rph_tfbs.c:371:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:351:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:819:5: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rphast.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RVowpalWabbit.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/scio.Rcheck/00install.out’ for details.
plot.srafit: no visible global function definition for ‘layout’
plot.srafit: no visible global function definition for ‘par’
sraData : vartruncGauss : ff: no visible global function definition for
  ‘dnorm’
sraData : vartruncGauss : ff: no visible global function definition for
  ‘pnorm’
sraData : vartruncGauss: no visible global function definition for
  ‘uniroot’
sraPlotMean: no visible global function definition for ‘axis’
sraPlotMean: no visible global function definition for ‘points’
sraPlotMean: no visible global function definition for ‘lines’
sraPlotMeanResid: no visible global function definition for ‘axis’
sraPlotMeanResid: no visible global function definition for ‘abline’
sraPlotMeanResid: no visible global function definition for ‘points’
sraPlotVar: no visible global function definition for ‘axis’
sraPlotVar: no visible global function definition for ‘points’
sraPlotVar: no visible global function definition for ‘lines’
sraPlotVarResid: no visible global function definition for ‘axis’
sraPlotVarResid: no visible global function definition for ‘abline’
sraPlotVarResid: no visible global function definition for ‘points’
sraPlotlegend: no visible global function definition for ‘legend’
sraStartingvalues : sraStartingvalues.mu0: no visible global function
  definition for ‘rnorm’
sraStartingvalues : sraStartingvalues.logvarA0: no visible global
  function definition for ‘rnorm’
sraStartingvalues : sraStartingvalues.logvarE0: no visible global
  function definition for ‘rnorm’
sraStartingvalues: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis dnorm layout legend lines par pnorm points rnorm uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "layout", "legend", "lines",
             "par", "points")
  importFrom("stats", "dnorm", "pnorm", "rnorm", "uniroot")
to your NAMESPACE file.
Found the following significant warnings:
  computeQ.cpp:75:15: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
  computeQ.cpp:134:15: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
  computeQ.cpp:142:17: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/strum.Rcheck/00install.out’ for details.
Rd file 'SyNet-package.rd':
  \examples lines wider than 100 characters:
       # Run NAM method on the previously inferred sympatry network                                           

Rd file 'acshgral.rd':
  \examples lines wider than 100 characters:
       #Display relationships into a parenthetical notation. You can track the indices of the species in the

Rd file 'gridinfer.rd':
  \examples lines wider than 100 characters:
       #are nested inside it. In a network analysis this kind of element will behave as intermediary node.  

Rd file 'reweight.rd':
  \examples lines wider than 100 characters:
       plot(unlist(ej),unlist(reweight(ej)), xlab = "Input matrix", ylab = "Reweighted matrix", main = "First reweighting")

These lines will be truncated in the PDF manual.
Running ‘testthat.R’ [14s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(textrecipes)
  Loading required package: recipes
  Loading required package: dplyr
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  
  Attaching package: 'recipes'
  
  The following object is masked from 'package:stats':
  
      step
  
  > 
  > test_check("textrecipes")
  ── 1. Failure: step_tfidf works as intended (@test-tfidf.R#44)  ────────────────
  as.matrix(rec_answer) not equal to as.matrix(manual_answer).
  29/68 mismatches (average diff: 0.123)
  [4]  0.201 - 0.0866 == 0.115
  [7]  0.201 - 0.0866 == 0.115
  [10] 0.268 - 0.1155 == 0.153
  [16] 0.201 - 0.0866 == 0.115
  [17] 0.106 - 0.0000 == 0.106
  [18] 0.141 - 0.0000 == 0.141
  [19] 0.106 - 0.0000 == 0.106
  [23] 0.201 - 0.0866 == 0.115
  [27] 0.201 - 0.0866 == 0.115
  ...
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 88 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 1 ]
  1. Failure: step_tfidf works as intended (@test-tfidf.R#44) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [13s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidytext)
  > 
  > test_check("tidytext")
  ── 3. Error: (unknown) (@test-corpus-tidiers.R#33)  ────────────────────────────
  Internal error: Trace data is not square.
  Backtrace:
    1. testthat::test_check("tidytext")
    2. testthat:::test_package_dir(...)
    3. testthat::test_dir(...)
    4. testthat:::test_files(...)
   10. base::lapply(...)
   11. testthat:::FUN(X[[i]], ...)
   17. testthat::source_file(...)
   18. testthat:::test_code(NULL, exprs, env)
   27. [ base::eval(...) ] with 1 more call
   29. testthat::test_that(...)
       ...
   40. testthat:::o_apply(...)
   41. base::lapply(objects, function(x) x[[method]](...))
   42. testthat:::FUN(X[[i]], ...)
   43. x[[method]](...)
   47. testthat:::failure_summary(result, self$n_fail)
   50. testthat:::format.expectation(x)
   51. testthat:::format_with_trace(x)
   53. rlang:::format.rlang_trace(...)
   54. rlang:::trace_format_branch(x, max_frames, dir, srcrefs)
   55. rlang:::branch_uncollapse_pipe(trace)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 274 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
  1. Error: Can tidy corpus from quanteda using accessor functions (@test-corpus-tidiers.R#38) 
  2. Error: Can tidy corpus from quanteda using accessor functions (@test-corpus-tidiers.R#33) 
  3. Error: (unknown) (@test-corpus-tidiers.R#33) 
  
  Error: testthat unit tests failed
  Execution halted
Documented arguments not in \usage in documentation object 'tags<-':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  libqhull/rboxlib.c:351:5: warning: ‘strncat’ output may be truncated copying between 0 and 199 bytes from a string of length 199 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TukeyRegion.Rcheck/00install.out’ for details.
Found the following significant warnings:
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<> >::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::MemoryPoolAllocator<> >’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<> >’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::CrtAllocator>’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/validatejsonr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  tabix/razf.c:188:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/WhopGenome.Rcheck/00install.out’ for details.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/x13binary.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘aaSEA_Documentation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in RColorBrewer::brewer.pal(N, "Set2") :
  n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors

Warning in RColorBrewer::brewer.pal(N, "Set2") :
  n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors

Quitting from lines 90-91 (aaSEA_Documentation.Rmd) 
Error: processing vignette 'aaSEA_Documentation.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘aaSEA_Documentation.Rmd’

SUMMARY: processing the following file failed:
  ‘aaSEA_Documentation.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    data       2.8Mb
    pictures   2.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R       1.5Mb
    data    1.3Mb
    files   1.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    doc   3.0Mb
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    data  20.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    4.8Mb
    help   1.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   2.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       2.9Mb
    extdata   1.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ahn.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 66-67 (ahn.Rmd) 
Error: processing vignette 'ahn.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘ahn.Rmd’

SUMMARY: processing the following file failed:
  ‘ahn.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘rsvg’
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    extdata  12.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown_notangle
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 49-64 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
--- failed re-building ‘Introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   3.4Mb
Packages suggested but not available for checking: 'ssh', 'aws.s3'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   2.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    testdata   5.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘antares.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘antares.Rmd’

--- re-building ‘antaresH5.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 38-72 (antaresH5.Rmd) 
Error: processing vignette 'antaresH5.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘antaresH5.Rmd’

SUMMARY: processing the following file failed:
  ‘antaresH5.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘kebabs’
Error(s) in re-building vignettes:
  ...
--- re-building ‘apcluster.Rnw’ using knitr

Attaching package: 'apcluster'

The following object is masked from 'package:stats':

    heatmap

Quitting from lines 387-408 (apcluster.Rnw) 
Error: processing vignette 'apcluster.Rnw' failed with diagnostics:
object 'apres2c' not found
--- failed re-building ‘apcluster.Rnw’

SUMMARY: processing the following file failed:
  ‘apcluster.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.3Mb
Package suggested but not available for checking: ‘qCBA’
Error(s) in re-building vignettes:
  ...
--- re-building ‘arkhe.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot5e4a5f915efe.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot5e4a5f915efe.png': No such file or directory
Quitting from lines 46-70 (arkhe.Rmd) 
Error: processing vignette 'arkhe.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘arkhe.Rmd’

SUMMARY: processing the following file failed:
  ‘arkhe.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    help   1.1Mb
installed size is  5.9Mb
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    data      1.1Mb
    extdata   3.8Mb
installed size is  5.1Mb
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    testdata   4.2Mb
Package suggested but not available for checking: ‘REBayes’
Error(s) in re-building vignettes:
  ...
--- re-building ‘asmapvignette.Rnw’ using knitr
Warning in summary.cross(cross) :
  Some markers at the same position on chr 1B1,1D,2B,2D1,3A,3B,3D,4A,5A,5B,5D,6D,7A,7B,7D; use jittermap().
Warning in summary.cross(cross) :
  Some chromosomes > 1000 cM in length; there may be a problem with the genetic map.
  (Perhaps it is in basepairs?)
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7,L.8,L.9; use jittermap().
Warning in heatMap(mapBC6, chr = c("L.3", "L.5", "L.8", "L.9"), lmax = 70) :
  Running est.rf.
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7; use jittermap().
installed size is  5.4Mb
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    full_doc   2.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Data_Analysis_with_augmentedRCBD.Rmd’ using rmarkdown_notangle
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 57-76 (Data_Analysis_with_augmentedRCBD.Rmd) 
Error: processing vignette 'Data_Analysis_with_augmentedRCBD.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
--- failed re-building ‘Data_Analysis_with_augmentedRCBD.Rmd’

SUMMARY: processing the following file failed:
  ‘Data_Analysis_with_augmentedRCBD.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 73.8Mb
  sub-directories of 1Mb or more:
    java  73.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   3.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘use-ballr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'janitor'

The following objects are masked from 'package:stats':

    chisq.test, fisher.test

Quitting from lines 62-63 (use-ballr.Rmd) 
Error: processing vignette 'use-ballr.Rmd' failed with diagnostics:
Timeout was reached: [www.basketball-reference.com] Operation timed out after 10063 milliseconds with 0 out of 0 bytes received
--- failed re-building ‘use-ballr.Rmd’

SUMMARY: processing the following file failed:
  ‘use-ballr.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘article2-vignette.Rnw’ using knitr
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-8'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.0Mb
    libs   1.8Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   4.2Mb
Package required but not available: ‘Rcsdp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    libs  20.3Mb
Running ‘testthat.R’ [23s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bcgam)
  Loading required package: nimble
  nimble version 0.9.0 is loaded.
  For more information on NIMBLE and a User Manual,
  please visit http://R-nimble.org.
  
  Attaching package: 'nimble'
  
  The following object is masked from 'package:stats':
  
      simulate
  
  > 
  > test_check("bcgam")
  thin = 1: tau, betalpha, sigma, eta
  ── 1. Error: (unknown) (@testthat.R#3)  ────────────────────────────────────────
  Failed to create the shared library.
  Backtrace:
   1. bcgam::bcgam(...)
   2. bcgam:::bcgam.fit(...)
   3. nimble::compileNimble(gaus)
   4. project$compileModel(units[[i]], control = control, showCompilerOutput = showCompilerOutput)
   5. cppProj$compileFile(compileList, showCompilerOutput)
   6. nimble:::compileDynamicRegistrations(showCompilerOutput = showCompilerOutput)
   7. nimble:::compileStaticCode(dllName, cppName, showCompilerOutput)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: (unknown) (@testthat.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Bclim.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.7Mb
Package suggested but not available for checking: ‘BRugs’
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Package suggested but not available for checking: ‘lumi’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Package suggested but not available for checking: ‘gifski’
Error(s) in re-building vignettes:
  ...
--- re-building ‘abcd-laagdrempelige_nederlandse_uitleg.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 53-74 (abcd-laagdrempelige_nederlandse_uitleg.Rmd) 
Error: processing vignette 'abcd-laagdrempelige_nederlandse_uitleg.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘abcd-laagdrempelige_nederlandse_uitleg.Rmd’

--- re-building ‘abcd.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘abcd.Rmd’

--- re-building ‘matrix-van-aspecten-van-de-psychologie.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘matrix-van-aspecten-van-de-psychologie.Rmd’

SUMMARY: processing the following file failed:
  ‘abcd-laagdrempelige_nederlandse_uitleg.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 124.9Mb
  sub-directories of 1Mb or more:
    include  124.9Mb
installed size is  5.9Mb
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    data   2.4Mb
    doc    1.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Removed 199 rows containing non-finite values (stat_contour).
Warning in normalizePath(f2) :
  path[1]="webshot566a54226b45.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot566a54226b45.png': No such file or directory
Quitting from lines 245-248 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘analysis.Rmd’

--- re-building ‘methodology.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘methodology.Rmd’

SUMMARY: processing the following file failed:
  ‘analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       3.1Mb
    extdata   2.5Mb
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘BioCircos.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 64-67 (BioCircos.Rmd) 
Error: processing vignette 'BioCircos.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘BioCircos.Rmd’

SUMMARY: processing the following file failed:
  ‘BioCircos.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 11.0Mb
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    doc       2.7Mb
    extdata   7.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    doc       1.4Mb
    extdata   1.7Mb
Running examples in ‘bioRad-Ex.R’ failed
The error most likely occurred in:

> ### Name: beam_profile_overlap
> ### Title: Calculate overlap between a vertical profile ('vp') of
> ###   biological scatterers and the vertical radiation profile emitted by
> ###   the radar
> ### Aliases: beam_profile_overlap
> 
> ### ** Examples
> 
> # locate example volume file:
> pvolfile <- system.file("extdata", "volume.h5", package = "bioRad")
> 
> # load the example polar volume file:
> pvol <- read_pvolfile(pvolfile)
Error in H5Fopen(file, "H5F_ACC_RDONLY", native = native) : 
  HDF5. File accessibilty. Unable to open file.
Calls: read_pvolfile ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bioRad.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building ‘bioRad.Rmd’

--- re-building ‘rad_aero_19.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Welcome to bioRad version 0.5.0
Warning: Docker daemon not found
Warning: bioRad functionality requiring Docker has been disabled

To enable Docker functionality, first install Docker
--- finished re-building ‘rad_aero_19.Rmd’

--- re-building ‘range_correction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 63-70 (range_correction.Rmd) 
Error: processing vignette 'range_correction.Rmd' failed with diagnostics:
HDF5. File accessibilty. Unable to open file.
--- failed re-building ‘range_correction.Rmd’

SUMMARY: processing the following file failed:
  ‘range_correction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    help   2.2Mb
Package suggested but not available for checking: ‘IHW’
Invalid maximum heap size: -Xmx4G
The specified size exceeds the maximum representable size.
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘gtools’ ‘knitr’ ‘nnet’ ‘parallel’ ‘rJava’ ‘reshape’
  ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
Missing or unexported object: ‘xgboost::predict’
Running examples in ‘blockcluster-Ex.R’ failed
The error most likely occurred in:

> ### Name: blockcluster
> ### Title: Co-Clustering Package
> ### Aliases: blockcluster
> 
> ### ** Examples
> 
> 
> ## Simple example with simulated binary data
> ## load data
> data(binarydata)
> ## usage of coclusterBinary function in its most simplest form
> out<-coclusterBinary(binarydata,nbcocluster=c(2,3))
Error(s) in re-building vignettes:
  ...
--- re-building ‘blockcluster_tutorial.Rnw’ using Sweave
Loading required package: rtkore
Loading required package: Rcpp

Attaching package: ‘rtkore’

The following object is masked from ‘package:Rcpp’:

    LdFlags

blockcluster version 4.4.3 loaded

----------------
Copyright (C)  <MODAL team @INRIA,Lille & U.M.R. C.N.R.S. 6599 Heudiasyc, UTC>
Please post questions and bugs at: <https://gforge.inria.fr/forum/forum.php?forum_id=11190&group_id=3679>


 *** caught segfault ***
address 38a566b4, cause 'memory not mapped'

 *** caught segfault ***
address 8195dc2, cause 'memory not mapped'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.0Mb
Running examples in ‘blockmodeling-Ex.R’ failed
The error most likely occurred in:

> ### Name: REGE
> ### Title: REGE - Algorithms for compiting (dis)similarities in terms of
> ###   regular equivalnece
> ### Aliases: REGE REGE.for REGE.nm.for REGE.ow REGE.ow.for REGE.ownm.for
> ###   REGD.for REGD.ow.for REGE.FC REGE.FC.ow REGD.ne.for REGD.ow.ne.for
> ###   REGE.ne.for REGE.nm.diag.for REGE.nm.ne.for REGE.ow.ne.for
> ###   REGE.ownm.diag.for REGE.ownm.ne.for
> ### Keywords: cluster graphs
> 
> ### ** Examples
> 
> n <- 20
> net <- matrix(NA, ncol = n, nrow = n)
> clu <- rep(1:2, times = c(5, 15))
> tclu <- table(clu)
> net[clu == 1, clu == 1] <- 0
> net[clu == 1, clu == 2] <- rnorm(n = tclu[1] * tclu[2], mean = 4, sd = 1) * sample(c(0, 1),
+    size = tclu[1] * tclu[2], replace = TRUE, prob = c(3/5, 2/5))
> net[clu == 2, clu == 1] <- 0
> net[clu == 2, clu == 2] <- 0
> 
> D <- REGE.for(M = net)$E # Any other REGE function can be used
> plot.mat(net, clu = cutree(hclust(d = as.dist(1 - D), method = "ward.D"),
+    k = 2))
> # REGE returns similarities, which have to be converted to
> # disimilarities
> 
> res <- optRandomParC(M = net, k = 2, rep = 10, approaches = "hom", homFun = "ss", blocks = "reg")


Starting optimization of the partiton 1 of 10 partitions.
Starting partition: 1 2 1 1 1 1 1 1 1 2 2 1 2 2 2 2 2 1 1 1 

 *** caught segfault ***
address 7d81d8dc, cause 'memory not mapped'

Traceback:
 1: optParC(M = M, clu = temppar, approaches = approaches, blocks = blocks,     useMulti = useMulti, save.initial.param = save.initial.param.opt,     ...)
 2: optRandomParC(M = net, k = 2, rep = 10, approaches = "hom", homFun = "ss",     blocks = "reg")
An irrecoverable exception occurred. R is aborting now ...
Error(s) in re-building vignettes:
  ...
--- re-building ‘BoolNet_package_vignette.Snw.Rnw’ using Sweave

Error: processing vignette 'BoolNet_package_vignette.Snw.Rnw' failed with diagnostics:
 chunk 13 
Error in net$interactions[[idx]][[functionIndices[idx]]] : 
  subscript out of bounds

--- failed re-building ‘BoolNet_package_vignette.Snw.Rnw’

SUMMARY: processing the following file failed:
  ‘BoolNet_package_vignette.Snw.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘break_caret.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: lattice
Loading required package: ggplot2
--- finished re-building ‘break_caret.Rmd’

--- re-building ‘break_glm.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘break_glm.Rmd’

--- re-building ‘break_lm.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘break_lm.Rmd’

--- re-building ‘break_randomForest.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘break_randomForest.Rmd’

Cpu Limit Exceeded - core dumped
--- re-building ‘break_ranger.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- re-building ‘break_svm.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘break_svm.Rmd’

--- re-building ‘break_xgboost.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘break_xgboost.Rmd’

SUMMARY: processing the following file failed:
  ‘break_ranger.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R     3.8Mb
    doc   2.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    bin    3.1Mb
    doc    1.3Mb
    libs   3.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   2.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘simple_plotting.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: Removed 4550 rows containing missing values (geom_path).
Quitting from lines 173-174 (simple_plotting.Rmd) 
Error: processing vignette 'simple_plotting.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘simple_plotting.Rmd’

SUMMARY: processing the following file failed:
  ‘simple_plotting.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'c3'

The following object is masked from 'package:dplyr':

    %>%

The following objects are masked from 'package:graphics':

    grid, legend

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot25611ac52086.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot25611ac52086.png': No such file or directory
Quitting from lines 56-65 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘examples.Rmd’

SUMMARY: processing the following file failed:
  ‘examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Package which this enhances but not available for checking: ‘FastRWeb’
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R        1.3Mb
    data     1.8Mb
    models   2.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘cartograflow.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 451-480 (cartograflow.Rmd) 
Error: processing vignette 'cartograflow.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘cartograflow.Rmd’

SUMMARY: processing the following file failed:
  ‘cartograflow.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
installed size is  9.9Mb
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    extdata   9.8Mb
installed size is  6.2Mb
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    doc    1.9Mb
Package suggested but not available for checking: ‘iptools’
installed size is  5.7Mb
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    data   1.0Mb
    doc    1.7Mb
    help   2.3Mb
Package suggested but not available for checking: ‘rggobi’
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Package which this enhances but not available for checking: ‘RWeka’
Error(s) in re-building vignettes:
  ...
--- re-building ‘the_clusterR_package.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 403-416 (the_clusterR_package.Rmd) 
Error: processing vignette 'the_clusterR_package.Rmd' failed with diagnostics:
std::bad_alloc
--- failed re-building ‘the_clusterR_package.Rmd’

SUMMARY: processing the following file failed:
  ‘the_clusterR_package.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.1Mb
    extdata   1.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Running-CoDiNA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 100-105 (Running-CoDiNA.Rmd) 
Error: processing vignette 'Running-CoDiNA.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
--- failed re-building ‘Running-CoDiNA.Rmd’

SUMMARY: processing the following file failed:
  ‘Running-CoDiNA.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
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    doc       3.0Mb
    extdata   2.3Mb
installed size is  5.4Mb
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    java   5.2Mb
Package suggested but not available for checking: ‘rscala’
installed size is  5.3Mb
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    doc   2.3Mb
installed size is  9.6Mb
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    data      6.5Mb
    extdata   2.8Mb
Package unavailable to check Rd xrefs: ‘fungible’
Error(s) in re-building vignettes:
  ...
--- re-building ‘chamber.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in for (i in seq_len(n)) { :
  closing unused connection 4 (http://www.camara.leg.br/SitCamaraWS/Proposicoes.asmx/ObterVotacaoProposicao?tipo=PL&numero=1992&ano=2007)
Quitting from lines 32-33 (chamber.Rmd) 
Error: processing vignette 'chamber.Rmd' failed with diagnostics:
HTTP error 500
--- failed re-building ‘chamber.Rmd’

--- re-building ‘senate.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

--- finished re-building ‘senate.Rmd’

SUMMARY: processing the following file failed:
  ‘chamber.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘cooccurNet-Ex.R’ failed
The error most likely occurred in:

> ### Name: coocnet
> ### Title: coocnet
> ### Aliases: coocnet
> 
> ### ** Examples
> 
> cooccurNetwork  = coocnet(dataFile=getexample(dataType="protein"), dataType="protein")
reading file......
completed. (10,329)
preprocess file......Error in if (pred >= memsize * alpha || ncol > 150 || (nrow > 30000 &  : 
  missing value where TRUE/FALSE needed
Calls: coocnet ... cooccur.dataprepreprocess.preprocess -> inmemoryflag
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Extending-cooccurNet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 176-178 (Extending-cooccurNet.Rmd) 
Error: processing vignette 'Extending-cooccurNet.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘Extending-cooccurNet.Rmd’

SUMMARY: processing the following file failed:
  ‘Extending-cooccurNet.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.4Mb
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    R     2.4Mb
    doc   5.9Mb
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    help   1.8Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
Package required but not available: ‘SNPRelate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 399-421 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.4Mb
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    doc   8.0Mb
installed size is  7.7Mb
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    doc    1.5Mb
    libs   5.1Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/csp.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/ctsem.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'Rmosek', 'gurobi', 'Rcplex', 'rcbc'
installed size is  6.5Mb
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    R      2.8Mb
    doc    1.3Mb
    help   1.1Mb
Running examples in ‘CVXR-Ex.R’ failed
The error most likely occurred in:

> ### Name: diag,Expression-method
> ### Title: Matrix Diagonal
> ### Aliases: diag,Expression-method diag
> 
> ### ** Examples
> 
> C <- Variable(3,3)
> obj <- Maximize(C[1,3])
> constraints <- list(diag(C) == 1, C[1,2] == 0.6, C[2,3] == -0.3, C == Variable(3,3, PSD = TRUE))
> prob <- Problem(obj, constraints)
> result <- solve(prob)

 *** caught segfault ***
address 0, cause 'memory not mapped'

Traceback:
 1: scs::scs(A = args$A, b = args$b, obj = args$c, cone = cones,     control = control)
 2: solve_via_data(object@solver, data, warm_start, verbose, feastol,     reltol, abstol, num_iter, solver_opts, problem@.solver_cache)
 3: solve_via_data(object@solver, data, warm_start, verbose, feastol,     reltol, abstol, num_iter, solver_opts, problem@.solver_cache)
 4: reduction_solve_via_data(object@.solving_chain, object, data,     warm_start, verbose, feastol, reltol, abstol, num_iter, list(...))
 5: reduction_solve_via_data(object@.solving_chain, object, data,     warm_start, verbose, feastol, reltol, abstol, num_iter, list(...))
 6: psolve(a, solver = NA, ...)
 7: psolve(a, solver = NA, ...)
 8: solve(prob)
 9: solve(prob)
An irrecoverable exception occurred. R is aborting now ...
Error(s) in re-building vignettes:
  ...
--- re-building ‘cycling_data_analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 177-179 (cycling_data_analysis.Rmd) 
Error: processing vignette 'cycling_data_analysis.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘cycling_data_analysis.Rmd’

SUMMARY: processing the following file failed:
  ‘cycling_data_analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.4Mb
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    libs   6.2Mb
installed size is  5.2Mb
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    doc   4.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 27-38 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
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    img   4.7Mb
installed size is  5.2Mb
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    Pied_Flycatchers_2   1.3Mb
    doc                  1.2Mb
installed size is  7.8Mb
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    java   7.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘get_started.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 26-34 (get_started.Rmd) 
Error: processing vignette 'get_started.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘get_started.Rmd’

SUMMARY: processing the following file failed:
  ‘get_started.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.5Mb
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    doc       2.5Mb
    extdata   5.7Mb
installed size is  5.2Mb
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    doc    1.3Mb
    libs   2.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘applications.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘applications.Rmd’

--- re-building ‘data.tree.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 513-516 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘data.tree.Rmd’

SUMMARY: processing the following file failed:
  ‘data.tree.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘RPostgres’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    sample_data   3.6Mb
installed size is  5.1Mb
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    extdata   4.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘RC_units.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘RC_units.Rmd’

--- re-building ‘decoder.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘decoder.Rmd’

--- re-building ‘sjukhus.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Joining, by = "key"
Joining, by = "key"
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 102-122 (sjukhus.Rmd) 
Error: processing vignette 'sjukhus.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘sjukhus.Rmd’

SUMMARY: processing the following file failed:
  ‘sjukhus.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘delayed.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 97-98 (delayed.Rmd) 
Error: processing vignette 'delayed.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘delayed.Rmd’

SUMMARY: processing the following file failed:
  ‘delayed.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is  7.3Mb
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    doc   5.9Mb
installed size is  7.5Mb
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    extdata   2.3Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.0Mb
    help   1.4Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'Rmosek', 'Rsymphony'
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    1.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘DGVM3D.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: rgl
Loading required namespace: rmarkdown
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 230-234 (DGVM3D.Rmd) 
Error: processing vignette 'DGVM3D.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘DGVM3D.Rmd’

SUMMARY: processing the following file failed:
  ‘DGVM3D.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 17.7Mb
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    htmlwidgets   6.2Mb
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installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
Package suggested but not available for checking: ‘RcppRedis’
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    include  15.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   2.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Running examples in ‘dmdScheme-Ex.R’ failed
The error most likely occurred in:

> ### Name: report
> ### Title: Generic function for creating a report from an object 'x'
> ### Aliases: report report.character report.dmdScheme_validation
> 
> ### ** Examples
> 
> ## Report of `dmdScheme_validation`
> report( scheme_path_xlsx() )
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Running ‘testthat.R’ [29s/68s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(magrittr)
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  > ##
  > library(dmdScheme)
  
  #############################################
  The cache will be in a temporary location and be deleted when you quit R.
  It is located at
     /tmp/Rtmparays2/working_dir/RtmpygaqzR/dmdScheme_56ca17e13919
  To make it permanent, call
     cache(createPermanent = TRUE)
  and restart R
  and a permanent cache will be created which will survive restarts.
  #############################################
  
  
  trying URL 'https://github.com/Exp-Micro-Ecol-Hub/dmdSchemeRepository/raw/master/schemes/dmdScheme_0.9.5.tar.gz'
  Content type 'application/octet-stream' length 27511 bytes (26 KB)
  ==================================================
  downloaded 26 KB
  
  Scheme definition `/tmp/Rtmparays2/working_dir/RtmpygaqzR/file56ca581c2789/dmdScheme_0.9.5.tar.gz, installed with
  name:    dmdScheme
  version: 0.9.5
  Theme switched to dmdScheme_0.9.5
  > ##
  > test_check("dmdScheme")
  terminate called after throwing an instance of 'Rcpp::exception'
    what():  Start tag expected, '<' not found [4]
Running ‘runit.R’ [17s/21s]
  Running ‘testthat.R’ [18s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > running_on_my_machines <- function() {
  +     sys_info <- Sys.info()
  +     r <- sys_info[["nodename"]] %in% c("h6", "h7") &&
  +         sys_info[["effective_user"]] == "qwer" &&
  +         .Platform[["OS.type"]] == "unix"
  +     return(r)
  + }
  > 
  > set_NOT_CRAN  <- function() {
  +     is_unset <- is.na(Sys.getenv("NOT_CRAN", unset = NA))
  +     if (running_on_my_machines() && is_unset)
  +         Sys.setenv("NOT_CRAN" = TRUE)
  + }
  > 
  > set_NOT_CRAN()
  > library("testthat")
  > library("document")
  > test_check("document")
  ── R CMD build ─────────────────────────────────────────────────────────────────
  * checking for file ‘.../DESCRIPTION’ ... OK
  * preparing ‘mini.mal’:
  * checking DESCRIPTION meta-information ... OK
  * checking for LF line-endings in source and make files and shell scripts
  * checking for empty or unneeded directories
  * building ‘mini.mal_2.0.0.tar.gz’
  
  ── 1. Error: (unknown) (@test_basic.R#13)  ─────────────────────────────────────
  Still alive
  Backtrace:
   1. document::document(file_name, check_package = TRUE, runit = TRUE)
   2. document:::check_package(...)
   3. rcmdcheck::rcmdcheck(...)
   4. rcmdcheck:::build_package(...)
   7. proc$get_built_file()
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: (unknown) (@test_basic.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Packages which this enhances but not available for checking:
  'gurobi', 'Rmosek'
Package suggested but not available for checking: ‘doRedis’
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    DRomics-shiny   1.8Mb
    extdata         3.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘userGuide.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Using constraints: b = 1
Using constraints: b = 1
Running default monotherapy fitting. Note that if constraints are needed, run mono fitting manually first
Using constraints: b = 1
Using constraints: b = 1
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot6bde48e13ba6.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot6bde48e13ba6.png': No such file or directory
Quitting from lines 357-358 (userGuide.Rmd) 
Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘userGuide.Rmd’

SUMMARY: processing the following file failed:
  ‘userGuide.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    appinformation   4.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘dsa-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 37-38 (dsa-vignette.Rmd) 
Error: processing vignette 'dsa-vignette.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
--- failed re-building ‘dsa-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘dsa-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Designing-33PC.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 163-164 (Designing-33PC.Rmd) 
Error: processing vignette 'Designing-33PC.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Designing-33PC.Rmd’

SUMMARY: processing the following file failed:
  ‘Designing-33PC.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    doc    1.8Mb
    libs   2.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.8Mb
Running ‘testthat.R’ [63s/55s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("dynutils")
  Loading required package: dynutils
  
  Attaching package: 'dynutils'
  
  The following object is masked from 'package:testthat':
  
      has_names
  
  ── 1. Error: write_h5 and read_h5 works (@test-h5.R#11)  ───────────────────────
  HDF5-API H5T.c in H5Tget_class(): line 1876: not a datatype
          class: HDF5
          major: Invalid arguments to routine
          minor: Inappropriate type
  Backtrace:
   1. dynutils::read_h5(file)
   2. dynutils::read_h5_(file_h5)
   3. hdf5r::h5attr(file_h5, "object_class")
   4. attr_obj$read()
   5. hdf5r:::H5ToR_Pre(mem_type, nelem)
  
  ❌ Unable to read hdf5 files
  ── 2. Error: test_h5_installation works (@test-h5.R#17)  ───────────────────────
  HDF5-API H5T.c in H5Tget_class(): line 1876: not a datatype
          class: HDF5
          major: Invalid arguments to routine
          minor: Inappropriate type
  Backtrace:
   1. testthat::expect_true(test_h5_installation())
   4. dynutils::test_h5_installation()
   5. dynutils:::test_h5_installation_read(detailed, file)
   6. base::tryCatch(...)
   7. base:::tryCatchList(expr, classes, parentenv, handlers)
   8. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   9. value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 402 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 2 ]
  1. Error: write_h5 and read_h5 works (@test-h5.R#11) 
  2. Error: test_h5_installation works (@test-h5.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc       5.3Mb
    extdata   5.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘EHRtemporalVariability.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Joining, by = "diagcode1"
Warning: Column `diagcode1` joining factor and character vector, coercing into character vector
# Missing values: 0 cases ( 0%)
# External causes codes: 0 cases ( 0%)
# V codes not mapped: 74330 cases ( 22.82%)
# Total ICD9-CM codes mapped: 146262 cases ( 44.9%)
# Unique ICD9-CM codes mapped: 3020
# Total PheWAS codes: 757
# ICD9 codes not mapped: 105180 cases ( 32.29%)
Quitting from lines 317-322 (EHRtemporalVariability.Rmd) 
Error: processing vignette 'EHRtemporalVariability.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘EHRtemporalVariability.Rmd’

SUMMARY: processing the following file failed:
  ‘EHRtemporalVariability.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    examples   4.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    xsd   4.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.6Mb
Running examples in ‘eNetXplorer-Ex.R’ failed
The error most likely occurred in:

> ### Name: plotContingency
> ### Title: generates plot of response vs out-of-bag predictions across
> ###   classes
> ### Aliases: plotContingency
> 
> ### ** Examples
> 
> ## Don't show: 
> set.seed(123)
> fit = eNetXplorer(x=matrix(rnorm(120),ncol=4),y=c(rep(0,15),rep(1,15)),
+ family="binomial",n_run=5, n_perm_null=4,alpha=c(0.5,1))
Error during execution of alpha =  0.5 
> plot(x=fit,plot.type="contingency")
Error in if (x$family %in% c("binomial", "multinomial")) { : 
  argument is of length zero
Calls: plot -> plot.eNetXplorer
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    doc    3.4Mb
    help   3.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘epicontacts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘epicontacts.Rmd’

--- re-building ‘epicontacts_class.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘epicontacts_class.Rmd’

SUMMARY: processing the following file failed:
  ‘epicontacts.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘epiflows-class.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘epiflows-class.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 117-120 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘EpiSignalDetection-Ex.R’ failed
The error most likely occurred in:

> ### Name: runEpiSDReport
> ### Title: Run the EpiSignalDetection report (HTML markdown)
> ### Aliases: runEpiSDReport
> 
> ### ** Examples
> 
> #---> OR
> 
> #-- First setting the parameters to run the report for
> input <- list(
+ disease = "Salmonellosis",
+ country = "Portugal",
+ indicator = "Reported cases",
+ stratification = "Confirmed cases",
+ unit = "Month",
+ daterange = c("2011-01-01", "2016-12-31"),
+ algo = "FarringtonFlexible",
+ testingperiod = 6
+ )
> 
> #-- Second running the report based on the EpiSignalDetection::SignalData dataset
> #-- and store it in a temporary folder
> runEpiSDReport(input = input)
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Running ‘sleep.R’
  Comparing ‘sleep.Rout’ to ‘sleep.Rout.save’ ... OK
  Running ‘testthat.R’ [61s/80s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(estimatr)
  > 
  > test_check("estimatr")
  ── 1. Failure: Handle perfect fits appropriately (@test-lm-robust-fes.R#682)  ──
  tidy(rfo)[rfo$term == "X", ] not equivalent to tidy(ro)[ro$term == "X", ].
  Component "std.error": 'is.NA' value mismatch: 1 in current 0 in target
  Component "statistic": 'is.NA' value mismatch: 1 in current 0 in target
  Component "p.value": 'is.NA' value mismatch: 1 in current 0 in target
  Component "conf.low": 'is.NA' value mismatch: 1 in current 0 in target
  Component "conf.high": 'is.NA' value mismatch: 1 in current 0 in target
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1326 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Handle perfect fits appropriately (@test-lm-robust-fes.R#682) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.1Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    exiftool  14.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_genExPrior.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 58-59 (using_genExPrior.Rmd) 
Error: processing vignette 'using_genExPrior.Rmd' failed with diagnostics:
Failed to create the shared library.
--- failed re-building ‘using_genExPrior.Rmd’

SUMMARY: processing the following file failed:
  ‘using_genExPrior.Rmd’

Error: Vignette re-building failed.
Execution halted
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Package suggested but not available for checking: ‘RWeka’
Package unavailable to check Rd xrefs: ‘RWeka’
Running ‘run-all.R’
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("farff")
  Loading required package: farff
  ── 1. Error: quick test with small arffs (@test_quick.R#6)  ────────────────────
  there is no package called 'RWeka'
  Backtrace:
   1. farff:::compareRWeka(INST_ARFF_DIR, "iris.arff", data.reader = dreader)
   2. RWeka::read.arff /home/ripley/R/packages/tests32/farff.Rcheck/tests/helper.R:17:2
   3. base::getExportedValue(pkg, name)
   4. base::asNamespace(ns)
   5. base::getNamespace(ns)
   6. base::loadNamespace(name)
   7. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   8. base:::withOneRestart(expr, restarts[[1L]])
   9. base:::doWithOneRestart(return(expr), restart)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: quick test with small arffs (@test_quick.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
Package suggested but not available for checking: ‘Rserve’
Installation failed.
See ‘/home/ripley/R/packages/tests32/FastRWeb.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘quick_charts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 125-134 (quick_charts.Rmd) 
Error: processing vignette 'quick_charts.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘quick_charts.Rmd’

SUMMARY: processing the following file failed:
  ‘quick_charts.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘lifeExpectancy.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 76-77 (lifeExpectancy.Rmd) 
Error: processing vignette 'lifeExpectancy.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘lifeExpectancy.Rmd’

--- re-building ‘selectIndicatorsRedRed.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘selectIndicatorsRedRed.Rmd’

SUMMARY: processing the following file failed:
  ‘lifeExpectancy.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    help   3.2Mb
Package suggested but not available for checking: ‘multipanelfigure’
Running examples in ‘float-Ex.R’ failed
The error most likely occurred in:

> ### Name: eigen
> ### Title: eigen
> ### Aliases: eigen eigen,float32-method
> 
> ### ** Examples
> 
> library(float)
> 
> s = flrunif(10, 3)
> cp = crossprod(s)
> 
> eigen(cp)
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    fonts   6.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    fonts   7.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘formattable-data-frame.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 168-169 (formattable-data-frame.Rmd) 
Error: processing vignette 'formattable-data-frame.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘formattable-data-frame.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘formattable-data-frame.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction-to-formulaic.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 127-132 (Introduction-to-formulaic.Rmd) 
Error: processing vignette 'Introduction-to-formulaic.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Introduction-to-formulaic.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction-to-formulaic.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2', 'Rsymphony'
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    help   1.6Mb
    libs   5.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R   5.8Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
    doc    2.1Mb
Package unavailable to check Rd xrefs: ‘RMark’
Packages suggested but not available for checking: 'RWeka', 'FSelector'
Package unavailable to check Rd xrefs: ‘FSelector’
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    data  16.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘futureheatwaves.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 604-605 (futureheatwaves.Rmd) 
Error: processing vignette 'futureheatwaves.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘futureheatwaves.Rmd’

--- re-building ‘starting_from_netcdf.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘starting_from_netcdf.Rmd’

SUMMARY: processing the following file failed:
  ‘futureheatwaves.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc   9.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘chart_themes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
g3viz: visualizing gene/genome/gentics data for fun.
Any questions, please send emails to <g3viz.group@gmail.com>
Please send questions to cbioportal@googlegroups.com
Quitting from lines 48-58 (chart_themes.Rmd) 
Error: processing vignette 'chart_themes.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘chart_themes.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
g3viz: visualizing gene/genome/gentics data for fun.
Any questions, please send emails to <g3viz.group@gmail.com>
Quitting from lines 103-114 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘chart_themes.Rmd’ ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   3.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      1.9Mb
Running ‘testthat.R’ [0m/16m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(gbfs)
  > 
  > test_check("gbfs")
  ── 1. Error: find feed from top level works (@test-utils.R#62)  ────────────────
  Timeout was reached: [biketownpdx.socialbicycles.com] Resolving timed out after 10000 milliseconds
  Backtrace:
    1. testthat::expect_equal(...)
    4. gbfs:::find_feed_from_top_level(...)
    5. jsonlite::fromJSON(txt = top_level_)
    6. jsonlite:::parse_and_simplify(...)
    7. jsonlite:::parseJSON(txt, bigint_as_char)
    8. jsonlite:::parse_con(txt, bigint_as_char)
   10. base::open.connection(con, "rb")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 27 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: find feed from top level works (@test-utils.R#62) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gcbd.Rnw’ using Sweave
Warning in packageDescription("gputools") :
  no package 'gputools' was found
Error: processing vignette 'gcbd.Rnw' failed with diagnostics:
at gcbd.Rnw:860, subscript out of bounds
--- failed re-building ‘gcbd.Rnw’

SUMMARY: processing the following file failed:
  ‘gcbd.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    L8NY18   2.1Mb
    doc      1.0Mb
    libs     2.3Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R  10.3Mb
Package suggested but not available for checking: ‘reactome.db’
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    data  27.2Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R         9.1Mb
    extdata   1.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘geosample-vignette.Rnw’ using knitr
Loading required package: sf
Linking to GEOS 3.6.3, GDAL 2.2.4, PROJ 5.2.0
Loading required package: sp
Loading required package: maxLik
Loading required package: miscTools

Please cite the 'maxLik' package as:
Henningsen, Arne and Toomet, Ott (2011). maxLik: A package for maximum likelihood estimation in R. Computational Statistics 26(3), 443-458. DOI 10.1007/s00180-010-0217-1.

If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/
Loading required package: raster

Attaching package: 'raster'

The following object is masked from 'package:maxLik':

    maxValue

Loading required package: pdist
Loading required package: Matrix
Quitting from lines 476-516 (geosample-vignette.Rnw) 
Error: processing vignette 'geosample-vignette.Rnw' failed with diagnostics:
cannot allocate vector of size 3.0 Gb
--- failed re-building ‘geosample-vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘geosample-vignette.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown_notangle
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 53-60 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
--- failed re-building ‘Introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    help   1.6Mb
Packages suggested but not available for checking: 'av', 'gifski'
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggBubbles.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: knitr
Loading required package: ggplot2
Loading required package: ggBubbles
Quitting from lines 30-40 (ggBubbles.Rmd) 
Error: processing vignette 'ggBubbles.Rmd' failed with diagnostics:
could not find function "CRANpkg"
--- failed re-building ‘ggBubbles.Rmd’

SUMMARY: processing the following file failed:
  ‘ggBubbles.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc         3.0Mb
    tutorials   1.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggPredict.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra

Attaching package: 'ggiraphExtra'

The following objects are masked from 'package:moonBook':

    addLabelDf, getMapping

Loading required package: plyr
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 45-49 (ggPredict.Rmd) 
Error: processing vignette 'ggPredict.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘ggPredict.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot3254152e7656.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot3254152e7656.png': No such file or directory
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘ggPredict.Rmd’ ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   4.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘extending-ggplot2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘extending-ggplot2.Rmd’

--- re-building ‘ggplot2-specs.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘ggplot2-specs.Rmd’

Profiling Timer Expired
--- re-building ‘profiling.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
SUMMARY: processing the following file failed:
  ‘profiling.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   9.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: Matrix
Quitting from lines 185-186 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggseas.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 125-126 (ggseas.Rmd) 
Error: processing vignette 'ggseas.Rmd' failed with diagnostics:
Process terminated
--- failed re-building ‘ggseas.Rmd’

SUMMARY: processing the following file failed:
  ‘ggseas.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc         1.3Mb
    libs        1.8Mb
    test_data   1.3Mb
Running examples in ‘glmnet-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot.cv.glmnet
> ### Title: plot the cross-validation curve produced by cv.glmnet
> ### Aliases: plot.cv.glmnet plot.cv.relaxed
> ### Keywords: models regression
> 
> ### ** Examples
> 
> 
> set.seed(1010)
> n = 1000
> p = 100
> nzc = trunc(p/10)
> x = matrix(rnorm(n * p), n, p)
> beta = rnorm(nzc)
> fx = (x[, seq(nzc)] %*% beta)
> eps = rnorm(n) * 5
> y = drop(fx + eps)
> px = exp(fx)
> px = px/(1 + px)
> ly = rbinom(n = length(px), prob = px, size = 1)
> cvob1 = cv.glmnet(x, y)
Error in intI(j, n = x@Dim[2], dn[[2]], give.dn = FALSE) : 
  'NA' indices are not (yet?) supported for sparse Matrices
Calls: cv.glmnet ... NextMethod -> predict.glmnet -> [ -> [ -> subCsp_cols -> intI
Execution halted
Packages required but not available: 'SeqArray', 'SeqVarTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/ripley/R/packages/tests32/gof.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    3.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘gprofiler2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 239-240 (gprofiler2.Rmd) 
Error: processing vignette 'gprofiler2.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘gprofiler2.Rmd’

SUMMARY: processing the following file failed:
  ‘gprofiler2.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   1.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘profiling.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Running ‘testthat.R’ [22s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(gwsem)
  Loading required package: OpenMx
  To take full advantage of multiple cores, use:
    mxOption(key='Number of Threads', value=parallel::detectCores()) #now
    Sys.setenv(OMP_NUM_THREADS=parallel::detectCores()) #before library(OpenMx)
  > 
  > test_check("gwsem")
  Error: C stack usage  207197300 is too close to the limit
  ── 1. Error: (unknown) (@test-covariate.R#36)  ─────────────────────────────────
  This model has 5 matrices, but the backend has returned 0 values
  Backtrace:
   1. gwsem::GWAS(...)
   2. OpenMx::mxRun(model)
   3. OpenMx:::runHelper(...)
   4. OpenMx:::updateModelMatrices(model, flatModel, output$matrices)
  
  ── 2. Error: (unknown) (@test-model.R#75)  ─────────────────────────────────────
  incompatible dimensions
  Backtrace:
   1. testthat::expect_equal(cor(ml$P, pgen$P), 1, tolerance = 0.001)
   4. stats::cor(ml$P, pgen$P)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 47 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 2 ]
  1. Error: (unknown) (@test-covariate.R#36) 
  2. Error: (unknown) (@test-model.R#75) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘growth.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: OpenMx
To take full advantage of multiple cores, use:
  mxOption(key='Number of Threads', value=parallel::detectCores()) #now
  Sys.setenv(OMP_NUM_THREADS=parallel::detectCores()) #before library(OpenMx)
Error: C stack usage  256545908 is too close to the limit
Quitting from lines 173-175 (growth.Rmd) 
Error: processing vignette 'growth.Rmd' failed with diagnostics:
This model has 4 matrices, but the backend has returned 0 values
--- failed re-building ‘growth.Rmd’

SUMMARY: processing the following file failed:
  ‘growth.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 130.8Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    java  128.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    HaDeX   4.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 40-43 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘overview.Rmd’

SUMMARY: processing the following file failed:
  ‘overview.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    data   9.5Mb
prepare_Rd: it is not known that wchar_t is Unicode on this platform
Warning in deparse(ce, width.cutoff = 0.75 * getOption("width")) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(ce, width.cutoff = 0.75 * getOption("width")) :
  it is not known that wchar_t is Unicode on this platform
Error(s) in re-building vignettes:
  ...
--- re-building ‘Basic_use.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 122-128 (Basic_use.Rmd) 
Error: processing vignette 'Basic_use.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Basic_use.Rmd’

SUMMARY: processing the following file failed:
  ‘Basic_use.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  readstat/readstat_convert.c:18:42: warning: passing argument 2 of ‘libiconv’ from incompatible pointer type [-Wincompatible-pointer-types]
  src/spss/readstat_sav_parse.rl:89:17: warning: passing argument 2 of ‘libiconv’ from incompatible pointer type [-Wincompatible-pointer-types]
  src/spss/readstat_sav_parse.rl:197:17: warning: passing argument 2 of ‘libiconv’ from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/ripley/R/packages/tests32/haven.Rcheck/00install.out’ for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc           2.8Mb
    htmlwidgets   2.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hchinamap.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'https://czxb.github.io/br/chinadf.rda'
Content type 'application/octet-stream' length 3992 bytes
==================================================
downloaded 3992 bytes

Quitting from lines 50-58 (hchinamap.Rmd) 
Error: processing vignette 'hchinamap.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘hchinamap.Rmd’

SUMMARY: processing the following file failed:
  ‘hchinamap.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    CWrappers_1.10.2   2.4Mb
    CWrappers_1.10.3   2.4Mb
    R                  1.1Mb
Running examples in ‘hdf5r-Ex.R’ failed
The error most likely occurred in:

> ### Name: H5A-class
> ### Title: Class for representing HDF5 attributes
> ### Aliases: H5A-class H5A
> 
> ### ** Examples
> 
> fname <- tempfile(fileext = ".h5")
> file <- H5File$new(fname, mode = "a")
> h5attr(file, "attr_numeric") <- rnorm(10)
> a <- file$attr_open("attr_numeric")
> a$get_info()
  corder_valid corder cset data_size
1            0      0    0        80
> a$attr_name()
[1] "attr_numeric"
> a$get_space()
Class: H5S
Type: Simple
Dims: 10
Maxdims: 10
> a$get_type()
Class: H5T_FLOAT
Datatype: H5T_IEEE_F64LE
> a$get_storage_size()
[1] 80
> a$read()
Error in H5ToR_Pre(mem_type, nelem) : HDF5-API Errors:
    error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
        class: HDF5
        major: Invalid arguments to routine
        minor: Inappropriate type
Calls: <Anonymous> -> H5ToR_Pre
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hdf5r.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 159-160 (hdf5r.Rmd) 
Error: processing vignette 'hdf5r.Rmd' failed with diagnostics:
HDF5-API Errors:
    error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
        class: HDF5
        major: Invalid arguments to routine
        minor: Inappropriate type

--- failed re-building ‘hdf5r.Rmd’

SUMMARY: processing the following file failed:
  ‘hdf5r.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hdnom.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

(process:16497): Pango-WARNING **: failed to create cairo scaled font, expect ugly output. the offending font is 'Helvetica Medium 10.5'

(process:16497): Pango-WARNING **: font_face status is: no error has occurred

(process:16497): Pango-WARNING **: scaled_font status is: invalid matrix (not invertible)

(process:16497): Pango-WARNING **: shaping failure, expect ugly output. shape-engine='BasicEngineFc', font='Helvetica Medium 10.5', text='M'
Quitting from lines 367-379 (hdnom.Rmd) 
Error: processing vignette 'hdnom.Rmd' failed with diagnostics:
NA/NaN/Inf in foreign function call (arg 16)
--- failed re-building ‘hdnom.Rmd’

SUMMARY: processing the following file failed:
  ‘hdnom.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘heatmaply.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

The following object is masked from 'package:stats':

    filter

The following object is masked from 'package:graphics':

    layout

Loading required package: viridis
Loading required package: viridisLite

======================
Welcome to heatmaply version 1.0.0

Type citation('heatmaply') for how to cite the package.
Type ?heatmaply for the main documentation.

The github page is: https://github.com/talgalili/heatmaply/
Please submit your suggestions and bug-reports at: https://github.com/talgalili/heatmaply/issues
Or contact: <tal.galili@gmail.com>
======================

Quitting from lines 108-110 (heatmaply.Rmd) 
Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘heatmaply.Rmd’

SUMMARY: processing the following file failed:
  ‘heatmaply.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.9Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    4.9Mb
    libs   1.8Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc           3.7Mb
    htmlwidgets   4.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
Found the following significant warnings:
  mapping.cpp:95:58: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
See ‘/home/ripley/R/packages/tests32/hilbertSimilarity.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘RProtoBuf’
Package unavailable to check Rd xrefs: ‘RProtoBuf’
Error(s) in re-building vignettes:
  ...
--- re-building ‘hpackedbubble.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 35-49 (hpackedbubble.Rmd) 
Error: processing vignette 'hpackedbubble.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘hpackedbubble.Rmd’

SUMMARY: processing the following file failed:
  ‘hpackedbubble.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   8.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.6Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   8.4Mb
    doc    2.4Mb
Running ‘testthat.R’ [5s/61s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("httr")
  Loading required package: httr
  ── 1. Failure: if request_perform() throws an error, RETRY passes it on (@test-r
  `RETRY(...)` threw an error with unexpected message.
  Expected match: "resolve host"
  Actual message: "Could not resolve: 98d90a2a254647889e2e4c236fb576cd.com (Domain name not found)"
  Backtrace:
   1. testthat::expect_error(...)
   6. httr::RETRY(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 158 | SKIPPED: 2 | WARNINGS: 4 | FAILED: 1 ]
  1. Failure: if request_perform() throws an error, RETRY passes it on (@test-retry.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'https://arxiv.org/e-print/1406.4806v1'
Content type 'application/x-eprint-tar' length 29273 bytes (28 KB)
==================================================
downloaded 28 KB

Quitting from lines 161-165 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hwordcloud.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 48-53 (hwordcloud.Rmd) 
Error: processing vignette 'hwordcloud.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘hwordcloud.Rmd’

SUMMARY: processing the following file failed:
  ‘hwordcloud.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
Running examples in ‘IAPWS95-Ex.R’ failed
The error most likely occurred in:

> ### Name: TDh
> ### Title: Temperature, Function of Density and Enthalpy
> ### Aliases: TDh
> 
> ### ** Examples
> 
> D <- 838.025
> h <- 977.181624
> T_Dh <- TDh(D,h)
Error(s) in re-building vignettes:
  ...
--- re-building ‘ibmsunburst.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 25-37 (ibmsunburst.Rmd) 
Error: processing vignette 'ibmsunburst.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘ibmsunburst.Rmd’

SUMMARY: processing the following file failed:
  ‘ibmsunburst.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘BSgenome.Mmusculus.UCSC.mm10’
Package unavailable to check Rd xrefs: ‘BSgenome.Mmusculus.UCSC.mm10’
Error(s) in re-building vignettes:
  ...
--- re-building ‘example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 62-70 (example.Rmd) 
Quitting from lines 62-70 (example.Rmd) 
Error: processing vignette 'example.Rmd' failed with diagnostics:
invalid connection
--- failed re-building ‘example.Rmd’

SUMMARY: processing the following file failed:
  ‘example.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   1.5Mb
    doc    1.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘model_details.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 25-32 (model_details.Rmd) 
Error: processing vignette 'model_details.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘model_details.Rmd’

--- re-building ‘parameter_details.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 24-31 (parameter_details.Rmd) 
Error: processing vignette 'parameter_details.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘parameter_details.Rmd’

--- re-building ‘resources.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘resources.Rmd’

SUMMARY: processing the following files failed:
  ‘model_details.Rmd’ ‘parameter_details.Rmd’

Error: Vignette re-building failed.
Execution halted
XIO:  fatal IO error 146 (Connection refused) on X server ":5.0"
      after 0 requests (0 known processed) with 0 events remaining.
Running examples in ‘ifa-Ex.R’ failed
The error most likely occurred in:

> ### Name: ifa.bic
> ### Title: A function to compute the BIC
> ### Aliases: ifa.bic
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> data(memory)

 *** caught segfault ***
address 144959bc, cause 'memory not mapped'

Traceback:
 1: sub(".*\\.", "", x)
 2: fileExt(file)
 3: data(memory)
An irrecoverable exception occurred. R is aborting now ...
Error(s) in re-building vignettes:
  ...
--- re-building ‘pritikin-schmidt.Rnw’ using knitr
Quitting from lines 1347-1404 (pritikin-schmidt.Rnw) 
Error: processing vignette 'pritikin-schmidt.Rnw' failed with diagnostics:
Fit not achieved
--- failed re-building ‘pritikin-schmidt.Rnw’

SUMMARY: processing the following file failed:
  ‘pritikin-schmidt.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.2Mb
    libs   6.5Mb
Package suggested but not available for checking: ‘tesseract’
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    doc       1.2Mb
    extdata   1.2Mb
    include   3.0Mb
    libs      6.3Mb
*** caught segfault ***
address f1000015, cause 'memory not mapped'

Traceback:
 1: dyn.load(file, DLLpath = DLLpath, ...)
 2: library.dynam(lib, package, package.lib)
 3: loadNamespace(p)
 4: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
 5: suppressMessages(loadNamespace(p))
 6: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
 7: suppressWarnings(suppressMessages(loadNamespace(p)))
 8: doTryCatch(return(expr), name, parentenv, handler)
 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(suppressWarnings(suppressMessages(loadNamespace(p))),     error = function(e) e)
12: tools:::.check_packages_used(package = "imager")
An irrecoverable exception occurred. R is aborting now ...
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    R  10.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    help   1.8Mb
Package unavailable to check Rd xrefs: ‘minfi’
Running examples in ‘Inflation-Ex.R’ failed
The error most likely occurred in:

> ### Name: INFL.core_tf
> ### Title: Computes the triple filter core inflation
> ### Aliases: INFL.core_tf
> ### Keywords: core filter triple
> 
> ### ** Examples
> 
> ipca <- ipca_sub
> INFL.core_tf(subits.var=ipca$ipca_ts, weights = ipca$weights_ts)
Unsupported platform: SunOS 5.10
For this platform, the path to the binary executable of X-13
has to be manually specified. See ?seasonal for details.
No path to the binary executable of X-13 specified.

You can set 'X13_PATH' manually if you intend to use your own
binaries. See ?seasonal for details.

Error in checkX13(fail = TRUE, fullcheck = FALSE, htmlcheck = FALSE) : 
  Process terminated
Calls: INFL.core_tf -> <Anonymous> -> checkX13
Execution halted
Running ‘spelling.R’
  Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(inplace)
  > 
  > test_check("inplace")
  ── 1. Failure: in-place operators work in common cases (@test-operators.R#57)  ─
  `X` not identical to `X2`.
  Objects equal but not identical
  
  ── 2. Failure: in-place operators work in common cases (@test-operators.R#56)  ─
  `X` not identical to `X2`.
  Objects equal but not identical
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 806 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: in-place operators work in common cases (@test-operators.R#57) 
  2. Failure: in-place operators work in common cases (@test-operators.R#56) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    java   4.4Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/IOHexperimenter.Rcheck/00install.out’ for details.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(stringr)
  > library(io)
  Loading required package: filenamer
  > 
  > test_check("io")
  ── 1. Error: (unknown) (@test_read-write-read.R#8)  ────────────────────────────
  HDF5. File accessibilty. Unable to open file.
  Backtrace:
    1. io:::test_read_write_read(f)
    2. io::qread(infile) /home/ripley/R/packages/tests32/io.Rcheck/tests/helper.R:47:8
    4. io:::qread.hdf5(...)
   10. rhdf5::h5ls(file)
   11. rhdf5:::h5checktypeOrOpenLoc(file, readonly = TRUE, native = native)
   12. rhdf5::H5Fopen(file, "H5F_ACC_RDONLY", native = native)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test_read-write-read.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   7.7Mb
Package suggested but not available for checking: ‘redux’
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-started-with-irg.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
ndvi                    package:irg                    R Documentation

_R_a_w _N_D_V_I _T_i_m_e _S_e_r_i_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     A data.table containing NDVI samples for ten points over ten years
     (2002-2012).

_F_o_r_m_a_t:

     A data.table with 2530 rows and 5 variables:

        • id - individual identifier

        • yr - year of sample

        • DayOfYear - julian day/day of year of sample

        • NDVI - sampled value

        • SummaryQA - Summary quality assessment value

     SummaryQA details:

        • 0 - Good data, use with confidence

        • 1 - Marginal data, useful but look at detailed QA for more
          information

        • 2 - Pixel covered with snow/ice

        • 3 - Pixel is cloudy

_E_x_a_m_p_l_e_s:

     # Load data.table
     library(data.table)
     
     # Read example data
     ndvi <- fread(system.file("extdata", "ndvi.csv", package = "irg"))
     

Quitting from lines 99-153 (getting-started-with-irg.Rmd) 
Error: processing vignette 'getting-started-with-irg.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘getting-started-with-irg.Rmd’

SUMMARY: processing the following file failed:
  ‘getting-started-with-irg.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    dict   5.0Mb
Package suggested but not available for checking: ‘RProtoBuf’
Running examples in ‘joinet-Ex.R’ failed
The error most likely occurred in:

> ### Name: coef.joinet
> ### Title: Extract Coefficients
> ### Aliases: coef.joinet
> 
> ### ** Examples
> 
> n <- 50; p <- 100; q <- 3
> X <- matrix(rnorm(n*p),nrow=n,ncol=p)
> Y <- replicate(n=q,expr=rnorm(n=n,mean=rowSums(X[,1:5])))
> object <- joinet(Y=Y,X=X)
Error in approx(lambda, seq(lambda), sfrac) : 
  need at least two non-NA values to interpolate
Calls: joinet ... NextMethod -> predict.glmnet -> lambda.interp -> approx
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(joinet)
  > 
  > testthat::test_check(package="joinet",stop_on_warning=FALSE)
  ── 1. Error: (unknown) (@test.R#24)  ───────────────────────────────────────────
  need at least two non-NA values to interpolate
  Backtrace:
    1. joinet::joinet(...)
    2. glmnet::cv.glmnet(...)
    3. glmnet:::cv.glmnet.raw(...)
    5. glmnet:::buildPredmat.default(...)
    9. glmnet::predict.glmnet(...)
   10. glmnet:::lambda.interp(lambda, s)
   11. stats::approx(lambda, seq(lambda), sfrac)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 3 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: (unknown) (@test.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘article.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building ‘article.Rmd’

--- re-building ‘joinet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 105-106 (joinet.Rmd) 
Error: processing vignette 'joinet.Rmd' failed with diagnostics:
need at least two non-NA values to interpolate
--- failed re-building ‘joinet.Rmd’

SUMMARY: processing the following file failed:
  ‘joinet.Rmd’

Error: Vignette re-building failed.
Execution halted
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘kgc-fine.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: shiny
Loading required package: shinythemes
Loading required package: plyr
Quitting from lines 37-53 (kgc-fine.Rmd) 
Error: processing vignette 'kgc-fine.Rmd' failed with diagnostics:
cannot allocate vector of size 640.7 Mb
--- failed re-building ‘kgc-fine.Rmd’

--- re-building ‘kgc-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: shiny
Loading required package: shinythemes
Loading required package: plyr
--- finished re-building ‘kgc-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘kgc-fine.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘advanced.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Matrix
Loaded glmnet 3.0-2

--- finished re-building ‘advanced.Rmd’

--- re-building ‘fixed.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘fixed.Rmd’

--- re-building ‘hiv.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘hiv.Rmd’

Cpu Limit Exceeded - core dumped
--- re-building ‘knockoff.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Matrix
Loaded glmnet 3.0-2

SUMMARY: processing the following file failed:
  ‘knockoff.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(KRIG)
  > 
  > test_check("KRIG")
  ── 1. Failure: Same result sequencial and parallel code (@test1.R#15)  ─────────
  `kw` not equal to `nw`.
  1/1 mismatches
  [1] 12632 - 6316 == 6316
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Same result sequencial and parallel code (@test1.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘copper_mining_2d.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

The following object is masked from 'package:stats':

    filter

The following object is masked from 'package:graphics':

    layout

Quitting from lines 120-123 (copper_mining_2d.Rmd) 
Error: processing vignette 'copper_mining_2d.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘copper_mining_2d.Rmd’

--- re-building ‘ordinary_kriging.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘ordinary_kriging.Rmd’

--- re-building ‘simple_kriging.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘simple_kriging.Rmd’

--- re-building ‘universal_kriging.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘universal_kriging.Rmd’

SUMMARY: processing the following file failed:
  ‘copper_mining_2d.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   8.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   3.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    2.3Mb
    help   1.2Mb
Running ‘config.R’
  Running ‘testthat.R’
Running the tests in ‘tests/config.R’ failed.
Complete output:
  > mac_dir <- "~/Documents/Rtest/"
  > win_dir <- "C:/Rtest"
  > linux_dir <- "~/Documents/Rtest"
  > 
  > switch(Sys.info()['sysname'],
  +        "Darwin" = {working_dir <- mac_dir},
  +        "Windows" = {working_dir <- win_dir},
  +        "Linux" = {working_dir <- linux_dir})
  > 
  > rds_file_name <- "./ranListSmall.rds"
  > llo_file_name <- "./ranListSmall.llo"
  > repeat_time <- 20
  > original <- FALSE
  > compress <- TRUE
  > 
  > # rds_file_name <- "./ranListMid.rds"
  > # llo_file_name <- "./ranListMid.llo"
  > # repeat_time <- 20
  > # original <- FALSE
  > # compress <- TRUE
  > 
  > options(list(largeList.report.progress = FALSE))
  > 
  > if (dir.exists(working_dir)) {
  +   setwd(working_dir)
  +   if (file.exists(rds_file_name)) {
  +     library(futile.logger)
  +     ready_to_test <- TRUE
  +   } else {
  +     ready_to_test <- FALSE
  +   }
  + } else {
  +   ready_to_test <- FALSE
  + }
  Error in dir.exists(working_dir) : object 'working_dir' not found
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro_to_lavaanPlot.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 41-42 (Intro_to_lavaanPlot.Rmd) 
Error: processing vignette 'Intro_to_lavaanPlot.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Intro_to_lavaanPlot.Rmd’

SUMMARY: processing the following file failed:
  ‘Intro_to_lavaanPlot.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘gof’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.7Mb
    libs   2.3Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    geojson  11.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 67-77 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.9Mb
Compilation used the following non-portable flag(s):
  ‘-mt’
Error(s) in re-building vignettes:
  ...
--- re-building ‘batch_import.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘batch_import.Rmd’

--- re-building ‘renormalise.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘renormalise.Rmd’

--- re-building ‘true_example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 59-62 (true_example.Rmd) 
Error: processing vignette 'true_example.Rmd' failed with diagnostics:
object 'params' not found
--- failed re-building ‘true_example.Rmd’

SUMMARY: processing the following file failed:
  ‘true_example.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Understanding_lime.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 262-263 (Understanding_lime.Rmd) 
Error: processing vignette 'Understanding_lime.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Understanding_lime.Rmd’

SUMMARY: processing the following file failed:
  ‘Understanding_lime.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘linkspotterVignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 109-112 (linkspotterVignette.Rmd) 
Error: processing vignette 'linkspotterVignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘linkspotterVignette.Rmd’

SUMMARY: processing the following file failed:
  ‘linkspotterVignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.3Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R          1.6Mb
    doc        2.8Mb
    testdata   1.8Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/lmSubsets.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘Rsymphony’
Error(s) in re-building vignettes:
  ...
--- re-building ‘lspline.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 18-23 (lspline.Rmd) 
Error: processing vignette 'lspline.Rmd' failed with diagnostics:
object 'params' not found
--- failed re-building ‘lspline.Rmd’

SUMMARY: processing the following file failed:
  ‘lspline.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘LUCIDus-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 63-64 (LUCIDus-vignette.Rmd) 
Error: processing vignette 'LUCIDus-vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘LUCIDus-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘LUCIDus-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help   1.3Mb
Running examples in ‘lvmcomp-Ex.R’ failed
The error most likely occurred in:

> ### Name: StEM_mirt
> ### Title: Stochastic EM algorithm for solving multivariate item response
> ###   theory model
> ### Aliases: StEM_mirt
> 
> ### ** Examples
> 
> # run a toy example based on the M2PL model
> 
> # load a simulated dataset
> attach(data_sim_mirt)
> 
> # generate starting values for the algorithm
> A0 <- Q
> d0 <- rep(0, J)
> theta0 <- matrix(rnorm(N*K, 0, 1),N)
> sigma0 <- diag(1, K) 
> 
> # do the confirmatory MIRT analysis
> # to enable multicore processing, set parallel = T
> mirt_res <- StEM_mirt(response, Q, A0, d0, theta0, sigma0)

Step  1	| 
Step  2	| 
Step  3	| 
Step  4	| 
Step  5	| 
Step  6	|
Running examples in ‘lvnet-Ex.R’ failed
The error most likely occurred in:

> ### Name: lvnet
> ### Title: Confirmatory Latent Variable Network Models
> ### Aliases: lvnet
> 
> ### ** Examples
> 
> # Load dataset:
> library("lavaan")
This is lavaan 0.6-5
lavaan is BETA software! Please report any bugs.

Attaching package: ‘lavaan’

The following object is masked from ‘package:OpenMx’:

    vech

> data(HolzingerSwineford1939)
> Data <- HolzingerSwineford1939[,7:15]
> 
> # Measurement model:
> Lambda <- matrix(0, 9, 3)
> Lambda[1:3,1] <- NA
> Lambda[4:6,2] <- NA
> Lambda[7:9,3] <- NA
> 
> # Fit CFA model:
> CFA <- lvnet(Data, lambda = Lambda)
Error: C stack usage  333747348 is too close to the limit
Error: The job for model 'model' exited abnormally with the error message: User interrupt
Execution halted
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    TS_files     6.0Mb
    base_files   6.5Mb
Packages suggested but not available for checking:
  'av', 'rsvg', 'tesseract', 'gifski'
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
Packages unavailable to check Rd xrefs: ‘rsvg’, ‘tesseract’, ‘gifski’, ‘av’
Running examples in ‘magick-Ex.R’ failed
The error most likely occurred in:

> ### Name: analysis
> ### Title: Image Analysis
> ### Aliases: analysis image_compare image_compare_dist image_fft
> 
> ### ** Examples
> 
> out1 <- image_blur(logo, 3)

 *** caught segfault ***
address 2c, cause 'memory not mapped'

Traceback:
 1: magick_image_blur(image, radius, sigma)
 2: image_blur(logo, 3)
An irrecoverable exception occurred. R is aborting now ...
Warning in find_bad_exprs(exprs[[i]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in find_bad_exprs(exprs[[i]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in find_bad_exprs(exprs[[i]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in find_bad_exprs(exprs[[i]]) :
  it is not known that wchar_t is Unicode on this platform
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘manhattanly.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

The following object is masked from 'package:stats':

    filter

The following object is masked from 'package:graphics':

    layout

Quitting from lines 95-96 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘manhattanly.Rmd’

SUMMARY: processing the following file failed:
  ‘manhattanly.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘manipulateWidgets.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="webshot4f9e9582434.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot4f9e9582434.png': No such file or directory
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘manipulateWidgets.Rmd’

SUMMARY: processing the following file failed:
  ‘manipulateWidgets.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.2Mb
    help   1.6Mb
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    mapdata  33.8Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data          1.0Mb
    doc           1.3Mb
    htmlwidgets   1.6Mb
    libs          3.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 95-100 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    mapdata   4.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    java   3.4Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘MBNMAtime.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Reference treatment is `plac`

ET50 parameters (beta.2) are on exponential scale to ensure they take positive values on the natural scale
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   3.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   6.0Mb
Package required but not available: ‘gdsfmt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    doc   3.1Mb
Package required but not available: ‘metagenomeSeq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [0m/180m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(metaSEM)
  Loading required package: OpenMx
  To take full advantage of multiple cores, use:
    mxOption(key='Number of Threads', value=parallel::detectCores()) #now
    Sys.setenv(OMP_NUM_THREADS=parallel::detectCores()) #before library(OpenMx)
  "SLSQP" is set as the default optimizer in OpenMx.
  mxOption(NULL, "Gradient algorithm") is set at "central".
  mxOption(NULL, "Optimality tolerance") is set at "6.3e-14".
  mxOption(NULL, "Gradient iterations") is set at "2".
  > 
  > test_check("metaSEM")
  ── 1. Failure: metaFIML() works correctly (@test_utilities.R#479)  ─────────────
  vcov(fit1a) not equal to vcov(fit1b)[names1, names1].
  4/25 mismatches (average diff: 0.104)
  [13] -1.07e-11 -  0.1202 == -0.1202
  [14]  3.14e-12 - -0.1033 ==  0.1033
  [18]  3.14e-12 - -0.1033 ==  0.1033
  [19] -2.18e-11 -  0.0891 == -0.0891
  
  Error in running mxModel:
  <simpleError: The job for model 'Meta analysis with FIML' exited abnormally with the error message: Non-conformable matrices in horizontal concatenation (cbind). First argument has 4 rows, and argument #2 has 0 rows.>
  ── 2. Error: metaFIML() works correctly (@test_utilities.R#484)  ───────────────
  The job for model 'Meta analysis with FIML' exited abnormally with the error message: Non-conformable matrices in horizontal concatenation (cbind). First argument has 4 rows, and argument #2 has 0 rows.
  Backtrace:
   1. metaSEM::metaFIML(y = r, v = r_v, x = JP_alpha, av = IDV, data = Jaramillo05)
  
  
   *** caught segfault ***
  address 3ff00018, cause 'memory not mapped'
  
   *** caught segfault ***
  address 14eff004, cause 'memory not mapped'
installed size is  5.2Mb
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    doc    2.6Mb
    help   2.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.7Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.1Mb
    libs   1.7Mb
    misc   1.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mgwrsar-basic_examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 91-94 (mgwrsar-basic_examples.Rmd) 
Error: processing vignette 'mgwrsar-basic_examples.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘mgwrsar-basic_examples.Rmd’

SUMMARY: processing the following file failed:
  ‘mgwrsar-basic_examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
*** This is beta software. Please report any bugs!
*** See the NEWS file for recent changes.
Loading required package: Matrix
Quitting from lines 109-112 (Analysis.Rmd) 
Error: processing vignette 'Analysis.Rmd' failed with diagnostics:
objective in x0 returns NA
--- failed re-building ‘Analysis.Rmd’

--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
*** This is beta software. Please report any bugs!
*** See the NEWS file for recent changes.

(process:14354): Pango-WARNING **: failed to create cairo scaled font, expect ugly output. the offending font is 'Helvetica Medium 9.9599609375'

(process:14354): Pango-WARNING **: font_face status is: <unknown error status>

(process:14354): Pango-WARNING **: scaled_font status is: invalid matrix (not invertible)

(process:14354): Pango-WARNING **: shaping failure, expect ugly output. shape-engine='BasicEngineFc', font='Helvetica Medium 9.9599609375', text='m'
Loading required package: Matrix
--- finished re-building ‘Introduction.Rmd’

--- re-building ‘Level2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
*** This is beta software. Please report any bugs!
*** See the NEWS file for recent changes.
--- finished re-building ‘Level2.Rmd’

SUMMARY: processing the following file failed:
  ‘Analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'REBayes', 'Rmosek'
Packages unavailable to check Rd xrefs: ‘REBayes’, ‘Rmosek’
Packages suggested but not available for checking:
  'minfi', 'IlluminaHumanMethylation450kmanifest'
Error(s) in re-building vignettes:
  ...
--- re-building ‘comparison_mlr3pipelines_mlr_sklearn.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘comparison_mlr3pipelines_mlr_sklearn.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 172-173 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘FSelector’
Packages suggested but not available for checking:
  'classiFunc', 'FSelector', 'RWeka'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    data   2.4Mb
    help   1.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mnlogit.Rnw’ using Sweave
Package: mnlogit
Version: 1.2.6
Multinomial Logit Choice Models.
Scientific Computing Group, Sentrana Inc.
Loading required package: Formula
Loading required package: zoo

Attaching package: 'zoo'

The following object is masked from 'package:mnlogit':

    index

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

Loading required package: lmtest

Attaching package: 'mlogit'

The following objects are masked from 'package:mnlogit':

    hmftest, scoretest
Running ‘testthat.R’ [10s/117s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Run all unit tests
  > 
  > # This is a wrapper around all the tests specified
  > # in the tests/testthat directory. These tests are visible
  > # to users and serve as small examples as well.
  > testthat::test_check("MODISTools")
  Loading required package: MODISTools
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |===================================                                   |  50%
    |                                                                            
    |======================================================================| 100%
  ── 1. Error: test mt_batch_subset() (@test_download_functions.R#218)  ──────────
  one node produced an error: $ operator is invalid for atomic vectors
  Backtrace:
   1. testthat::expect_is(...)
   4. MODISTools::mt_batch_subset(...)
   5. parallel::parRapply(...)
   7. parallel::clusterApply(...)
   8. parallel:::staticClusterApply(cl, fun, length(x), argfun)
   9. parallel:::checkForRemoteErrors(val)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 24 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: test mt_batch_subset() (@test_download_functions.R#218) 
  
  Error: testthat unit tests failed
  In addition: Warning messages:
  1: In for (i in seq_len(n)) { :
    closing unused connection 5 (<-localhost:11319)
  2: In for (i in seq_len(n)) { :
    closing unused connection 4 (<-localhost:11319)
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   5.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
Running examples in ‘monoreg-Ex.R’ failed
The error most likely occurred in:

> ### Name: monoreg
> ### Title: Bayesian monotonic regression
> ### Aliases: monoreg
> 
> ### ** Examples
> 
> library(monoreg)
> set.seed(1)
> # nobs <- 1000
> nobs <- 50
> sigma <- 0.01
> x1 <- runif(nobs)
> x2 <- runif(nobs)
> 
> # 6 different monotonic regression surfaces:
> # mu <- sqrt(x1)
> mu <- 0.5 * x1 + 0.5 * x2
> # mu <- pmin(x1, x2)
> # mu <- 0.25 * x1 + 0.25 * x2 + 0.5 * (x1 + x2 > 1.0)
> # mu <- 0.25 * x1 + 0.25 * x2 + 0.5 * (pmax(x1, x2) > 0.5)
> # mu <- ifelse((x1 - 1.0)^2 + (x2 - 1.0)^2 < 1.0, sqrt(1.0 - (x1 - 1.0)^2 - (x2 - 1.0)^2), 0.0)
> 
> y <- rnorm(nobs, mu, sigma)
> 
> # results <- monoreg(niter=15000, burnin=5000, adapt=5000, refresh=10, 
> results <- monoreg(niter=5000, burnin=2500, adapt=2500, refresh=10, 
+                    thin=5, birthdeath=10, seed=1, rhoa=0.1, rhob=0.1, 
+                    deltai=0.1, drange=2.0, predict=rep(1.0, nobs), 
+                    include=rep(1.0, nobs), response=y, offset=NULL, 
+                    axes=cbind(x1,x2), covariates=rep(1.0, nobs), 
+                    settozero=getcmat(2), package=rep(1,3)) 
Point process configuration:
1 0 1 
1 1 0 
1 0 0 
     
Packages:
1 
0 
Starting Gibbs sampler:

 *** caught segfault ***
address 6, cause 'memory not mapped'

Traceback:
 1: monoreg(niter = 5000, burnin = 2500, adapt = 2500, refresh = 10,     thin = 5, birthdeath = 10, seed = 1, rhoa = 0.1, rhob = 0.1,     deltai = 0.1, drange = 2, predict = rep(1, nobs), include = rep(1,         nobs), response = y, offset = NULL, axes = cbind(x1,         x2), covariates = rep(1, nobs), settozero = getcmat(2),     package = rep(1, 3))
An irrecoverable exception occurred. R is aborting now ...
Installation failed.
See ‘/home/ripley/R/packages/tests32/mpMap2.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   3.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘msaR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 30-37 (msaR.Rmd) 
Error: processing vignette 'msaR.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘msaR.Rmd’

SUMMARY: processing the following file failed:
  ‘msaR.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘msir.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="webshot2931d025061.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot2931d025061.png': No such file or directory
Quitting from lines 102-104 (msir.Rmd) 
Error: processing vignette 'msir.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘msir.Rmd’

SUMMARY: processing the following file failed:
  ‘msir.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘muHVT.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: unable to access index for repository http://cran.us.r-project.org/src/contrib:
  cannot open URL 'http://cran.us.r-project.org/src/contrib/PACKAGES'
Warning: package 'R.utils' is not available (for R version 3.6.3 RC)
Quitting from lines 18-121 (muHVT.Rmd) 
Error: processing vignette 'muHVT.Rmd' failed with diagnostics:
there is no package called 'R.utils'
--- failed re-building ‘muHVT.Rmd’

SUMMARY: processing the following file failed:
  ‘muHVT.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/MultiBD.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/multicross.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    java  14.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    2.6Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    extdata  16.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.9Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   9.5Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ncmeta)
  > skip_on_os("solaris")
  Error: Reason: On Solaris
  Execution halted
Running examples in ‘NCutYX-Ex.R’ failed
The error most likely occurred in:

> ### Name: ancut
> ### Title: Cluster the Columns of Y into K Groups with the Help of External
> ###   Features X.
> ### Aliases: ancut
> 
> ### ** Examples
> 
> #This sets up the initial parameters for the simulation.
> library(MASS)#for mvrnorm
> library(fields)
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.5-1 (2019-12-12) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: ‘spam’

The following objects are masked from ‘package:base’:

    backsolve, forwardsolve

Loading required package: maps
See https://github.com/NCAR/Fields for
 an extensive vignette, other supplements and source code 
> n=30 #Sample size
> B=50 #Number of iterations in the simulated annealing algorithm.
> L=10000 #Temperature coefficient.
> p=50 #Number of columns of Y.
> q=p #Number of columns of X.
> h1=0.15
> h2=0.25
> 
> S=matrix(0.2,q,q)
> S[1:(q/2),(q/2+1):q]=0
> S[(q/2+1):q,1:(q/2)]=0
> S=S-diag(diag(S))+diag(q)
> 
> mu=rep(0,q)
> 
> W0=matrix(1,p,p)
> W0[1:(p/2),1:(p/2)]=0
> W0[(p/2+1):p,(p/2+1):p]=0
> Denum=sum(W0)
> 
> B2=matrix(0,q,p)
> for (i in 1:(p/2)){
+    B2[1:(q/2),i]=runif(q/2,h1,h2)
+    in1=sample.int(q/2,6)
+    B2[-in1,i]=0
+ }
> 
> for (i in (p/2+1):p){
+    B2[(q/2+1):q,i]=runif(q/2,h1,h2)
+    in2=sample(seq(q/2+1,q),6)
+    B2[-in2,i]=0
+ }
> 
> X=mvrnorm(n, mu, S)
> Z=X%*%B2
> Y=Z+matrix(rnorm(n*p,0,1),n,p)
> #Our method
> Res=ancut(Y=Y,X=X,B=B,L=L,alpha=0,ncv=3)
Error in if (J2 > J) { : missing value where TRUE/FALSE needed
Calls: ancut
Execution halted
Found the following significant warnings:
  generateData.cpp:105:18: warning: passing NULL to non-pointer argument 1 of ‘Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ [-Wconversion-null]
See ‘/home/ripley/R/packages/tests32/NestedCategBayesImpute.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘NetRep.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: C stack usage  234230536 is too close to the limit

 *** caught
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 57-64 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'PCIT'
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introducing_nhanesA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 156-160 (Introducing_nhanesA.Rmd) 
Error: processing vignette 'Introducing_nhanesA.Rmd' failed with diagnostics:
Timeout was reached: [wwwn.cdc.gov] Resolving timed out after 10000 milliseconds
--- failed re-building ‘Introducing_nhanesA.Rmd’

SUMMARY: processing the following file failed:
  ‘Introducing_nhanesA.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    extdata   5.9Mb
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    CppCode  10.4Mb
    R         6.2Mb
    include   5.3Mb
    libs      2.8Mb
    tests     1.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘geocode.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 127-133 (geocode.Rmd) 
Error: processing vignette 'geocode.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘geocode.Rmd’

SUMMARY: processing the following file failed:
  ‘geocode.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [80s/106s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > Sys.setenv("nlmixr_silent"="TRUE")
  > library(testthat)
  > library(nlmixr)
  > 
  > test_check("nlmixr")
  ── 1. Error: parsing functions fix drake compatibility (@test-drake.R#51)  ─────
  object 'progress_bar' not found
  Backtrace:
    1. testthat::expect_equal(make(plan, cache = .cache), NULL)
    4. drake::make(plan, cache = .cache)
    6. drake::drake_config(...)
    7. drake:::logger(verbose = verbose, file = log_make)
    8. refclass_logger$new(verbose = verbose, file = file, progress_bar = progress_bar)
    9. methods::new(def, ...)
   11. methods::initialize(value, ...)
   12. methods::initRefFields(.Object, classDef, selfEnv, list(...))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 253 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: parsing functions fix drake compatibility (@test-drake.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data      4.4Mb
    doc       1.2Mb
    reports   3.8Mb
Found the following significant warnings:
  WrapperNMFGPU.cpp:96:12: warning: converting ‘false’ to pointer type for argument 1 of ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const _CharT*, const _Alloc&) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’ [-Wconversion-null]
See ‘/home/ripley/R/packages/tests32/nmfgpu4R.Rcheck/00install.out’ for details.
Running examples in ‘NMF-Ex.R’ failed
The error most likely occurred in:

> ### Name: NMFfitX-class
> ### Title: Virtual Class to Handle Results from Multiple Runs of NMF
> ###   Algorithms
> ### Aliases: NMFfitX-class
> 
> ### ** Examples
> 
> ## Don't show: 
> # roxygen generated flag
> options(R_CHECK_RUNNING_EXAMPLES_=TRUE)
> ## End(Don't show)
> 
> # generate a synthetic dataset with known classes
> n <- 20; counts <- c(5, 2, 3);
> V <- syntheticNMF(n, counts)
> 
> # perform multiple runs of one algorithm (default is to keep only best fit)
> res <- nmf(V, 3, nrun=3)
# NOTE - CRAN check detected: limiting maximum number of cores [2/16]
Error in big.matrix(nrow = nrow(x), ncol = ncol(x), type = type, init = NULL,  : 
  Error: memory could not be allocated for instance of type big.matrix
Calls: nmf ... gVariable -> <Anonymous> -> <Anonymous> -> big.matrix
Timing stopped at: 0.03 0.033 0.064
Execution halted
Package unavailable to check Rd xrefs: ‘redux’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    7.5Mb
    libs   1.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R            1.7Mb
    test_files   4.4Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    data   1.0Mb
    doc    2.5Mb
    help   2.8Mb
Packages suggested but not available for checking: 'RMark', 'R2ucare'
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    R        2.7Mb
    data     1.0Mb
    libs     4.1Mb
    models   4.4Mb
Running examples in ‘OpenMx-Ex.R’ failed
The error most likely occurred in:

> ### Name: mxModelAverage
> ### Title: Information-Theoretic Model-Averaging and Multimodel Inference
> ### Aliases: mxModelAverage omxAkaikeWeights omxAICWeights
> 
> ### ** Examples
> 
> require(OpenMx)
> data(demoOneFactor)
> factorModel1 <- mxModel(
+ 	"OneFactor1",
+ 	mxMatrix(
+ 		"Full", 5, 1, values=0.8, 
+ 		labels=paste("a",1:5,sep=""),
+ 		free=TRUE, name="A"),
+ 	mxMatrix(
+ 		"Full", 5, 1, values=1,
+ 		labels=paste("u",1:5,sep=""),
+ 		free=TRUE, name="Udiag"),
+ 	mxMatrix(
+ 		"Symm", 1, 1, values=1,
+ 		free=FALSE, name="L"),
+ 	mxAlgebra(vec2diag(Udiag),name="U"),
+ 	mxAlgebra(A %*% L %*% t(A) + U, name="R"),
+ 	mxExpectationNormal(
+ 		covariance = "R",
+ 		dimnames = names(demoOneFactor)),
+ 	mxFitFunctionML(),
+ 	mxData(cov(demoOneFactor), type="cov", numObs=500))
> factorFit1 <- mxRun(factorModel1)
Running OneFactor1 with 10 parameters
Error: C stack usage  204182676 is too close to the limit
Error: The job for model 'OneFactor1' exited abnormally with the error message: User interrupt
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    java     1.3Mb
    models   6.1Mb
Packages suggested but not available for checking:
  'gurobi', 'Rsymphony', 'lpsymphony'
Package required but not available: ‘optiSolve’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [14s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(ordinalNet)
  > testthatInst <- require(testthat)
  Loading required package: testthat
  > 
  > if (testthatInst) test_check("ordinalNet")
  ── 1. Failure: Elastic net sratio matches glmnetcr::glmnet.cr (@test-ordinalNet.
  coef(o) not equal to `coefg`.
  3/7 mismatches (average diff: 0.475)
  [1] -0.572 - 0 == -0.572
  [3] -0.440 - 0 == -0.440
  [4] -0.413 - 0 == -0.413
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 34 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 1 ]
  1. Failure: Elastic net sratio matches glmnetcr::glmnet.cr (@test-ordinalNet.R#213) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘OriGen/libs/OriGen.so’:
  Found ‘__f90_close’, possibly from ‘close’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__f90_esfr’, possibly from ‘read’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__f90_open’, possibly from ‘open’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__f90_rewind’, possibly from ‘rewind’ (Fortran)
    Object: ‘OriGen.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R       1.1Mb
    nifti   4.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Rcpp_API.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘Rcpp_API.Rmd’

--- re-building ‘customisation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘customisation.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 185-198 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘overview.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘ssh’
Package unavailable to check Rd xrefs: ‘ssh’
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(oxcAAR)
  > 
  > test_check("oxcAAR")
  sh: /home/ripley/R/packages/tests32/oxcAAR.Rcheck/tests/testthat/ox_output.js: cannot execute
  ── 1. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_util
  `quickSetupOxcal()` threw an error.
  Message: argument is of length zero
  Class:   simpleError/error/condition
  Backtrace:
   1. testthat::expect_error(quickSetupOxcal(), NA)
   6. oxcAAR::quickSetupOxcal()
  
  ── 2. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_util
  dir.exists("OxCal/bin/") isn't true.
  
  ── 3. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_util
  `%in%`(...) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 94 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_utility_functions.R#30) 
  2. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_utility_functions.R#31) 
  3. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_utility_functions.R#32) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘basic-usage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 24-30 (basic-usage.Rmd) 
Error: processing vignette 'basic-usage.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘basic-usage.Rmd’

SUMMARY: processing the following file failed:
  ‘basic-usage.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.