Crm: no visible global function definition for ‘integrate’
Crm : <anonymous>: no visible global function definition for
  ‘integrate’
Crm: no visible global function definition for ‘optimize’
ail1: no visible global function definition for ‘uniroot’
ail2 : fu : <anonymous>: no visible global function definition for
  ‘integrate’
ail2: no visible global function definition for ‘uniroot’
aip : fu : <anonymous>: no visible global function definition for
  ‘integrate’
aip: no visible global function definition for ‘uniroot’
ait1: no visible global function definition for ‘uniroot’
ait2 : fu : <anonymous>: no visible global function definition for
  ‘integrate’
ait2: no visible global function definition for ‘uniroot’
sim3p3: no visible global function definition for ‘rbinom’
simCrm: no visible global function definition for ‘rbinom’
simCrm: no visible global function definition for ‘palette’
simCrm: no visible global function definition for ‘gray’
simCrm: no visible global function definition for ‘plot’
simCrm: no visible global function definition for ‘abline’
simCrm: no visible global function definition for ‘lines’
ssim3p3: no visible global function definition for ‘txtProgressBar’
ssim3p3: no visible global function definition for ‘setTxtProgressBar’
ssimCrm: no visible global function definition for ‘txtProgressBar’
ssimCrm: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  abline gray integrate lines optimize palette plot rbinom
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("grDevices", "gray", "palette")
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "integrate", "optimize", "rbinom", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
rmd2pdf: no visible global function definition for ‘tail’
rnw2pdf: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Running examples in ‘umap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: predict.umap
> ### Title: project data points onto an existing umap embedding
> ### Aliases: predict.umap
> 
> ### ** Examples
> 
> # embedd iris dataset using default settings
> iris.umap = umap(iris[,1:4])
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
umap
 --- call from context --- 
knn.from.dist(d.dist, k)
 --- call from argument --- 
if (class(d) == "dist") {
    d = as.matrix(d)
}
 --- R stacktrace ---
where 1: knn.from.dist(d.dist, k)
where 2: knn.info(d, config)
where 3: implementations[[method]](d, config)
where 4: umap(iris[, 1:4])

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (d, k) 
{
    if (class(d) == "dist") {
        d = as.matrix(d)
    }
    k = floor(k)
    if (k > ncol(d)) {
        umap.error("number of neighbors must be smaller than number of items")
    }
    if (k <= 1) {
        umap.error("number of neighbors must be greater than 1")
    }
    items = 1:ncol(d)
    indexes = t(apply(d, 1, function(x) {
        items[order(x)][1:k]
    }))
    distances = matrix(0, ncol = k, nrow = nrow(d))
    for (i in 1:nrow(d)) {
        distances[i, ] = d[i, indexes[i, ]]
    }
    rownames(indexes) = rownames(distances) = rownames(d)
    list(indexes = indexes, distances = distances)
}
<bytecode: 0x55681190ae28>
<environment: namespace:umap>
 --- function search by body ---
Function knn.from.dist in namespace umap has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1
ubRacing : predCandidate: no visible global function definition for
  ‘predict’
ubRacing : aux2.friedman.edit: no visible global function definition
  for ‘pchisq’
ubRacing : aux2.friedman.edit: no visible global function definition
  for ‘qt’
ubRacing : aux.friedman.edit: no visible global function definition for
  ‘wilcox.test’
ubRacing : aux.ttest.edit: no visible global function definition for
  ‘t.test’
ubRacing : aux.ttest.edit: no visible global function definition for
  ‘p.adjust’
ubRacing : idFolds: no visible global function definition for
  ‘quantile’
ubRacing: no visible binding for global variable ‘sd’
ubSmoteExs: no visible global function definition for ‘runif’
Undefined global functions or variables:
  p.adjust pchisq predict qt quantile runif sd t.test wilcox.test
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "predict", "qt", "quantile",
             "runif", "sd", "t.test", "wilcox.test")
to your NAMESPACE file.
med: no visible global function definition for ‘quantile’
uh: no visible global function definition for ‘mad’
uh.bu: no visible global function definition for ‘mad’
Undefined global functions or variables:
  mad quantile
Consider adding
  importFrom("stats", "mad", "quantile")
to your NAMESPACE file.
Running examples in ‘ungroup-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pclm2D
> ### Title: Two-Dimensional Penalized Composite Link Model (PCLM-2D)
> ### Aliases: pclm2D
> 
> ### ** Examples
> 
> # Input data
> Dx <- ungroup.data$Dx
> Ex <- ungroup.data$Ex
> 
> # Aggregate data to ungroup it in the examples below
> x      <- c(0, 1, seq(5, 85, by = 5))
> nlast  <- 26
> n      <- c(diff(x), nlast)
> group  <- rep(x, n)
> y      <- aggregate(Dx, by = list(group), FUN = "sum")[, -1]
> offset <- aggregate(Ex, by = list(group), FUN = "sum")[, -1]
> 
> # Example 1 ---------------------- 
> # Fit model and ungroup data using PCLM-2D
> P1 <- pclm2D(x, y, nlast)
   Ungrouping data       ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
ungroup
 --- call from context --- 
eval(substitute(expr), data, enclos = parent.frame())
 --- call from argument --- 
if (L) f1(fit) else apply(fit, 2, FUN = f1)
 --- R stacktrace ---
where 1: eval(substitute(expr), data, enclos = parent.frame())
where 2: eval(substitute(expr), data, enclos = parent.frame())
where 3: with.default(M, if (L) f1(fit) else apply(fit, 2, FUN = f1))
where 4: with(M, if (L) f1(fit) else apply(fit, 2, FUN = f1))
where 5: delete.artificial.bin(R)
where 6: pclm2D(x, y, nlast)

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
 --- function search by body ---
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1
dudewicz.unif.test: no visible global function definition for ‘runif’
frosini.unif.test: no visible global function definition for ‘runif’
hegazy.unif.test: no visible global function definition for ‘runif’
kolmogorov.unif.test: no visible global function definition for ‘runif’
kuiper.unif.test: no visible global function definition for ‘runif’
neyman.unif.test: no visible global function definition for ‘runif’
quesenberry.unif.test: no visible global function definition for
  ‘runif’
sarkadi.unif.test: no visible global function definition for ‘runif’
sherman.unif.test: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
cumcount: no visible global function definition for ‘setNames’
uniqtag: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/unix.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘USAboundariesData’
readSEER: no visible global function definition for ‘read.fwf’
Undefined global functions or variables:
  read.fwf
Consider adding
  importFrom("utils", "read.fwf")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘UScensus2000cdp/R/zzz.R’:
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat(paste("copyright (c) 2009, Zack W. Almquist, University of California-Irvine\n",     sep = ""))
    cat("For citation information, type citation(\"UScensus2000cdp\").\n")
    cat("Type help(package=\"UScensus2000cdp\") to get started.\n")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘UScensus2000tract/R/zzz.R’:
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat(paste("copyright (c) 2009, Zack W. Almquist, University of California-Irvine\n",     sep = ""))
    cat("For citation information, type citation(\"UScensus2000tract\").\n")
    cat("Type help(package=\"UScensus2000tract\") to get started.\n")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.
Found the following hidden files and directories:
  data/.Rhistory
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘rgdal’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘foreign’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/uuid.Rcheck/00install.out’ for details.
File ‘uuid/libs/uuid.so’:
  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.
histw: no visible global function definition for ‘plot.new’
histw: no visible global function definition for ‘plot.window’
histw: no visible global function definition for ‘axis’
histw: no visible global function definition for ‘rect’
histw: no visible global function definition for ‘lines’
uwham.boot: no visible binding for global variable ‘var’
Undefined global functions or variables:
  axis lines plot.new plot.window rect var
Consider adding
  importFrom("graphics", "axis", "lines", "plot.new", "plot.window",
             "rect")
  importFrom("stats", "var")
to your NAMESPACE file.
Found the following significant warnings:
  'config' variable 'CXXCPP' is deprecated
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/V8.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘PredValidationPlots.pdf’ ‘RepStructValidationPlots.pdf’
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-devel-gcc/Work/PKGS/validatejsonr.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘validatejsonr.Rmd’
Package vignette with placeholder title ‘Vignette Title’:
  ‘intro-to-varbundle.Rmd’
Mammen: no visible global function definition for ‘runif’
PR2: no visible global function definition for ‘ar.burg’
PR2: no visible global function definition for ‘pt’
PR2: no visible global function definition for ‘pf’
PR3: no visible global function definition for ‘ar.burg’
PR3: no visible global function definition for ‘pt’
PR3: no visible global function definition for ‘pf’
VAR.FOR: no visible global function definition for ‘qnorm’
VAR.ForeB: no visible global function definition for ‘runif’
VAR.LRtest: no visible global function definition for ‘pchisq’
VAR.LRtest: no visible global function definition for ‘pf’
VAR.PI: no visible global function definition for ‘quantile’
VAR.Waldtest: no visible global function definition for ‘pf’
VAR.irf: no visible global function definition for ‘par’
VAR.irf: no visible global function definition for ‘plot’
VAR.irf: no visible global function definition for ‘abline’
VAR1.sim: no visible global function definition for ‘rnorm’
resamp: no visible global function definition for ‘runif’
Undefined global functions or variables:
  abline ar.burg par pchisq pf plot pt qnorm quantile rnorm runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "ar.burg", "pchisq", "pf", "pt", "qnorm",
             "quantile", "rnorm", "runif")
to your NAMESPACE file.
Found the following files/directories:
  ‘Output.txt’ ‘Overlap.csv’ ‘Polar coordinates.csv’
black_scholes: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
burdenPlot: no visible global function definition for ‘density’
burdenPlot: no visible global function definition for ‘axis’
burdenPlot: no visible global function definition for ‘points’
burdenPlot: no visible global function definition for ‘lines’
burdenPlot: no visible global function definition for ‘abline’
burdenPlot: no visible global function definition for ‘text’
burdenPlot: no visible global function definition for ‘sd’
burdenPlot: no visible global function definition for ‘segments’
vbdm: no visible global function definition for ‘var’
vbdm: no visible global function definition for ‘pchisq’
vbdmR : run_discrete_mixture_vanilla: no visible global function
  definition for ‘var’
vbdmR: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  abline axis density lines pchisq points sd segments text var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "points", "segments",
             "text")
  importFrom("stats", "density", "pchisq", "sd", "var")
to your NAMESPACE file.
compute_KL : rtnorm: no visible global function definition for ‘runif’
compute_KL : rtnorm: no visible global function definition for ‘dnorm’
compute_KL: no visible global function definition for ‘qnorm’
compute_KL: no visible global function definition for ‘dnorm’
compute_KL: no visible global function definition for ‘pnorm’
compute_KL: no visible global function definition for ‘var’
compute_KL: no visible global function definition for ‘rbinom’
compute_KL: no visible global function definition for ‘rnorm’
compute_KL: no visible global function definition for ‘sd’
vbsr: no visible global function definition for ‘qchisq’
vbsr: no visible global function definition for ‘var’
vbsr: no visible global function definition for ‘pchisq’
vbsr: no visible global function definition for ‘sd’
vbsr: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  dnorm pchisq pnorm qchisq qnorm rbinom rnorm runif sd var
Consider adding
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qchisq", "qnorm",
             "rbinom", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘VBTree_vignette.Rmd’
Running ‘testthat.R’ [11s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(vctrs)
  > 
  > test_check("vctrs")
  ── 1. Failure: vec_slice() unclasses input before calling `vec_restore()` (@test
  `class` not identical to "matrix".
  Lengths differ: 2 is not 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 2001 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: vec_slice() unclasses input before calling `vec_restore()` (@test-slice.R#255) 
  
  Error: testthat unit tests failed
  Execution halted
Compare2FDS: no visible global function definition for ‘runif’
Compare2FDS: no visible global function definition for ‘lm’
Compare2FDS: no visible global function definition for ‘model.matrix’
Compare2FDS: no visible global function definition for ‘plot’
Compare2FDS: no visible global function definition for ‘abline’
Compare2FDS: no visible global function definition for ‘lines’
Compare2FDS: no visible global function definition for ‘text’
Compare2Vdg: no visible global function definition for ‘par’
Compare2Vdg: no visible global function definition for ‘plot’
Compare2Vdg: no visible global function definition for ‘lines’
Compare2Vdg: no visible global function definition for ‘legend’
FDSPlot: no visible global function definition for ‘runif’
FDSPlot: no visible global function definition for ‘lm’
FDSPlot: no visible global function definition for ‘model.matrix’
FDSPlot: no visible global function definition for ‘plot’
FDSPlot: no visible global function definition for ‘abline’
Vdgraph: no visible global function definition for ‘par’
Vdgraph: no visible global function definition for ‘plot’
Vdgraph: no visible global function definition for ‘lines’
Vdgraph: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline legend lines lm model.matrix par plot runif text
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "plot",
             "text")
  importFrom("stats", "lm", "model.matrix", "runif")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘vdmR-vignette.Rnw’ using knitr
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Quitting from lines 189-193 (vdmR-vignette.Rnw) 
Error: processing vignette 'vdmR-vignette.Rnw' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘vdmR-vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘vdmR-vignette.Rnw’

Error: Vignette re-building failed.
Execution halted
calculateParameters,AffineTransformation: no visible global function
  definition for ‘lm’
calculateParameters,AffineTransformation: no visible global function
  definition for ‘coef’
calculateParameters,SimilarityTransformation: no visible global
  function definition for ‘lm’
calculateParameters,SimilarityTransformation: no visible global
  function definition for ‘coef’
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for ‘points’
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for ‘legend’
Undefined global functions or variables:
  coef legend lm points
Consider adding
  importFrom("graphics", "legend", "points")
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
DrawDensity3D: no visible global function definition for ‘colorRamp’
DrawDensity3D: no visible global function definition for ‘rgb’
ReadFromFile3D: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  colorRamp read.table rgb
Consider adding
  importFrom("grDevices", "colorRamp", "rgb")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' call to ‘stats’ which was already attached by Depends.
  Please remove these calls from your code.
H: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = H, func.arg = list(func.arg), boot.arg)):
  partial argument match of ‘arg’ to ‘args’
M.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = M.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
Rel.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = Rel.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
bootstrap: warning in do.call(what = func, arg = list(boots[, , i])):
  partial argument match of ‘arg’ to ‘args’
bootstrap: warning in do.call(what = func, arg = c(abundances =
  list(boots[, , i]), func.arg)): partial argument match of ‘arg’ to
  ‘args’
d: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = d, func.arg = list(func.arg), boot.arg)):
  partial argument match of ‘arg’ to ‘args’
sim.groups: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of ‘arg’ to ‘args’
sim.table: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of ‘arg’ to ‘args’
similarity: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = similarity, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
turnover: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = turnover, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
Found the following files/directories:
  ‘Fig3-1_triple_labels_sub_and_superscripts.tiff’
  ‘Fig3-2_Euler_3set_simple_with_subscripts.tiff’
  ‘Pairwise_Venn_diagram.tiff’ ‘Quad_Venn_diagram.tiff’
  ‘Quintuple_Venn_diagram.tiff’ ‘Single_Venn_diagram.tiff’
  ‘Triple_Venn_diagram.tiff’ ‘Venn_2set_complex.tiff’
  ‘Venn_4set_pretty.tiff’ ‘Venn_5set_pretty.tiff’
plot.VennDiagram : <anonymous>: no visible global function definition
  for ‘hcl’
plot.VennDiagram: no visible global function definition for ‘plot.new’
plot.VennDiagram: no visible global function definition for
  ‘plot.window’
plot.VennDiagram: no visible global function definition for ‘col2rgb’
plot.VennDiagram: no visible global function definition for ‘rgb’
plot.VennDiagram: no visible global function definition for ‘polygon’
plot.VennDiagram: no visible global function definition for ‘text’
plot.VennDiagram: no visible global function definition for ‘title’
Undefined global functions or variables:
  col2rgb hcl plot.new plot.window polygon rgb text title
Consider adding
  importFrom("grDevices", "col2rgb", "hcl", "rgb")
  importFrom("graphics", "plot.new", "plot.window", "polygon", "text",
             "title")
to your NAMESPACE file.
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 ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/VICmodel.Rcheck/00install.out’ for details.
vif: no visible global function definition for ‘sd’
vif: no visible global function definition for ‘lm’
vif: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  lm pnorm sd
Consider adding
  importFrom("stats", "lm", "pnorm", "sd")
to your NAMESPACE file.
hyperpara: no visible binding for global variable ‘var’
hyperpara: no visible global function definition for ‘hist’
Undefined global functions or variables:
  hist var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "var")
to your NAMESPACE file.
panel.meansdplot : meansdplot.stats: no visible global function
  definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
viopoints.default: no visible global function definition for ‘par’
viopoints.default: no visible global function definition for ‘plot.new’
viopoints.default: no visible global function definition for
  ‘plot.window’
viopoints.default: no visible global function definition for ‘axis’
viopoints.default: no visible global function definition for ‘arrows’
viopoints.default: no visible global function definition for
  ‘getFromNamespace’
viopoints.default: no visible global function definition for ‘title’
viopoints.default: no visible global function definition for ‘box’
Undefined global functions or variables:
  arrows axis box getFromNamespace par plot.new plot.window title
Consider adding
  importFrom("graphics", "arrows", "axis", "box", "par", "plot.new",
             "plot.window", "title")
  importFrom("utils", "getFromNamespace")
to your NAMESPACE file.
Missing or unexported object: ‘jsonlite::rbind.pages’
Decile.Plot: no visible global function definition for ‘barplot’
Decile.Plot: no visible global function definition for ‘axis’
Sliding.Window: no visible global function definition for ‘plot’
Sliding.Window: no visible global function definition for ‘lines’
Sliding.Window: no visible global function definition for ‘legend’
Undefined global functions or variables:
  axis barplot legend lines plot
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "plot")
to your NAMESPACE file.
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.
Found the following files/directories:
  ‘multinom_divorced.png’ ‘multinom_married.png’
  ‘multinom_patientsummary.png’ ‘multinom_patientsummary2.png’
  ‘multinom_widowed.png’ ‘multinomp_divorced.png’
  ‘multinomp_divorced_wing.png’ ‘multinomp_married.png’
  ‘multinomp_married_wing.png’ ‘multinomp_single.png’
  ‘multinomp_widowed.png’ ‘multinomp_widowed_wing.png’ ‘mysummary.Rnw’
  ‘mysummary.html’ ‘mysummary1.Rnw’ ‘mysummary1.html’
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘walker.Rmd’ using rmarkdown
Quitting from lines 76-78 (walker.Rmd) 
Error: processing vignette 'walker.Rmd' failed with diagnostics:
is_3d_array(x) is not TRUE
--- failed re-building ‘walker.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘test-all.R’ [7s/9s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("walkr")
  Loading required package: walkr
  ── 1. Failure: Testing Walkr Output (@test.walkr.output.R#35)  ─────────────────
  class(z1_har) not equal to "matrix".
  Lengths differ: 2 is not 1
  
  ── 2. Failure: Testing Walkr Output (@test.walkr.output.R#36)  ─────────────────
  class(z1_dikin) not equal to "matrix".
  Lengths differ: 2 is not 1
  
  ── 3. Failure: Testing Walkr Output (@test.walkr.output.R#37)  ─────────────────
  class(z2_har) not equal to "matrix".
  Lengths differ: 2 is not 1
  
  ── 4. Failure: Testing Walkr Output (@test.walkr.output.R#38)  ─────────────────
  class(z2_dikin) not equal to "matrix".
  Lengths differ: 2 is not 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 93 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: Testing Walkr Output (@test.walkr.output.R#35) 
  2. Failure: Testing Walkr Output (@test.walkr.output.R#36) 
  3. Failure: Testing Walkr Output (@test.walkr.output.R#37) 
  4. Failure: Testing Walkr Output (@test.walkr.output.R#38) 
  
  Error: testthat unit tests failed
  Execution halted
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.
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.
Found the following files/directories:
  ‘TESTLIST1.txt’ ‘TESTLIST2.txt’
  ‘kME_correlations_between_A_and_B_inMod.pdf’ ‘testEnrichment.csv’
Running examples in ‘whiboclustering-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.whibo_cluster
> ### Title: Plot WhiBo Cluster Representatives
> ### Aliases: plot.whibo_cluster
> 
> ### ** Examples
> 
> data <- iris[, 1:4] #Numerical data only
> 
> model <- whibo_clustering(data = data, k = 3)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
whiboclustering
 --- call from context --- 
wc_initialize(data = data, k = k, initialization_type = cluster_initialization_type)
 --- call from argument --- 
if (!(class(data) %in% c("data.frame", "matrix"))) {
    stop("Data should be data.frame or matrix")
}
 --- R stacktrace ---
where 1: wc_initialize(data = data, k = k, initialization_type = cluster_initialization_type)
where 2: whibo_clustering(data = data, k = 3)

 --- value of length: 2 type: logical ---
[1] FALSE  TRUE
 --- function from context --- 
function (data, k = 3, initialization_type) 
{
    if (!(tolower(initialization_type) %in% tolower(wc_init_types$Type))) {
        stop("Please enter initialization function that is available in wc_init_types data frame")
    }
    if (!(class(data) %in% c("data.frame", "matrix"))) {
        stop("Data should be data.frame or matrix")
    }
    if (!is.numeric(k)) {
        stop("k should be numeric")
    }
    centroids <- eval(call(name = as.character(wc_init_types$Method[tolower(wc_init_types$Type) == 
        tolower(initialization_type)]), data, k))
    return(centroids)
}
<bytecode: 0x55e160f94498>
<environment: namespace:whiboclustering>
 --- function search by body ---
Function wc_initialize in namespace whiboclustering has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1
dlog.norm: no visible global function definition for ‘rnorm’
fun.load.hals.a: no visible global function definition for ‘sfExport’
fun.load.hals.a: no visible global function definition for ‘sfLibrary’
fun.load.hals.fill: no visible global function definition for
  ‘sfExport’
fun.load.hals.fill: no visible global function definition for
  ‘sfLibrary’
fun.load.widals.a: no visible global function definition for ‘sfExport’
fun.load.widals.a: no visible global function definition for
  ‘sfLibrary’
fun.load.widals.fill: no visible global function definition for
  ‘sfExport’
fun.load.widals.fill: no visible global function definition for
  ‘sfLibrary’
unif.mh: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif sfExport sfLibrary
Consider adding
  importFrom("stats", "rnorm", "runif")
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.
Running examples in ‘windfarmGA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: barometric_height
> ### Title: Calculates Air Density, Air Pressure and Temperature according
> ###   to the Barometric Height Formula
> ### Aliases: barometric_height
> 
> ### ** Examples
> 
> data <- matrix(seq(0,5000,500));
> barometric_height(data)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
windfarmGA
 --- call from context --- 
barometric_height(data)
 --- call from argument --- 
if (class(data) != "data.frame") {
    data <- data.frame(data)
}
 --- R stacktrace ---
where 1: barometric_height(data)

 --- value of length: 2 type: logical ---
[1] TRUE TRUE
 --- function from context --- 
function (data, height, po = 101325, ro = 1.225) 
{
    if (is.numeric(data) || (ncol(data)) == 1) {
        ph <- as.numeric(po * exp(-data * 0.0001252))
        rh <- as.numeric(ro * exp(-data * 0.0001252))
        Th <- as.numeric(288.15 - ((6.5 * data)/1000))
    }
    else {
        if (missing(height)) {
            stop("Height column not given.")
        }
        data <- data[, height]
        ph <- po * exp(-data * 0.0001252)
        rh <- ro * exp(-data * 0.0001252)
        Th <- 288.15 - ((6.5 * data)/1000)
    }
    if (class(data) != "data.frame") {
        data <- data.frame(data)
    }
    colnames(data) <- "Height"
    celsius <- as.numeric(Th - 273.15)
    data$ph <- ph
    data$rh <- rh
    data$tempK <- Th
    data$tempC <- celsius
    return(data)
}
<bytecode: 0x55ef3f5569e0>
<environment: namespace:windfarmGA>
 --- function search by body ---
Function barometric_height in namespace windfarmGA has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1
Found the following files/directories:
  ‘foo’
Running examples in ‘wkb-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: readWKB
> ### Title: Convert WKB to Spatial Objects
> ### Aliases: readWKB
> ### Keywords: wkb
> 
> ### ** Examples
> 
> # create a list of WKB geometry representations of type Point
> wkb <- list(
+   as.raw(c(0x01, 0x01, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
+            0xf0, 0x3f, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x08, 0x40)),
+   as.raw(c(0x01, 0x01, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
+            0x00, 0x40, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x40))
+ )
> 
> # convert to object of class SpatialPoints
> obj <- readWKB(wkb)
> 
> 
> # create a list of WKB geometry representations of type MultiPoint
> wkb <- list(
+   as.raw(c(0x01, 0x04, 0x00, 0x00, 0x00, 0x01, 0x00, 0x00, 0x00, 0x01, 0x01,
+            0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0xf0, 0x3f,
+            0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x08, 0x40)),
+   as.raw(c(0x01, 0x04, 0x00, 0x00, 0x00, 0x01, 0x00, 0x00, 0x00, 0x01, 0x01,
+            0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x40,
+            0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x40)))
> 
> # convert to list of objects of class SpatialPoints
> obj <- readWKB(wkb)
Error in vapply(obj, class, character(1)) : values must be length 1,
 but FUN(X[[1]]) result is length 2
Calls: readWKB -> unique -> vapply
Execution halted
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(wkb)
  > 
  > test_check("wkb")
  ── 1. Error: little-endian WKB MultiPoint representation converts to list of Spa
  values must be length 1,
   but FUN(X[[1]]) result is length 2
  Backtrace:
   1. wkb::readWKB(refwkb)
   3. base::vapply(obj, class, character(1))
  
  ── 2. Error: big-endian WKB MultiPoint representation converts to list of Spatia
  values must be length 1,
   but FUN(X[[1]]) result is length 2
  Backtrace:
   1. wkb::readWKB(refwkbbe)
   3. base::vapply(obj, class, character(1))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 21 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: little-endian WKB MultiPoint representation converts to list of SpatialPoints objects (@testmultipoint.R#32) 
  2. Error: big-endian WKB MultiPoint representation converts to list of SpatialPoints objects (@testmultipoint.R#48) 
  
  Error: testthat unit tests failed
  Execution halted
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’
Found the following significant warnings:
  assp/dsputils.c:414:13: warning: value computed is not used [-Wunused-value]
  assp/labelobj.c:165:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/wrassp.Rcheck/00install.out’ for details.
Running examples in ‘WrightMap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ppPlot
> ### Title: Person probability plots
> ### Aliases: ppPlot cutLines kidmap
> 
> ### ** Examples
> 
> 	
> 	fpath <- system.file("extdata", package="WrightMap")
> 	model1 <- CQmodel(p.est = file.path(fpath,"ex2.eap"), show = file.path(fpath,"ex2.shw"))
> 	
> 	#Person histogram, modern item
> 	ppPlot(model1,est = 0, SE = 1) 
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
WrightMap
 --- call from context --- 
unpack.GIN(model$GIN)
 --- call from argument --- 
if (class(GIN) == "matrix") return(GIN) else {
    return(do.call(cbind, lapply(GIN, unpack.GIN)))
}
 --- R stacktrace ---
where 1: unpack.GIN(model$GIN)
where 2: itemData.CQmodel(thresholds, ...)
where 3: itemData(thresholds, ...)
where 4: wrightMap(thetas, thresholds, main.title = main.title, person.points = est, 
    person.range = c(est - SE, est + SE), cutpoints = cutpoints, 
    cut.lab.text = c("20%", "40%", "50%", "60%", "80%"), cut.left = cut.left, 
    cut.right = cut.right, cut.lab.adj = cut.lab.adj, ...)
where 5: ppPlot(model1, est = 0, SE = 1)

 --- value of length: 2 type: logical ---
[1]  TRUE FALSE
 --- function from context --- 
function (GIN) 
{
    if (class(GIN) == "matrix") 
        return(GIN)
    else {
        return(do.call(cbind, lapply(GIN, unpack.GIN)))
    }
}
<bytecode: 0x56060d7759a0>
<environment: 0x56060be291e8>
 --- function search by body ---
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1
Running examples in ‘wrMisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lrbind
> ### Title: rbind on lists
> ### Aliases: lrbind
> 
> ### ** Examples
> 
> lst1 <- list(matrix(1:9,nc=3,dimnames=list(letters[1:3],c("AA","BB","CC"))),
+   11:13,matrix(51:56,ncol=3))
> lrbind(lst1)
Error in matrix(lst[[i]], ncol = ncol(lst[[which(lclass == "matrix")[1]]])) : 
  non-numeric matrix extent
Calls: lrbind -> matrix
Execution halted
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:
  ‘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’
Found the following files/directories:
  ‘myXLfile.xlsx’ ‘myXLfile_2019_11_27_001302.xlsx’
  ‘myXLfile_2019_11_27_001304.xlsx’ ‘myXLfile_2019_11_27_001306.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.
Non-standard files/directories found at top level:
  ‘Bug.R’ ‘Bugs.html’ ‘Check’ ‘CodeDetails’ ‘DESCRIPTION.in’ ‘Docs’
  ‘FAQ.html’ ‘FIXME_NOW’ ‘GNUmakefile’ ‘GNUmakefile.admin’
  ‘Makevars.in’ ‘MemoryBug.R’ ‘NAMESPACE.in’ ‘NodeFuns’ ‘Notes’
  ‘QuestionSolutions’ ‘README.windows’ ‘Rsamples’ ‘TAGS’
  ‘Todo-orig.html’ ‘Todo.xml’ ‘VersionInfo’ ‘addFinalizer’ ‘checkLinks’
  ‘dotCalls’ ‘expat’ ‘index.html’ ‘index.html.in’ ‘libxml’
  ‘libxml2.9.R’ ‘scrapingData.xml’ ‘testRemoveFinalizers.R’
  ‘testRemoveFinalizers.c’ ‘xpathPointer.xml’
newXMLDoc: no visible binding for global variable ‘doc’
source: no visible binding for global variable ‘use_file’
xmlFlatListTree : f: no visible binding for global variable ‘nodeNames’
xmlFlatListTree : f: no visible binding for global variable ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘nodeSet’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘nodeSet’
xmlFlatListTree : addNode: no visible binding for global variable ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘nodeNames’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘nodeNames’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘parentCount’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘parentCount’
xmlFlatListTree : <anonymous>: no visible binding for global variable
  ‘e’
xmlFlatTree : <anonymous>: no visible binding for global variable ‘e’
Undefined global functions or variables:
  doc e idx nodeNames nodeSet parentCount use_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’
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’
Found the following significant warnings:
  emitter.c:28:6: warning: value computed is not used [-Wunused-value]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/yaml.Rcheck/00install.out’ for details.
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.
Running examples in ‘YPmodel-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: YPmodel-package
> ### Title: The short-term and long-term hazard ratio model for survival
> ###   data
> ### Aliases: YPmodel-package
> ### Keywords: Survival analysis
> 
> ### ** Examples
> 
> 	library(YPmodel)
> 	data(gastric)
> 	YPmodel(gastric, repNum=100)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
YPmodel
 --- call from context --- 
fun.flipud(s1)
 --- call from argument --- 
if (class(data) != "matrix") {
    data <- matrix(data, nrow = length(data), ncol = 1)
}
 --- R stacktrace ---
where 1: fun.flipud(s1)
where 2: fun.cumsum(fun.flipud(s1))
where 3: fun.flipud(fun.cumsum(fun.flipud(s1)))
where 4: fun.adlgrk(beta, r, Data)
where 5: YPmodel.adlgrk(data = data, Estimate = Estimate)
where 6: YPmodel.default(gastric, repNum = 100)
where 7: YPmodel(gastric, repNum = 100)

 --- value of length: 2 type: logical ---
[1] FALSE  TRUE
 --- function from context --- 
function (data) 
{
    if (class(data) != "matrix") {
        data <- matrix(data, nrow = length(data), ncol = 1)
    }
    size <- dim(data)
    Output <- data
    for (j in 1:size[2]) {
        for (i in 1:size[1]) {
            Output[i, j] <- data[size[1] + 1 - i, j]
        }
    }
    return(Output)
}
<bytecode: 0x55b061756e18>
<environment: namespace:YPmodel>
 --- function search by body ---
Function fun.flipud in namespace YPmodel has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1
Found the following files/directories:
  ‘installed_pkgs.rda’
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  5.3Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.4Mb
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  9.3Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
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  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
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: ‘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  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
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  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
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.
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.
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 18.4Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
Error(s) in re-building vignettes:
--- re-building ‘intro.Rmd’ using rmarkdown
Loading required package: R6
--- finished re-building ‘intro.Rmd’

--- re-building ‘traits.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'traits.Rmd' failed with diagnostics:
Failed to compile traits.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See traits.log for more info.
--- failed re-building ‘traits.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘jsonlite’ ‘rlang’
  All declared Imports should be used.
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
Error(s) in re-building vignettes:
--- re-building ‘Introduction.Rmd’ using rmarkdown_notangle
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
Failed to compile Introduction.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See Introduction.log for more info.
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘devtools’ ‘gridExtra’
  All declared Imports should be used.
File ‘AMORE/libs/AMORE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘shinyjs’
  All declared Imports should be used.
Found the following files/directories:
  ‘ORdensity_2019-11-23.jpeg’ ‘discordanceDelta_2019-11-23.txt’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘magrittr’
  All declared Imports should be used.
installed size is 26.8Mb
  sub-directories of 1Mb or more:
    libs  25.4Mb
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.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rgdal’
  All declared Imports should be used.
installed size is 56.8Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs    55.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   1.8Mb
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
Found the following files/directories:
  ‘res1.RData’ ‘res2.RData’ ‘res_alpha1.RData’ ‘res_alpha2.RData’
  ‘res_beta1.RData’ ‘res_beta2.RData’ ‘res_ns1.RData’ ‘res_ns2.RData’
Namespaces in Imports field not imported from:
  ‘MASS’ ‘evd’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Namespaces in Imports field not imported from:
  ‘curl’ ‘httr’
  All declared Imports should be used.
possible bashism in cleanup line 5 (brace expansion):
  rm -rf vignettes/rmd/auto/ vignettes/rmd/*.{log,aux,out,tex,blg,bbl,xwm} \
     vignettes/rmd/pinp.cls vignettes/rmd/jss.bst
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/apcf.Rcheck/00install.out’ for details.
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  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
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.
Namespace in Imports field not imported from: ‘sp’
  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  6.4Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.5Mb
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.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
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.
File ‘attrCUSUM/libs/attrCUSUM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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.
Error(s) in re-building vignettes:
--- re-building ‘Data_Analysis_with_augmentedRCBD.Rmd’ using rmarkdown_notangle
trying URL 'https://www.r-project.org/logo/Rlogo.png'
Content type 'image/png' length 48148 bytes (47 KB)
==================================================
downloaded 47 KB

trying URL 'https://raw.githubusercontent.com/aravind-j/augmentedRCBD/master/vignettes/rbase.png'
Content type 'image/png' length 57299 bytes (55 KB)
==================================================
downloaded 55 KB

trying URL 'https://github.com/aravind-j/augmentedRCBD/raw/master/vignettes/rstudio.png'
Content type 'image/png' length 91730 bytes (89 KB)
==================================================
downloaded 89 KB

trying URL 'https://github.com/aravind-j/augmentedRCBD/raw/master/vignettes/rstudio%20panes.png'
Content type 'image/png' length 86653 bytes (84 KB)
==================================================
downloaded 84 KB

! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'Data_Analysis_with_augmentedRCBD.Rmd' failed with diagnostics:
Failed to compile Data_Analysis_with_augmentedRCBD.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See Data_Analysis_with_augmentedRCBD.log for more info.
--- 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
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 13.4Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘jsonlite’
  All declared Imports should be used.
Found the following significant warnings:
  'config' variable 'CXXCPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/av.Rcheck/00install.out’ for details.
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  8.2Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   3.3Mb
Namespace in Imports field not imported from: ‘glpkAPI’
  All declared Imports should be used.
installed size is 75.6Mb
  sub-directories of 1Mb or more:
    libs  74.7Mb
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.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   2.0Mb
File ‘BAMMtools/libs/BAMMtools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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   4.6Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘docopt’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ranger’
  All declared Imports should be used.
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 10.6Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.1Mb
    libs   5.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.9Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
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.
installed size is 70.2Mb
  sub-directories of 1Mb or more:
    libs  69.3Mb
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.
Found the following significant warnings:
  Blasso.cpp:451:51: warning: assigning field to itself [-Wself-assign-field]
See ‘/data/gannet/ripley/R/packages/tests-clang/bayesCL.Rcheck/00install.out’ for details.
Running examples in ‘bayesCL-Ex.R’ failed
The error most likely occurred in:

> ### Name: lasso
> ### Title: Bayesian Lasso
> ### Aliases: lasso
> ### Keywords: regression
> 
> ### ** Examples
> 
> 
> set.seed(0)
> n_samples  <- 500
> n_features <- 40
> X <- matrix(rnorm(n_features * n_samples), nrow = n_samples)
> y <- 2 * X[,1] - 3 * X[,2] + rnorm(n_samples) # only features 1 & 2 are relevant
> 
> X_train <- X[1:400,]
> y_train <- y[1:400]
> X_test  <- X[401:500,]
> y_test  <- y[401:500]
> 
> 
> # START ------------------------------------------------------------------------
> 
> # first, standardize data !!!
> X_train <- scale(X_train)
> 
> tmp00 <- bayesCL::lasso(X = X_train, 
+                           y = y_train, 
+                           T = 500,  # number of Gibbs sampling iterations
+                           icept = T,
+                           device=0  ) # use constant term (intercept), we do
------------------------------
Platform and device selection

 *** caught segfault ***
address 0x1421c500, cause 'memory not mapped'

Traceback:
 1: prepare(precision = 0, device = device, parameters = parameters)
 2: bayesCL::lasso(X = X_train, y = y_train, T = 500, icept = T,     device = 0)
An irrecoverable exception occurred. R is aborting now ...
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.
File ‘bayesDccGarch/libs/bayesDccGarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 66.9Mb
  sub-directories of 1Mb or more:
    libs  66.1Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MatrixModels’
  All declared Imports should be used.
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs  14.9Mb
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 ‘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  6.6Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.3Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
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  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 31.3Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs  26.9Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   4.1Mb
Namespaces in Imports field not imported from:
  ‘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  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
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 117.0Mb
  sub-directories of 1Mb or more:
    libs  116.9Mb
File ‘BayHap/libs/BayHap.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘mcmc.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘mcmc.o’
File ‘BayHap/libs/BayHap.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 files/directories:
  ‘outhaplo231119064434619YDGABKNRWJ.txt’
  ‘outhaplo231119064437724XNBMRYFAHT.txt’
  ‘outhaplo231119064444775LOATCFJWUY.txt’
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘matrixStats’ ‘reshape2’ ‘scales’
  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.
Namespace in Imports field not imported from: ‘methods’
  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.
Error(s) in re-building vignettes:
--- re-building ‘BClustLonG.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'BClustLonG.Rmd' failed with diagnostics:
Failed to compile BClustLonG.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See BClustLonG.log for more info.
--- failed re-building ‘BClustLonG.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘bclust/libs/bclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rlang’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘BCSub.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'BCSub.Rmd' failed with diagnostics:
Failed to compile BCSub.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See BCSub.log for more info.
--- failed re-building ‘BCSub.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 98.7Mb
  sub-directories of 1Mb or more:
    libs  97.2Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
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 41.5Mb
  sub-directories of 1Mb or more:
    libs  40.5Mb
Namespace in Imports field not imported from: ‘compiler’
  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.
installed size is 153.5Mb
  sub-directories of 1Mb or more:
    include  153.4Mb
Found the following files/directories:
  ‘PceEstimates’ ‘mcmcDiagnostics’ ‘output.csv’ ‘plots’
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.
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 11.7Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   9.8Mb
File ‘bigalgebra/libs/bigalgebra.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 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.
possible bashism in configure line 399 (trap with signal numbers):
  trap 'rm -fr conftest* confdefs* core core.* *.core $ac_clean_files; exit 1' 1 2 15
  possible bashism in configure line 511 (unsafe echo with backslash):
  if (echo "testing\c"; echo 1,2,3) | grep c >/dev/null; then
  possible bashism in configure line 513 (echo -n):
    if (echo -n testing; echo 1,2,3) | sed s/-n/xn/ | grep xn >/dev/null; then
  possible bashism in configure line 526 (test -a/-o):
  if test /usr/local != "$exec_prefix" -a /usr/local != "$prefix" ; then
  possible bashism in configure line 595 (trap with signal numbers):
  trap '' 1 2 15
  possible bashism in configure line 643 (trap with signal numbers):
  trap 'rm -fr conftest* confdefs* core core.* *.core $ac_clean_files; exit 1' 1 2 15
  possible bashism in configure line 656 (trap with signal numbers):
  trap 'rm -f $CONFIG_STATUS conftest*; exit 1' 1 2 15
  possible bashism in cleanup line 10 (brace expansion):
  rm -f src/*.{o,so,d}
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
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  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
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  7.7Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   2.5Mb
    libs      1.9Mb
Error(s) in re-building vignettes:
--- re-building ‘bigMap_qckref.Rmd’ using rmarkdown
tlmgr search --file --global '/tikzlibrarytopaths.code.tex'
tlmgr search --file --global '/tikzlibraryshadows.code.tex'
tlmgr search --file --global '/tikzlibraryfadings.code.tex'
Trying to automatically install missing LaTeX packages...
tlmgr install pgf
tlmgr: package repository http://mirror.ox.ac.uk/sites/ctan.org/systems/texlive/tlnet (verified)
tlmgr install: package already present: pgf
tlmgr path add
add_link_dir_dir: /usr/local/share/info/dir exists; not making symlink.
tlmgr search --file --global '/tikzlibrarytopaths.code.tex'
tlmgr search --file --global '/tikzlibraryshadows.code.tex'
tlmgr search --file --global '/tikzlibraryfadings.code.tex'
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'bigMap_qckref.Rmd' failed with diagnostics:
Failed to compile bigMap_qckref.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See bigMap_qckref.log for more info.
--- failed re-building ‘bigMap_qckref.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
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 12.7Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      9.9Mb
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 17.1Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
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.
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  6.7Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
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.
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  6.2Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
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.
File ‘bit/libs/bit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘bitrugs/libs/bitrugs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Package suggested but not available for checking: ‘RQuantLib’
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘knitr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘getPass’
  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 49.8Mb
  sub-directories of 1Mb or more:
    libs  48.1Mb
Found the following files/directories:
  ‘lambda-20191123-142341.txt’
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 57.2Mb
  sub-directories of 1Mb or more:
    libs  55.9Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
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:
  ‘lhs’ ‘metR’ ‘methods’ ‘mvtnorm’ ‘numDeriv’ ‘viridis’
  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 33.7Mb
  sub-directories of 1Mb or more:
    libs  33.4Mb
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.
Found the following significant warnings:
  basic-probs.cpp:7:13: warning: 'bind2nd<std::__1::plus<double>, double>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/bnclassify.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Error(s) in re-building vignettes:
--- re-building ‘methods.Rmd’ using rmarkdown
--- finished re-building ‘methods.Rmd’

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

--- re-building ‘usage.rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'usage.rmd' failed with diagnostics:
Failed to compile usage.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See usage.log for more info.
--- failed re-building ‘usage.rmd’

SUMMARY: processing the following file failed:
  ‘usage.rmd’

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘fastDummies’
  All declared Imports should be used.
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.7Mb
installed size is 393.0Mb
  sub-directories of 1Mb or more:
    include    8.8Mb
    lib      383.8Mb
installed size is 76.9Mb
  sub-directories of 1Mb or more:
    libs  76.3Mb
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  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
File ‘bpkde/libs/bpkde.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 ‘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.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Namespaces in Imports field not imported from:
  ‘CCA’ ‘brainR’ ‘elasticnet’
  All declared Imports should be used.
Found the following files/directories:
  ‘MNI152_T1_8mm_brain.stl’ ‘Visit_1_8mm.stl’ ‘Visit_1_8mm_1.stl’
  ‘Visit_2_8mm.stl’ ‘Visit_2_8mm_1.stl’ ‘Visit_3_8mm.stl’
  ‘Visit_3_8mm_1.stl’ ‘Visit_4_8mm.stl’ ‘Visit_4_8mm_1.stl’
  ‘Visit_5_8mm.stl’ ‘Visit_5_8mm_1.stl’ ‘brain.stl’ ‘index_4D_stl.html’
  ‘xtk_edge.js’ ‘xtk_xdat.gui.js’
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 37.8Mb
  sub-directories of 1Mb or more:
    libs  37.6Mb
Namespace in Imports field not imported from: ‘lme4’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘BRETIGEA_basic.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'BRETIGEA_basic.Rmd' failed with diagnostics:
Failed to compile BRETIGEA_basic.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See BRETIGEA_basic.log for more info.
--- failed re-building ‘BRETIGEA_basic.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘profileModel’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R     2.9Mb
    doc   2.6Mb
Running examples in ‘broom.mixed-Ex.R’ failed
The error most likely occurred in:

> ### Name: glmmTMB_tidiers
> ### Title: Tidying methods for glmmTMB models
> ### Aliases: glmmTMB_tidiers tidy.glmmTMB augment.glmmTMB glance.glmmTMB
> 
> ### ** Examples
> 
> if (require("glmmTMB") && require("lme4")) {
+     data("sleepstudy",package="lme4")
+     ## original model:
+     ## Not run: 
+ ##D         lmm1 <- glmmTMB(Reaction ~ Days + (Days | Subject), sleepstudy)
+ ##D     
+ ## End(Not run)
+     ## load stored object
+     load(system.file("extdata","glmmTMB_example.rda",package="broom.mixed"))
+     tidy(lmm1)
+     tidy(lmm1, effects = "fixed")
+     tidy(lmm1, effects = "fixed", conf.int=TRUE)
+     tidy(lmm1, effects = "fixed", conf.int=TRUE, conf.method="uniroot")
+     ## FIX: tidy(lmm1, effects = "ran_vals", conf.int=TRUE)
+     head(augment(lmm1, sleepstudy))
+     glance(lmm1)
+ 
+     ## original model:
+     ##  glmm1 <- glmmTMB(incidence/size ~ period + (1 | herd),
+     ##                  data = cbpp, family = binomial, weights=size)
+     tidy(glmm1)
+     tidy(glmm1, effects = "fixed")
+     head(augment(glmm1, cbpp))
+     head(augment(glmm1, cbpp, type.residuals="pearson"))
+     glance(glmm1)
+ }
Loading required package: glmmTMB
Loading required package: lme4
Loading required package: Matrix
Error in do.call(`[`, c(list(x), indvecs, if (!is.null(dim(x))) list(drop = FALSE))) : 
  object 'Days' not found
Calls: head ... fbx -> fbx -> fbx -> head -> head.default -> do.call
Execution halted
Running ‘test-all.R’ [37s/115s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > test_check("broom.mixed")
  Loading required package: broom.mixed
  Registered S3 methods overwritten by 'broom.mixed':
    method         from 
    augment.lme    broom
    augment.merMod broom
    glance.lme     broom
    glance.merMod  broom
    glance.stanreg broom
    tidy.brmsfit   broom
    tidy.gamlss    broom
    tidy.lme       broom
    tidy.merMod    broom
    tidy.rjags     broom
    tidy.stanfit   broom
    tidy.stanreg   broom
  ── 1. Error: (unknown) (@test-alltibbles.R#53)  ────────────────────────────────
  object 'Days' not found
  Backtrace:
    1. broom.mixed:::testf("augment", z)
    6. broom.mixed:::augment.glmmTMB(obj)
    7. broom::augment_columns(x, data, newdata, ...)
   10. glmmTMB:::fitted.glmmTMB(...)
   12. glmmTMB:::predict.glmmTMB(object, type = "response")
   15. glmmTMB:::mkTMBStruc(...)
   16. glmmTMB:::getXReTrms(formula, mf, fr, contrasts = contrasts)
   17. glmmTMB::splitForm(formula)
   18. glmmTMB:::fbx(formula, debug, specials)
   19. glmmTMB:::fbx(term[[2]], debug, specials)
   20. glmmTMB:::fbx(term[[3]], debug, specials)
   22. utils:::head.default(term)
   23. base::do.call(`[`, c(list(x), indvecs, if (!is.null(dim(x))) list(drop = FALSE)))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 184 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 1 ]
  1. Error: (unknown) (@test-alltibbles.R#53) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    bin    2.5Mb
    doc    1.1Mb
    libs   2.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    AdminLTE3-3.0.0   1.0Mb
    doc               1.8Mb
    help              1.3Mb
Namespaces in Imports field not imported from:
  ‘rworldxtra’ ‘sp’
  All declared Imports should be used.
installed size is 37.5Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  35.4Mb
installed size is 99.1Mb
  sub-directories of 1Mb or more:
    libs  98.4Mb
File ‘BTR/libs/BTR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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.
Error(s) in re-building vignettes:
--- re-building ‘BTYDplus-HowTo.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'BTYDplus-HowTo.Rmd' failed with diagnostics:
Failed to compile BTYDplus-HowTo.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See BTYDplus-HowTo.log for more info.
--- failed re-building ‘BTYDplus-HowTo.Rmd’

SUMMARY: processing the following file failed:
  ‘BTYDplus-HowTo.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘buildmer.Rmd’ using rmarkdown
Fitting the final model
Fitting via lmer, with REML: f1 ~ following + vowel + timepoint + vowel:timepoint + following:timepoint + (1 + timepoint | word) + (1 + timepoint + following + timepoint:following | participant)
Finalizing by converting the model to lmerTest
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'buildmer.Rmd' failed with diagnostics:
Failed to compile buildmer.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See buildmer.log for more info.
--- failed re-building ‘buildmer.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
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  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
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 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
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.
Found the following significant warnings:
  rulebasedmodels.c:65:3: warning: expression result unused [-Wunused-value]
  rulebasedmodels.c:75:3: warning: expression result unused [-Wunused-value]
  rulebasedmodels.c:76:3: warning: expression result unused [-Wunused-value]
  rulebasedmodels.c:115:3: warning: expression result unused [-Wunused-value]
  rulebasedmodels.c:128:3: warning: expression result unused [-Wunused-value]
  rulebasedmodels.c:143:3: warning: expression result unused [-Wunused-value]
  rulebasedmodels.c:151:3: warning: expression result unused [-Wunused-value]
  rulebasedmodels.c:161:3: warning: expression result unused [-Wunused-value]
  rulebasedmodels.c:162:3: warning: expression result unused [-Wunused-value]
  rulebasedmodels.c:178:3: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/C50.Rcheck/00install.out’ for details.
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.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.1Mb
installed size is  6.6Mb
  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  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
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 ‘caTools/libs/caTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘rgdal’ ‘spatialEco’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      1.2Mb
    extdata   1.1Mb
    libs      2.6Mb
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  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
File ‘ccaPP/libs/ccaPP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 20.0Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
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  6.3Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.6Mb
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  6.2Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
File ‘cec2005benchmark/libs/cec2005benchmark.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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 11.5Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.7Mb
    libs   6.3Mb
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.
Error(s) in re-building vignettes:
--- re-building ‘ceRtainty.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'ceRtainty.Rmd' failed with diagnostics:
Failed to compile ceRtainty.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See ceRtainty.log for more info.
--- failed re-building ‘ceRtainty.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tools’
  All declared Imports should be used.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
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  7.5Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   5.1Mb
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 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Found the following significant warnings:
  'config' variable 'CXXCPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/cld3.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
File ‘clere/libs/clere.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘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.
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: ‘aws.signature’
  All declared Imports should be used.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/clpAPI.Rcheck/00install.out’ for details.
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  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
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  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
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.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   4.5Mb
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.
Namespaces in Imports field not imported from:
  ‘graphics’ ‘jsonlite’ ‘pander’ ‘rlang’
  All declared Imports should be used.
Missing or unexported object: ‘skimr::skim_with_defaults’
Running examples in ‘codebook-Ex.R’ failed
The error most likely occurred in:

> ### Name: codebook
> ### Title: Generate rmarkdown codebook
> ### Aliases: codebook
> 
> ### ** Examples
> 
> # will generate figures in a temporary directory
> old_base_dir <- knitr::opts_knit$get("base.dir")
> knitr::opts_knit$set(base.dir = tempdir())
> on.exit(knitr::opts_knit$set(base.dir = old_base_dir))
> data("bfi")
> bfi <- bfi[, c("BFIK_open_1", "BFIK_open_1")]
> md <- codebook(bfi, survey_repetition = "single", metadata_table = FALSE)
No missing values.
Warning: 'skimr::skim_to_wide' is deprecated.
Use 'skim()' instead.
See help("Deprecated")
Error: 'skim_with_defaults' is not an exported object from 'namespace:skimr'
Execution halted
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  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
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 28.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs  26.4Mb
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  20.7Mb
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.
Found the following significant warnings:
  Utility.c:162:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:187:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:211:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:392:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:417:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:442:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/CompRandFld.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
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.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
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.
Error(s) in re-building vignettes:
--- re-building ‘confSAM.Rmd’ using rmarkdown
Loading required package: survival
Welcome to penalized. For extended examples, see vignette("penalized").
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'confSAM.Rmd' failed with diagnostics:
Failed to compile confSAM.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See confSAM.log for more info.
--- failed re-building ‘confSAM.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘chamber.Rmd’ using rmarkdown
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 ‘chamber.Rmd’

--- re-building ‘senate.Rmd’ using rmarkdown
Quitting from lines 93-94 (senate.Rmd) 
Error: processing vignette 'senate.Rmd' failed with diagnostics:
Request failed. Please check the validity of the information you requested.
--- failed re-building ‘senate.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Error(s) in re-building vignettes:
--- re-building ‘Compare-methods.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'Compare-methods.Rmd' failed with diagnostics:
Failed to compile Compare-methods.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See Compare-methods.log for more info.
--- failed re-building 'Compare-methods.Rmd'

--- re-building ‘Compare-node-supports.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'Compare-node-supports.Rmd' failed with diagnostics:
Failed to compile Compare-node-supports.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See Compare-node-supports.log for more info.
--- failed re-building 'Compare-node-supports.Rmd'

--- re-building ‘Conduct-analyses.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'Conduct-analyses.Rmd' failed with diagnostics:
Failed to compile Conduct-analyses.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See Conduct-analyses.log for more info.
--- failed re-building ‘Conduct-analyses.Rmd’

SUMMARY: processing the following files failed:
  ‘Compare-methods.Rmd’ ‘Compare-node-supports.Rmd’
  ‘Conduct-analyses.Rmd’

Error: Vignette re-building failed.
Execution halted
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 64.7Mb
  sub-directories of 1Mb or more:
    libs  63.5Mb
Namespaces in Imports field not imported from:
  ‘geosphere’ ‘igraph’ ‘methods’ ‘rgdal’ ‘sf’
  All declared Imports should be used.
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 10.0Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   5.6Mb
Found the following files/directories:
  ‘module1.pdf’
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.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Running ‘test.R’ [202s/130s]
Running the tests in ‘tests/test.R’ failed.
Complete output:
  > library(testthat)
  > library(mockr)
  
  Attaching package: 'mockr'
  
  The following object is masked from 'package:testthat':
  
      with_mock
  
  > library(corehunter)
  Loading required package: rJava
  > 
  > test_check("corehunter")
  ── 1. Error: arguments are checked (@testAnalysis.R#12)  ───────────────────────
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(...)
   14. rlang::cnd_entrace(cnd)
   17. rJava:::`$.Throwable`(cnd, "trace")
   18. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ── 2. Error: arguments are checked (@testData.R#532)  ──────────────────────────
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(...)
   13. rlang::cnd_entrace(cnd)
   16. rJava:::`$.Throwable`(cnd, "trace")
   17. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 2416 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: arguments are checked (@testAnalysis.R#12) 
  2. Error: arguments are checked (@testData.R#532) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘forcats’ ‘ggplot2’ ‘re2r’ ‘rmarkdown’ ‘shinyWidgets’
  ‘shinycssloaders’ ‘shinydashboard’ ‘shinyjs’ ‘tidyr’ ‘zoo’
  All declared Imports should be used.
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  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  8.9Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   6.0Mb
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  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
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’ ‘markdown’ ‘shinyjs’ ‘tidyr’
  All declared Imports should be used.
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 17.2Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
Namespace in Imports field not imported from: ‘coxme’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
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.
File ‘coxsei/libs/coxsei.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
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  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
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 27.7Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  25.7Mb
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.
Namespace in Imports field not imported from: ‘tea’
  All declared Imports should be used.
installed size is 105.0Mb
  sub-directories of 1Mb or more:
    data    1.9Mb
    libs  101.0Mb
Namespace in Imports field not imported from: ‘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.
Found the following significant warnings:
  rulebasedmodels.c:95:3: warning: expression result unused [-Wunused-value]
  rulebasedmodels.c:105:3: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/Cubist.Rcheck/00install.out’ for details.
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.
File ‘CUSUMdesign/libs/CUSUMdesign.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘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.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    libs   5.2Mb
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 24.5Mb
  sub-directories of 1Mb or more:
    libs  23.7Mb
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
Note: found 4 marked Latin-1 strings
  Note: found 21 marked UTF-8 strings
Package suggested but not available for checking: ‘metagenomeFeatures’
Namespace in Imports field not imported from: ‘ape’
  All declared Imports should be used.
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.
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
Namespace in Imports field not imported from: ‘DatabaseConnectorJars’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   3.8Mb
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  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
.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.
Namespaces in Imports field not imported from:
  ‘future’ ‘iterators’ ‘readr’
  All declared Imports should be used.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc       2.2Mb
    extdata   5.5Mb
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
installed size is 46.9Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  44.8Mb
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.
browse: no visible global function definition for ‘slot’
browse: no visible global function definition for ‘page’
default.options: no visible binding for global variable ‘object.size’
heat.view: no visible global function definition for ‘head’
heat.view: no visible global function definition for ‘tail’
whos: no visible global function definition for ‘slotNames’
whos : <anonymous> : <anonymous>: no visible global function definition
  for ‘slot’
Undefined global functions or variables:
  head object.size page slot slotNames tail
Consider adding
  importFrom("methods", "slot", "slotNames")
  importFrom("utils", "head", "object.size", "page", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dbplyr)
  > 
  > test_check("dbplyr")
  Registering testing src: df OK
  Registering testing src: sqlite OK
  Registering testing src: mysql OK
  Registering testing src: MariaDB 
   *** caught segfault ***
  address 0x1c1, cause 'memory not mapped'
  
  Traceback:
   1: result_release(res@ptr)
   2: dbClearResult(rs)
   3: dbClearResult(rs)
   4: dbExecute(con, "SET time_zone = '+00:00'")
   5: dbExecute(con, "SET time_zone = '+00:00'")
   6: .local(drv, ...)
   7: DBI::dbConnect(...)
   8: DBI::dbConnect(...)
   9: paste0("src_", class(con)[[1]])
  10: src_dbi(DBI::dbConnect(...), auto_disconnect = TRUE)
  11: test_srcs$add(name, src)
  12: doTryCatch(return(expr), name, parentenv, handler)
  13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  14: tryCatchList(expr, classes, parentenv, handlers)
  15: tryCatch({    test_srcs$add(name, src)    message("OK")}, error = function(e) message("\n* ", conditionMessage(e)))
  16: test_register_src(name, src_dbi(DBI::dbConnect(...), auto_disconnect = TRUE))
  17: test_register_con("MariaDB", RMariaDB::MariaDB(), dbname = "test",     host = "localhost", user = Sys.getenv("USER"))
  18: eval(exprs, env)
  19: eval(exprs, env)
  20: FUN(X[[i]], ...)
  21: lapply(files, source_file, env = env, chdir = chdir, wrap = wrap)
  22: source_dir(path, "^helper.*\\.[rR]$", env = env, wrap = FALSE)
  23: source_test_helpers(path, env)
  24: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,     ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     wrap = wrap)
  25: test_package_dir(package = package, test_path = test_path, filter = filter,     reporter = reporter, ..., stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  26: test_check("dbplyr")
  An irrecoverable exception occurred. R is aborting now ...
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
File ‘dcemriS4/libs/dcemriS4.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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   4.1Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘gridExtra’ ‘latticeExtra’
  All declared Imports should be used.
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.
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 21.8Mb
  sub-directories of 1Mb or more:
    libs  21.7Mb
Namespace in Imports field not imported from: ‘DiagrammeR’
  All declared Imports should be used.
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.
installed size is 80.8Mb
  sub-directories of 1Mb or more:
    libs  78.1Mb
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.
Bootstrapping.CI: no visible global function definition for ‘quantile’
D.Jost: no visible global function definition for ‘read.table’
D.Jost: no visible global function definition for ‘write.table’
Dv.locis.corrected.calc: no visible global function definition for
  ‘p.adjust’
Gst.Nei: no visible global function definition for ‘read.table’
Gst.Nei: no visible global function definition for ‘write.table’
H.out: no visible global function definition for ‘write.table’
Hardy.calc: no visible global function definition for ‘chisq.test’
critical.ci.values: no visible global function definition for
  ‘quantile’
inputformat: no visible global function definition for ‘read.table’
inputformat: no visible global function definition for ‘write.table’
over.all.pops: no visible global function definition for ‘write.table’
p.value.correcture: no visible global function definition for
  ‘p.adjust’
pair.pops: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  chisq.test p.adjust quantile read.table write.table
Consider adding
  importFrom("stats", "chisq.test", "p.adjust", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘Example.t.H.values.txt’ ‘Example.t.Hest_loci.values.txt’
  ‘Example.t.Hest_mean.values.txt’
  ‘Example.t.allelefreq.2019-11-23.txt’
  ‘Example.t.overall.Dest.loci.2019-11-23.txt’
  ‘Example.t.overall.Dest.loci.ci2019-11-23.txt’
  ‘Example.t.overall.Dest.loci.p.2019-11-23.txt’
  ‘Example.t.overall.Dest.mean.2019-11-23.txt’
  ‘Example.t.overall.Dest.mean.ci2019-11-23.txt’
  ‘Example.t.overall.Dest.mean.p.2019-11-23.txt’
  ‘Example.t.sample.sizes.2019-11-23.txt’ ‘Example.u.H.values.txt’
  ‘Example.u.Hest_loci.values.txt’ ‘Example.u.Hest_mean.values.txt’
  ‘Example.u.allelefreq.2019-11-23.txt’
  ‘Example.u.pairwise.Gst.loci.2019-11-23.txt’
  ‘Example.u.pairwise.Gst.mean.2019-11-23.txt’
  ‘Example.u.sample.sizes.2019-11-23.txt’ ‘Output-Inputformat.txt’
Running ‘test-all.R’ [30s/32s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > 
  > library(dendextend)
  
  ---------------------
  Welcome to dendextend version 1.12.0
  Type citation('dendextend') for how to cite the package.
  
  Type browseVignettes(package = 'dendextend') for the package vignette.
  The github page is: https://github.com/talgalili/dendextend/
  
  Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
  Or contact: <tal.galili@gmail.com>
  
  	To suppress this message use:  suppressPackageStartupMessages(library(dendextend))
  ---------------------
  
  
  Attaching package: 'dendextend'
  
  The following object is masked from 'package:stats':
  
      cutree
  
  > test_check("dendextend")
  Bootstrap (r = 0.4)... Done.
  Bootstrap (r = 0.6)... Done.
  Bootstrap (r = 0.8)... Done.
  Bootstrap (r = 1.0)... Done.
  Bootstrap (r = 1.2)... Done.
  Bootstrap (r = 1.4)... Done.
  ── 1. Failure: extract au (@test-pvclust_extract.R#12)  ────────────────────────
  round(pvclust_edges(dend)[, 3], digits = 2) not identical to c(0.97, 1, 1).
  2/3 mismatches (average diff: 0.11)
  [1] 0.76 - 0.97 == -0.21
  [2] 0.99 - 1.00 == -0.01
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 409 | SKIPPED: 0 | WARNINGS: 10 | FAILED: 1 ]
  1. Failure: extract au (@test-pvclust_extract.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Error(s) in re-building vignettes:
--- re-building ‘denoiSeq-vignette.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'denoiSeq-vignette.Rmd' failed with diagnostics:
Failed to compile denoiSeq-vignette.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See denoiSeq-vignette.log for more info.
--- failed re-building ‘denoiSeq-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘denoiSeq-vignette.Rmd’

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

It is 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  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
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.
Error(s) in re-building vignettes:
--- re-building ‘derivmkts-vignette.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

tlmgr search --file --global '/tikzlibrarytopaths.code.tex'
tlmgr search --file --global '/tikzlibrarypositioning.code.tex'
Trying to automatically install missing LaTeX packages...
tlmgr install pgf
tlmgr: package repository http://mirror.ox.ac.uk/sites/ctan.org/systems/texlive/tlnet (verified)
tlmgr install: package already present: pgf
tlmgr path add
add_link_dir_dir: /usr/local/share/info/dir exists; not making symlink.
tlmgr search --file --global '/tikzlibrarytopaths.code.tex'
tlmgr search --file --global '/tikzlibrarypositioning.code.tex'
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'derivmkts-vignette.Rmd' failed with diagnostics:
Failed to compile derivmkts-vignette.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See derivmkts-vignette.log for more info.
--- failed re-building ‘derivmkts-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘derivmkts-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.8Mb
    help   1.4Mb
    libs   2.7Mb
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  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.2Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   6.8Mb
Found the following significant warnings:
  'config' variable 'CXXCPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/dfmta.Rcheck/00install.out’ for details.
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 49.1Mb
  sub-directories of 1Mb or more:
    libs  48.6Mb
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  21.9Mb
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.
Error(s) in re-building vignettes:
--- re-building ‘DHARMa.Rmd’ using rmarkdown
Loading required package: Matrix
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
Quitting from lines 394-400 (DHARMa.Rmd) 
Error: processing vignette 'DHARMa.Rmd' failed with diagnostics:
object 'group' not found
--- failed re-building ‘DHARMa.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘diagis.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'diagis.Rmd' failed with diagnostics:
Failed to compile diagis.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See diagis.log for more info.
--- failed re-building ‘diagis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
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  6.6Mb
  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 10.8Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
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.
Error(s) in re-building vignettes:
--- re-building ‘vignette.Rmd’ using rmarkdown_notangle
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'vignette.Rmd' failed with diagnostics:
Failed to compile vignette.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See vignette.log for more info.
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
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.
Namespaces in Imports field not imported from:
  ‘R6’ ‘R62S3’ ‘pracma’
  All declared Imports should be used.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/diversitree.Rcheck/00install.out’ for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
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  8.8Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   2.1Mb
    libs   3.9Mb
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 13.8Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs  10.5Mb
File ‘doRedis/libs/doRedis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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’ ‘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 29.7Mb
  sub-directories of 1Mb or more:
    libs  27.4Mb
Namespaces in Imports field not imported from:
  ‘bit64’ ‘rstudioapi’
  All declared Imports should be used.
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.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    appinformation   3.6Mb
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.
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.
Found the following files/directories:
  ‘iris2_2019-11-23.tsv’
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/dti.Rcheck/00install.out’ for details.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.2Mb
Namespaces in Imports field not imported from:
  ‘digest’ ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs  29.0Mb
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  6.2Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.5Mb
Namespace in Imports field not imported from: ‘desc’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘hdf5r’ ‘jsonlite’
  All declared Imports should be used.
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 10.7Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   3.2Mb
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.
Namespace in Imports field not imported from: ‘rprojroot’
  All declared Imports should be used.
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’ ‘rappdirs’ ‘rgdal’ ‘scales’ ‘tools’
  All declared Imports should be used.
File ‘EBMAforecast/libs/EBMAforecast.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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   1.2Mb
    hac    4.0Mb
Namespace in Imports field not imported from: ‘lubridate’
  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  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
File ‘EDR/libs/EDR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘rmarkdown’
  All declared Imports should be used.
installed size is 102.4Mb
  sub-directories of 1Mb or more:
    libs  101.7Mb
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.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data  11.5Mb
Error(s) in re-building vignettes:
--- re-building ‘elisatools-vignette.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'elisatools-vignette.Rmd' failed with diagnostics:
Failed to compile elisatools-vignette.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See elisatools-vignette.log for more info.
--- failed re-building ‘elisatools-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘elisatools-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘EloRating_tutorial.Rmd’ using rmarkdown
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: sna
Loading required package: statnet.common

Attaching package: 'statnet.common'

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

    order

Loading required package: network
network: Classes for Relational Data
Version 1.15 created on 2019-04-01.
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.

sna: Tools for Social Network Analysis
Version 2.4 created on 2016-07-23.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
 For citation information, type citation("sna").
 Type help(package="sna") to get started.

! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'EloRating_tutorial.Rmd' failed with diagnostics:
Failed to compile EloRating_tutorial.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See EloRating_tutorial.log for more info.
--- failed re-building ‘EloRating_tutorial.Rmd’

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

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

> ### Name: runPCA
> ### Title: Perform an Principal Component Analysis
> ### Aliases: runPCA
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> data("marty")
> 
> ## PCA on sample with inertia plot and sample plot colored by tumour type
> 
> example.subset <- marty[1:100,]
> pca <- runPCA(t(example.subset), verbose = FALSE, lab.sample = marty.type.cl)
dev.new(): using pdf(file="Rplots9.pdf")
dev.new(): using pdf(file="Rplots10.pdf")
Error in strwidth(legend, units = "user", cex = cex, font = text.font) : 
  plot.new has not been called yet
Calls: runPCA -> plotSample -> legend -> strwidth
Execution halted
Namespaces in Imports field not imported from:
  ‘AER’ ‘pROC’ ‘pander’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘EMbC_qckref.Rmd’ using rmarkdown
Loading required package: geosphere
Loading required package: sp
Loading required package: raster
Loading required package: rgdal
rgdal: version: 1.4-7, (SVN revision 845)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.3.2, released 2018/09/21
 Path to GDAL shared files: /usr/share/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 5.2.0, September 15th, 2018, [PJ_VERSION: 520]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.3-2 
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'EMbC_qckref.Rmd' failed with diagnostics:
Failed to compile EMbC_qckref.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See EMbC_qckref.log for more info.
--- failed re-building ‘EMbC_qckref.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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 18.3Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  16.1Mb
File ‘emIRT/libs/emIRT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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' 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.
Found the following significant warnings:
  emmix.cpp:351:195: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/EMMIXgene.Rcheck/00install.out’ for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.6Mb
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  7.1Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.5Mb
Note: found 23639 marked Latin-1 strings
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    lib    3.6Mb
    libs   1.1Mb
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.
Error(s) in re-building vignettes:
--- re-building ‘eNetXplorer_vignette.Rmd’ using rmarkdown
Loading required package: Matrix

Attaching package: 'expm'

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

    expm


Attaching package: 'gplots'

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

    lowess

! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'eNetXplorer_vignette.Rmd' failed with diagnostics:
Failed to compile eNetXplorer_vignette.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See eNetXplorer_vignette.log for more info.
--- failed re-building ‘eNetXplorer_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘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.
Found the following significant warnings:
  motor_optim.cpp:556:52: warning: 'mem_fun_ref<void, optim>' is deprecated [-Wdeprecated-declarations]
  motor_optim.cpp:559:52: warning: 'mem_fun_ref<void, optim>' is deprecated [-Wdeprecated-declarations]
  motor_optim.cpp:564:65: warning: 'mem_fun_ref<void, optim, double>' is deprecated [-Wdeprecated-declarations]
  motor_optim.cpp:564:52: warning: 'bind2nd<std::__1::mem_fun1_ref_t<void, optim, double>, double>' is deprecated [-Wdeprecated-declarations]
  motor_param.cpp:257:5: warning: explicitly assigning value of variable of type 'arma::vec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/episode.Rcheck/00install.out’ for details.
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘testthat’ ‘tidyr’
  All declared Imports should be used.
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  5.6Mb
  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.
File ‘esaddle/libs/esaddle.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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’ ‘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.
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 25.6Mb
  sub-directories of 1Mb or more:
    libs  25.2Mb
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.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘msm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘EnvStats’
  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.
Namespaces in Imports field not imported from:
  ‘eva’ ‘evir’ ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘methods’
  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 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
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  6.5Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.5Mb
Namespace in Imports field not imported from: ‘pkgload’
  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.
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  5.2Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.0Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Namespace in Imports field not imported from: ‘RobustGaSP’
  All declared Imports should be used.
installed size is 39.5Mb
  sub-directories of 1Mb or more:
    libs  39.4Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
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 16.7Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  15.3Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.2Mb
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  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      6.8Mb
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.
Found the following files/directories:
  ‘descriptive_statistics2019-11-23_16.53.41.txt’
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  5.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.0Mb
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 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is 46.4Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs  42.8Mb
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    libs  22.4Mb
File ‘fdaPDE/libs/fdaPDE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘fdaMatlabPath.m’
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   8.0Mb
File ‘FDGcopulas/libs/FDGcopulas.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 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.
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  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
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.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/fftw.Rcheck/00install.out’ for details.
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.
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘mapproj’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   2.1Mb
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.
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  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
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.
Error(s) in re-building vignettes:
--- re-building ‘FixedPoint.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'FixedPoint.Rmd' failed with diagnostics:
Failed to compile FixedPoint.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See FixedPoint.log for more info.
--- failed re-building ‘FixedPoint.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   2.8Mb
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 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
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 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
Namespaces in Imports field not imported from:
  ‘stats’ ‘utils’
  All declared Imports should be used.
File ‘FME/libs/FME.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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 33.1Mb
  sub-directories of 1Mb or more:
    libs  31.8Mb
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  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
Running ‘testthat.R’ [163s/178s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > if (require(testthat)) {
  +   test_check("forecast")
  + }
  Loading required package: testthat
  Loading required package: forecast
  Registered S3 methods overwritten by 'forecast':
    method             from    
    fitted.fracdiff    fracdiff
    residuals.fracdiff fracdiff
  ── 1. Error: tests for autoplot/gg functions (@test-ggplot.R#64)  ──────────────
  need at least two non-NA values to interpolate
  Backtrace:
   1. forecast::ggseasonplot(...)
   2. ggplot2::scale_color_gradientn(colours = col)
   5. scales::gradient_n_pal(colours, values, space)
   6. scales::colour_ramp(colours)
   7. stats::approxfun(x_in, lab_in[, 1])
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 774 | SKIPPED: 5 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: tests for autoplot/gg functions (@test-ggplot.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Error(s) in re-building vignettes:
--- re-building ‘Vignette.Rmd’ using rmarkdown
Quitting from lines 896-920 (Vignette.Rmd) 
Error: processing vignette 'Vignette.Rmd' failed with diagnostics:
could not find function "doColorRamp"
--- failed re-building ‘Vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
Error(s) in re-building vignettes:
--- re-building ‘pcl-vignette.Rmd’ using rmarkdown
Quitting from lines 43-49 (pcl-vignette.Rmd) 
Error: processing vignette 'pcl-vignette.Rmd' failed with diagnostics:
need at least two non-NA values to interpolate
--- failed re-building ‘pcl-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘pcl-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘fpCompare.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'fpCompare.Rmd' failed with diagnostics:
Failed to compile fpCompare.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See fpCompare.log for more info.
--- failed re-building ‘fpCompare.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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  9.4Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   5.6Mb
Error(s) in re-building vignettes:
--- re-building ‘freealg.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'freealg.Rmd' failed with diagnostics:
Failed to compile freealg.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See freealg.log for more info.
--- failed re-building ‘freealg.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
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 65.9Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs  64.1Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   6.9Mb
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 50.7Mb
  sub-directories of 1Mb or more:
    libs  50.2Mb
Found the following files/directories:
  ‘coelli.dta’ ‘coelli.ins’ ‘front41.000’
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.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
Found the following significant warnings:
  ./MatOp.h:122:44: warning: 'bind2nd<std::__1::minus<float>, float>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/fssemR.Rcheck/00install.out’ for details.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
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.
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 30.4Mb
  sub-directories of 1Mb or more:
    libs  30.2Mb
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.
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  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.8Mb
Found the following significant warnings:
  'config' variable 'CXXCPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/gaselect.Rcheck/00install.out’ for details.
PKG_CFLAGS set in ‘src/Makevars’ without any corresponding files
   PKG_CFLAGS set in ‘src/Makevars.in’ without any corresponding files
   PKG_CFLAGS set in ‘src/Makevars.win’ without any corresponding files
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   9.4Mb
installed size is 106.1Mb
  sub-directories of 1Mb or more:
    libs  105.7Mb
Namespaces in Imports field not imported from:
  ‘methods’ ‘rstantools’
  All declared Imports should be used.
installed size is 75.7Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     72.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
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 18.3Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  16.9Mb
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 40.9Mb
  sub-directories of 1Mb or more:
    L8NY18   2.3Mb
    libs    37.2Mb
Found the following files/directories:
  ‘output_aspect.tif’ ‘output_hillshade.tif’ ‘output_slope.tif’
  ‘tahoe_highrez_tiled.tif’ ‘tahoe_highrez_utm11.tif’
  ‘test_mosaic.envi’ ‘test_mosaic.hdr’
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
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.
File ‘geepack/libs/geepack.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 12.5Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
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.
Error(s) in re-building vignettes:
--- re-building ‘GenomicTools-Vignette.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'GenomicTools-Vignette.Rmd' failed with diagnostics:
Failed to compile GenomicTools-Vignette.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See GenomicTools-Vignette.log for more info.
--- failed re-building ‘GenomicTools-Vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘GenomicTools-Vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
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  8.5Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   5.0Mb
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:
  ‘maptools’ ‘rgdal’ ‘rgeos’
  All declared Imports should be used.
File ‘GeoGenetix/libs/GeoGenetix.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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    1.3Mb
    libs   3.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   6.7Mb
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 13.0Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  11.3Mb
Namespace in Imports field not imported from: ‘velociraptr’
  All declared Imports should be used.
Found the following assignments to the global environment:
File ‘geoR/R/auxiliar.R’:
  assign(".objfuncQQ", objfunc, pos = 1)
  assign(".bounds.list", .bounds.list, pos = 1)
  assign("madtonormalQQ", madtonormalQQ, pos = 1)
File ‘geoR/R/likGRF.R’:
  assign(".likGRF.dists.vec", lapply(split(as.data.frame(coords), 
    realisations), vecdist), pos = 1)
  assign(".likGRF.dists.vec", lapply(split(as.data.frame(coords), 
    realisations), vecdist), pos = 1)
  assign(".likGRF.dists.vec", lapply(split(as.data.frame(coords.c), 
    temp.list$realisations), vecdist), pos = 1)
  assign(".temp.lower.lambda", -2, pos = 1)
  assign(".temp.upper.lambda", 2, pos = 1)
File ‘geoR/R/profiles.R’:
  assign(".temp.list", list(n = n, z = data, beta.size = dim(trend)[2], 
    kappa = obj.likfit$kappa, xmat = trend, method.lik = obj.likfit$method.lik, 
    dists.lowertri = dists.vec, cov.model = obj.likfit$cov.model, 
    fix.lambda = obj.likfit$transform.info$fix.lambda, lambda = obj.likfit$lambda, 
    lower.phi = lower.phi, upper.phi = upper.phi, lower.sigmasq = lower.sigmasq, 
    phi.est = phi, tausq.rel.est = tausq.rel, tausq.est = tausq, 
    sigmasq.est = sigmasq), pos = 1)
  assign(".temp.temp.list", get(".temp.list", pos = 1), pos = 1)
  assign(".temp.list", .temp.temp.list, pos = 1)
  assign(".temp.lambda", lambda, pos = 1)
  assign(".temp.lambda", lambda, pos = 1)
File ‘geoR/R/simul.R’:
  assign("setRF", geoR2RF(cov.model = cov.model, cov.pars = cov.pars, 
    nugget = nugget, kappa = kappa, aniso.pars = aniso.pars), 
    pos = 1)
File ‘geoR/R/variofit.R’:
  assign(".temp.theta", NULL, pos = 1)
  assign(".temp.theta", theta, pos = 1)
  assign(".IND.geoR.variog.model.env", TRUE, pos = 1)
File ‘geoR/R/variogram.R’:
  assign(".variog4.nomessage", TRUE, pos = 1)
File ‘geoR/libs/geoR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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:
    data   3.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R         2.4Mb
    extdata   2.3Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘utils’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
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.
Namespaces in Imports field not imported from:
  ‘ggforce’ ‘plyr’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
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 19.9Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  18.0Mb
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:
  ‘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.
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  7.5Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.6Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
Namespaces in Imports field not imported from:
  ‘reshape2’ ‘rosm’
  All declared Imports should be used.
File ‘ghyp/libs/ghyp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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:
    doc    1.6Mb
    libs   3.2Mb
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.
Found the following files/directories:
  ‘gridded_sample.jpg’ ‘gridded_sample_dead.jpg’ ‘sample.jpg.dat’
  ‘sample_dead.jpg.dat’
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
File ‘GLDEX/libs/GLDEX.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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 28.0Mb
  sub-directories of 1Mb or more:
    libs  26.9Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
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  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
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 38.5Mb
  sub-directories of 1Mb or more:
    libs  37.9Mb
installed size is 45.5Mb
  sub-directories of 1Mb or more:
    libs  44.6Mb
Error(s) in re-building vignettes:
--- re-building ‘glmmsr-vignette.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'glmmsr-vignette.Rmd' failed with diagnostics:
Failed to compile glmmsr-vignette.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See glmmsr-vignette.log for more info.
--- failed re-building ‘glmmsr-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘glmmsr-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 45.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  43.0Mb
Running examples in ‘glmmTMB-Ex.R’ failed
The error most likely occurred in:

> ### Name: VarCorr.glmmTMB
> ### Title: Extract variance and correlation components
> ### Aliases: VarCorr.glmmTMB VarCorr
> ### Keywords: internal
> 
> ### ** Examples
> 
> ## Comparing variance-covariance matrix with manual computation
> data("sleepstudy",package="lme4")
> fm4 <- glmmTMB(Reaction ~ Days + (Days|Subject), sleepstudy)
Error in do.call(`[`, c(list(x), indvecs, if (!is.null(dim(x))) list(drop = FALSE))) : 
  object 'Days' not found
Calls: glmmTMB ... fbx -> fbx -> fbx -> head -> head.default -> do.call
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Coxnet.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'Coxnet.Rmd' failed with diagnostics:
Failed to compile Coxnet.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See Coxnet.log for more info.
--- failed re-building ‘Coxnet.Rmd’

--- re-building ‘glmnet.Rmd’ using rmarkdown
Loading required package: lars
Loaded lars 1.2

! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'glmnet.Rmd' failed with diagnostics:
Failed to compile glmnet.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See glmnet.log for more info.
--- failed re-building ‘glmnet.Rmd’

--- re-building ‘relax.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'relax.Rmd' failed with diagnostics:
Failed to compile relax.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See relax.log for more info.
--- failed re-building ‘relax.Rmd’

SUMMARY: processing the following files failed:
  ‘Coxnet.Rmd’ ‘glmnet.Rmd’ ‘relax.Rmd’

Error: Vignette re-building failed.
Execution halted
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:
  ‘MASS’ ‘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.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/glpkAPI.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘rworldmap’ ‘shape’
  All declared Imports should be used.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
File ‘gMWT/libs/gMWT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  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.
Found the following significant warnings:
  ./matrix.h:4401:3: warning: 'bind1st<std::__1::multiplies<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./matrix.h:4401:3: warning: 'bind2nd<std::__1::multiplies<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./matrix.h:2180:31: warning: 'bind1st<std::__1::multiplies<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./matrix.h:2183:13: warning: 'bind2nd<std::__1::multiplies<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./matrix.h:4436:3: warning: 'bind1st<std::__1::divides<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./matrix.h:4436:3: warning: 'bind2nd<std::__1::divides<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./matrix.h:4365:3: warning: 'bind1st<std::__1::minus<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./matrix.h:4365:3: warning: 'bind2nd<std::__1::minus<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./matrix.h:4330:3: warning: 'bind1st<std::__1::plus<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./matrix.h:4330:3: warning: 'bind2nd<std::__1::plus<double>, double>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/goftte.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘DT’ ‘processx’ ‘remotes’ ‘rsconnect’
  All declared Imports should be used.
File ‘GPB/libs/GPB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘gpclib/libs/gpclib.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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   1.4Mb
    libs   5.0Mb
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  5.7Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    4.0Mb
installed size is 31.0Mb
  sub-directories of 1Mb or more:
    R  30.8Mb
Running ‘testthat.R’ [87s/103s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(gqlr)
  > 
  > test_check("gqlr")
  ── 1. Failure: pryr fails (@test-aaa-pryr-unenclose.R#25)  ─────────────────────
  ans$A() == "A" isn't false.
  
  ── 2. Failure: pryr fails (@test-aaa-pryr-unenclose.R#26)  ─────────────────────
  ans$B() == "B" isn't false.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 541 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 2 ]
  1. Failure: pryr fails (@test-aaa-pryr-unenclose.R#25) 
  2. Failure: pryr fails (@test-aaa-pryr-unenclose.R#26) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘gRain/libs/gRain.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘MPG_algorithm.Rmd’ using rmarkdown
Warning in get_engine(options$engine) :
  Unknown language engine 'cpp' (must be registered via knit_engines$set()).
--- finished re-building ‘MPG_algorithm.Rmd’

--- re-building ‘grainscape_vignette.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'grainscape_vignette.Rmd' failed with diagnostics:
Failed to compile grainscape_vignette.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See grainscape_vignette.log for more info.
--- failed re-building ‘grainscape_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
Found the following files/directories:
  ‘cat.expressions.dir.2019-11-23.1.1’
  ‘cat.expressions.dir.2019-11-23.1.2’
  ‘cat.expressions.dir.2019-11-23.1.3’
  ‘cat.expressions.dir.2019-11-23.1.4’
  ‘cat.expressions.dir.2019-11-23.1.5’
  ‘cat.expressions.dir.2019-11-23.1.6’
  ‘cat.expressions.dir.2019-11-23.1.7’
  ‘cat.expressions.dir.2019-11-23.1.8’
  ‘cat.expressions.dir.2019-11-23.1.9’
  ‘cat.expressions.dir.2019-11-23.2’
  ‘cat.expressions.dir.2019-11-23.2.1’
  ‘cat.expressions.dir.2019-11-23.2.2’
  ‘cat.expressions.dir.2019-11-23.2.3’
  ‘cat.expressions.dir.2019-11-23.2.4’
  ‘cat.expressions.dir.2019-11-23.2.5’
  ‘cat.expressions.dir.2019-11-23.2.6’
  ‘cat.expressions.dir.2019-11-23.2.7’ ‘graphfactorD - 10-08-2016 -
  Function Viz1.png’ ‘graphfactorD - 10-08-2016 - Function Viz10.png’
  ‘graphfactorD - 10-08-2016 - Function Viz11.png’ ‘graphfactorD -
  10-08-2016 - Function Viz12.png’ ‘graphfactorD - 10-08-2016 -
  Function Viz2.png’ ‘graphfactorD - 10-08-2016 - Function Viz3.png’
  ‘graphfactorD - 10-08-2016 - Function Viz4.png’ ‘graphfactorD -
  10-08-2016 - Function Viz5.png’ ‘graphfactorD - 10-08-2016 - Function
  Viz6.png’
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    help   2.4Mb
    libs   2.8Mb
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 13.6Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Namespace in Imports field not imported from: ‘BiasedUrn’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
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 17.4Mb
  sub-directories of 1Mb or more:
    libs  17.0Mb
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  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
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.
Running ‘testthat.R’ [7s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(GSODR)
  > 
  > test_check("GSODR")
  ── 1. Failure: The 'max_missing' parameter filters out improper stations (@test-
  `get_GSOD(years = 1929, max_missing = 1)` threw an error with unexpected message.
  Expected match: "There were no stations that had a max of."
  Actual message: "attempt to set an attribute on NULL"
  Backtrace:
   1. testthat::expect_error(...)
   6. GSODR::get_GSOD(years = 1929, max_missing = 1)
   7. GSODR:::.validate_missing_days(max_missing, file_list)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 31 | SKIPPED: 9 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: The 'max_missing' parameter filters out improper stations (@test-get_GSOD.R#128) 
  
  Error: testthat unit tests failed
  Execution halted
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  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.7Mb
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.
Namespace in Imports field not imported from: ‘urca’
  All declared Imports should be used.
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  5.5Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.2Mb
Namespaces in Imports field not imported from:
  ‘broom’ ‘dplyr’ ‘ggrepel’ ‘kableExtra’ ‘knitr’ ‘nnet’ ‘plotROC’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/gwsem.Rcheck/00install.out’ for details.
File ‘gyriq/libs/gyriq.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘outGyriq.out’
installed size is 127.0Mb
  sub-directories of 1Mb or more:
    java  125.0Mb
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.
Found the following files/directories:
  ‘exmpl_data_preproc_gen.RData’ ‘exmpl_data_preproc_gen.ffData’
  ‘exmpl_haplin_data_gen.RData’ ‘exmpl_haplin_data_gen.ffData’
  ‘exmpl_ped_data_gen.RData’ ‘exmpl_ped_data_gen.ffData’
  ‘exmpl_ped_data_part_gen.RData’ ‘exmpl_ped_data_part_gen.ffData’
  ‘gen_data_men_only_gen.RData’ ‘gen_data_men_only_gen.ffData’
  ‘my_data_part_gen.RData’ ‘my_data_part_gen.ffData’
  ‘poo_exmpl_data_preproc_gen.RData’
  ‘poo_exmpl_data_preproc_gen.ffData’ ‘poo_exmpl_data_read_gen.RData’
  ‘poo_exmpl_data_read_gen.ffData’ ‘trial_data_gen.RData’
  ‘trial_data_gen.ffData’
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
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 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
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 10.1Mb
  sub-directories of 1Mb or more:
    data  10.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   1.2Mb
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 34.6Mb
  sub-directories of 1Mb or more:
    libs  34.1Mb
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  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is 26.8Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs  21.3Mb
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.
File ‘hier.part/libs/hier.part.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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  7.1Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
Found the following significant warnings:
  codegenerator.cpp:464:4: warning: 'auto_ptr<Matcher>' is deprecated [-Wdeprecated-declarations]
  codegenerator.cpp:1742:4: warning: 'auto_ptr<Pattern>' is deprecated [-Wdeprecated-declarations]
  codegenerator.cpp:1743:4: warning: 'auto_ptr<Matcher>' is deprecated [-Wdeprecated-declarations]
  languagedefinition.cpp:100:3: warning: 'auto_ptr<Matcher>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/highlight.Rcheck/00install.out’ for details.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    highlight   1.1Mb
    libs        7.9Mb
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  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
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  7.1Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   5.2Mb
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  7.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   4.1Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
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  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
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
Found the following significant warnings:
  sar.cpp:210:32: warning: explicitly assigning value of variable of type 'arma::sp_mat' (aka 'SpMat<double>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/HSAR.Rcheck/00install.out’ for details.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
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 62.1Mb
  sub-directories of 1Mb or more:
    libs  61.6Mb
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 13.1Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   8.1Mb
    doc    2.5Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
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  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
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  8.1Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   5.5Mb
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 ‘HWxtest/libs/HWxtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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.
Found the following files/directories:
  ‘pcp-monthly.txt’
installed size is  5.1Mb
  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  8.5Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   5.4Mb
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.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm10'
Packages unavailable to check Rd xrefs: ‘BSgenome.Hsapiens.1000genomes.hs37d5’, ‘BSgenome.Hsapiens.UCSC.hg38’, ‘BSgenome.Mmusculus.UCSC.mm10’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
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.
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
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 12.0Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   1.4Mb
    libs   7.4Mb
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 15.1Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
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.
Found the following significant warnings:
  RccpSource_.cpp:978:54: warning: explicitly assigning value of variable of type 'Rcpp::NumericVector' (aka 'Vector<14>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/icosa.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      2.8Mb
installed size is 75.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  73.2Mb
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  23.8Mb
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  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
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.
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 16.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  13.5Mb
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 50.4Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       5.3Mb
    extdata   1.0Mb
    include   2.8Mb
    libs     39.2Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
Error(s) in re-building vignettes:
--- re-building ‘imbalance.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'imbalance.Rmd' failed with diagnostics:
Failed to compile imbalance.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See imbalance.log for more info.
--- failed re-building ‘imbalance.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
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:
  ‘methods’ ‘plyr’ ‘qpdf’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘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.
File ‘inarmix/libs/inarmix.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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:
    doc    1.9Mb
    libs   4.8Mb
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.
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
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: ‘gridExtra’
  All declared Imports should be used.
Found the following files/directories:
  ‘1-Reasonableness_ID_var_check_errors_20191123.xlsx’
  ‘1-Reasonableness_Var2_check_errors_20191123.xlsx’
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 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
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.
installed size is 26.8Mb
  sub-directories of 1Mb or more:
    libs  26.5Mb
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 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘bsplus’ ‘colourpicker’ ‘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.
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  8.7Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
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.
File ‘IsingSampler/libs/IsingSampler.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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    1.1Mb
    libs   7.3Mb
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.
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.
Namespace in Imports field not imported from: ‘comtradr’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'gurobi', 'Rcplex', 'cplexAPI'
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          17.9Mb
Found the following significant warnings:
  jaguar.cpp:352:84: warning: 'bind2nd<std::__1::less<double>, double>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/JAGUAR.Rcheck/00install.out’ for details.
File ‘JAGUAR/libs/JAGUAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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’ ‘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.
Found the following significant warnings:
  ../inst/include/lib/limonp/StringUtil.hpp:83:70: warning: 'ptr_fun<int, int>' is deprecated [-Wdeprecated-declarations]
  ../inst/include/lib/limonp/StringUtil.hpp:88:61: warning: 'ptr_fun<int, int>' is deprecated [-Wdeprecated-declarations]
  ../inst/include/lib/limonp/StringUtil.hpp:97:70: warning: 'bind2nd<std::__1::equal_to<char>, char>' is deprecated [-Wdeprecated-declarations]
  ../inst/include/lib/limonp/StringUtil.hpp:102:61: warning: 'bind2nd<std::__1::equal_to<char>, char>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/jiebaR.Rcheck/00install.out’ for details.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
possible bashism in configure line 44 ($BASH_SOMETHING):
  if test -z "$BASH_VERSION$ZSH_VERSION" \
      && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
  possible bashism in configure line 334 ([^] should be [!]):
      sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
  possible bashism in configure line 338 ([^] should be [!]):
  	  /^X\(\/\/\)[^/].*/{
  possible bashism in configure line 442 ([^] should be [!]):
      sed '/^.*\/\([^/][^/]*\)\/*$/{
  possible bashism in configure line 500 (echo -n):
  case `echo -n x` in #(((((
  possible bashism in configure line 502 (unsafe echo with backslash):
    case `echo 'xy\c'` in
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Found the following significant warnings:
  znorm.cpp:44:59: warning: 'bind2nd<std::__1::minus<double>, double>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/jmotif.Rcheck/00install.out’ for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   6.6Mb
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.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   4.3Mb
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.
Namespace in Imports field not imported from: ‘survC1’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   5.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    include   1.2Mb
    libs      4.6Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘nlme’ ‘zoo’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
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 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  14.8Mb
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  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
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.
Error(s) in re-building vignettes:
--- re-building ‘tutorial.Rmd’ using rmarkdown
Warning in get_engine(options$engine) :
  Unknown language engine 'eval' (must be registered via knit_engines$set()).
Writing 5 Bibtex entries ... OK
Results written to file 'references.bib'
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
Failed to compile tutorial.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See tutorial.log for more info.
--- failed re-building ‘tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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  7.2Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.4Mb
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.
Error(s) in re-building vignettes:
--- re-building ‘scrartcl.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'scrartcl.Rmd' failed with diagnostics:
Failed to compile scrartcl.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See scrartcl.log for more info.
--- failed re-building ‘scrartcl.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    java   6.0Mb
Found the following files/directories:
  ‘KoNLP_dic’
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  6.8Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   3.0Mb
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/KSgeneral.Rcheck/00install.out’ for details.
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 18.3Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  15.7Mb
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  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.0Mb
Namespaces in Imports field not imported from:
  ‘collections’ ‘repr’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    2.4Mb
    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 ‘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’ ‘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: ‘leaflet’
  All declared Imports should be used.
File ‘leaps/libs/leaps.so’:
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Object: ‘leaps.o’
File ‘leaps/libs/leaps.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 ‘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  7.9Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  5.4Mb
  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.
Namespaces in Imports field not imported from:
  ‘methods’ ‘tools’
  All declared Imports should be used.
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.
Found the following files/directories:
  ‘temp.cns’ ‘temp.ea’
Namespace in Imports field not imported from: ‘stringdist’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   9.3Mb
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  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs      19.9Mb
    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: ‘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 12.1Mb
  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 25.3Mb
  sub-directories of 1Mb or more:
    libs  23.7Mb
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.
Running examples in ‘lori-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot.lori
> ### Title: plot 2D displays of the row-column interactions
> ### Aliases: plot.lori
> 
> ### ** Examples
> 
> X = matrix(rnorm(rep(0, 15)), 5)
> Y <- matrix(rpois(length(c(X)), exp(c(X))), 5)
> res_lori <- lori(Y, cov=cbind(c(X),c(X)), lambda1=1, lambda2=1)
> p <- plot(res_lori)
Error in if (nullxlimylim & diff(xlim)/diff(ylim) > 3) ylim <- (ylim -  : 
  missing value where TRUE/FALSE needed
Calls: plot -> plot.lori -> <Anonymous>
Execution halted
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  5.5Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
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 50.8Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  48.2Mb
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  5.8Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.5Mb
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘raster’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.1Mb
    libs   1.6Mb
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/lwgeom.Rcheck/00install.out’ for details.
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 24.9Mb
  sub-directories of 1Mb or more:
    libs  24.6Mb
Namespaces in Imports field not imported from:
  ‘nnls’ ‘reshape2’ ‘stats’
  All declared Imports should be used.
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.
Found the following significant warnings:
  'config' variable 'CXXCPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/magick.Rcheck/00install.out’ for details.
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs   6.2Mb
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.
Packages required but not available: 'pdInfoBuilder', 'oligo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs  18.8Mb
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  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
installed size is 45.6Mb
  sub-directories of 1Mb or more:
    doc           1.2Mb
    htmlwidgets   1.5Mb
    libs         41.5Mb
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.
Found the following significant warnings:
  cuts.c:24:2: warning: expression result unused [-Wunused-value]
  cuts.c:24:5: warning: expression result unused [-Wunused-value]
  cuts.c:24:9: warning: expression result unused [-Wunused-value]
  cuts.c:32:2: warning: expression result unused [-Wunused-value]
  cuts.c:32:6: warning: expression result unused [-Wunused-value]
  cuts.c:32:10: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/mapproj.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
File ‘maptpx/libs/maptpx.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘brew’ ‘svglite’ ‘uuid’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘betareg’
  All declared Imports should be used.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Found the following significant warnings:
  ./matrix.h:4401:3: warning: 'bind1st<std::__1::multiplies<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./matrix.h:4401:3: warning: 'bind2nd<std::__1::multiplies<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./matrix.h:4365:3: warning: 'bind1st<std::__1::minus<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./matrix.h:4365:3: warning: 'bind2nd<std::__1::minus<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./matrix.h:4330:3: warning: 'bind1st<std::__1::plus<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./matrix.h:4330:3: warning: 'bind2nd<std::__1::plus<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./matrix.h:4436:3: warning: 'bind1st<std::__1::divides<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./matrix.h:4436:3: warning: 'bind2nd<std::__1::divides<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./matrix.h:4365:3: warning: 'bind1st<std::__1::minus<int>, int>' is deprecated [-Wdeprecated-declarations]
  ./matrix.h:4365:3: warning: 'bind2nd<std::__1::minus<int>, int>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/MasterBayes.Rcheck/00install.out’ for details.
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs  10.5Mb
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 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
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.
Error(s) in re-building vignettes:
--- re-building ‘Introduction_to_mbbefd.Rmd’ using rmarkdown
Loading required package: fitdistrplus
Loading required package: MASS
Loading required package: survival
Loading required package: npsurv
Loading required package: lsei
Loading required package: alabama
Loading required package: numDeriv
Loading required package: Rcpp
Package:  mbbefd
Version:  0.8.8.5
Date:     2019-01-02 11:50:03 UTC
BugReport: http://github.com/spedygiorgio/mbbefd/issues


Warning in fitdist(x, distr = dist, method = method, start = start, lower = 0,  :
  The doiunif function should return a vector of with NaN values when input has inconsistent values and not raise an error
Read 44 items
Read 22 items
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'Introduction_to_mbbefd.Rmd' failed with diagnostics:
Failed to compile Introduction_to_mbbefd.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See Introduction_to_mbbefd.log for more info.
--- failed re-building ‘Introduction_to_mbbefd.Rmd’

--- re-building ‘test-beta.Rmd’ using rmarkdown
Loading required package: fitdistrplus
Loading required package: MASS
Loading required package: survival
Loading required package: npsurv
Loading required package: lsei
Loading required package: alabama
Loading required package: numDeriv
Loading required package: Rcpp
Package:  mbbefd
Version:  0.8.8.5
Date:     2019-01-02 11:50:03 UTC
BugReport: http://github.com/spedygiorgio/mbbefd/issues


--- finished re-building ‘test-beta.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘vignette.Rmd’ using rmarkdown
Warning in (function (filename = "Rplot%03d.png", width = 480, height = 480,  :
  cairo error 'invalid value (typically too big) for the size of the input (surface, pattern, etc.)'
Quitting from lines 39-41 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
unable to start device 'png'
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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 13.5Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  11.1Mb
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  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
installed size is 45.4Mb
  sub-directories of 1Mb or more:
    libs  44.3Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
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.
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.
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
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 28.1Mb
  sub-directories of 1Mb or more:
    libs  26.4Mb
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.
File ‘MEET/libs/MEET.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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’ ‘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  5.2Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   3.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.8Mb
Namespace in Imports field not imported from: ‘KernSmooth’
  All declared Imports should be used.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   5.5Mb
installed size is 111.8Mb
  sub-directories of 1Mb or more:
    libs  111.3Mb
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.
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘DT’ ‘GEOmetadb’ ‘RMySQL’ ‘RSQLite’ ‘gplots’ ‘pheatmap’
  ‘readr’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘MetaLonDA.Rmd’ using rmarkdown
Quitting from lines 28-43 (MetaLonDA.Rmd) 
Error: processing vignette 'MetaLonDA.Rmd' failed with diagnostics:
non-numeric argument to binary operator
--- failed re-building ‘MetaLonDA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘shiny’
  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 75.0Mb
  sub-directories of 1Mb or more:
    libs  74.7Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   2.2Mb
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 25.8Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    1.1Mb
    libs  21.2Mb
    misc   1.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
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 26.0Mb
  sub-directories of 1Mb or more:
    libs  25.0Mb
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 20.7Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  19.1Mb
Error(s) in re-building vignettes:
--- re-building ‘estimation-mhmm.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'estimation-mhmm.Rmd' failed with diagnostics:
Failed to compile estimation-mhmm.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See estimation-mhmm.log for more info.
--- failed re-building ‘estimation-mhmm.Rmd’

--- re-building ‘tutorial-mhmm.Rmd’ using rmarkdown
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "parameter" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "parameter" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "parameter" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "parameter" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "parameter" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "parameter" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "parameter" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "parameter" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "parameter" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "parameter" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "parameter" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "parameter" is not a graphical parameter
--- finished re-building ‘tutorial-mhmm.Rmd’

SUMMARY: processing the following file failed:
  ‘estimation-mhmm.Rmd’

Error: Vignette re-building failed.
Execution halted
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  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
File ‘microclass/libs/microclass.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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’ ‘ggiraph’ ‘ggplot2’ ‘grid’ ‘gtools’ ‘scales’ ‘shinyBS’
  ‘shinyWidgets’ ‘tidyr’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘microsamplingDesign.Rmd’ using rmarkdown
Loading required package: Rcpp
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'microsamplingDesign.Rmd' failed with diagnostics:
Failed to compile microsamplingDesign.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See microsamplingDesign.log for more info.
--- failed re-building ‘microsamplingDesign.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘MigClim/libs/MigClim.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Objects: ‘genclust.o’, ‘migrate.o’, ‘src_cell.o’, ‘validate.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Objects: ‘genclust.o’, ‘migrate.o’
File ‘MigClim/libs/MigClim.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: ‘mipfp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘softImpute’
  All declared Imports should be used.
Found the following files/directories:
  ‘..md’ ‘NA.R’ ‘NA.mm’ ‘md-2019-11-23-20-08-31.mm’ ‘md.R’ ‘md.mm’
  ‘mindr.md’ ‘mindr.mm’ ‘mm.md’ ‘outline-2019-11-23-20-08-31.md’
  ‘outline.md’ ‘r.R’ ‘r.Rmd’
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    libs  20.3Mb
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  8.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   6.9Mb
File ‘misclassGLM/libs/misclassGLM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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.
Found the following significant warnings:
  GLMM_Deviance.cpp:153:8: warning: expression result unused [-Wunused-value]
  GLMM_Deviance.cpp:708:10: warning: expression result unused [-Wunused-value]
  GLMM_Deviance2.cpp:173:8: warning: expression result unused [-Wunused-value]
  GLMM_Deviance2.cpp:780:10: warning: expression result unused [-Wunused-value]
  GLMM_newData.cpp:183:8: warning: expression result unused [-Wunused-value]
  GLMM_updateRanEf.cpp:161:8: warning: expression result unused [-Wunused-value]
  GLMM_updateRanEf.cpp:626:6: warning: expression result unused [-Wunused-value]
  GLMM_updateRanEf_QR.cpp:124:8: warning: expression result unused [-Wunused-value]
  GLMM_updateRanEf_QR.cpp:328:10: warning: expression result unused [-Wunused-value]
  MCMC_Moments_NormalApprox_QR.cpp:104:10: warning: expression result unused [-Wunused-value]
  MCMC_Moments_NormalApprox_QR.cpp:209:10: warning: expression result unused [-Wunused-value]
  NMix_updateMeansVars.cpp:516:9: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/mixAK.Rcheck/00install.out’ for details.
installed size is 40.1Mb
  sub-directories of 1Mb or more:
    libs  37.8Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
File ‘MixedDataImpute/libs/MixedDataImpute.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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   4.9Mb
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.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘foreach’
  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.
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.
Missing link or links in documentation object 'makeMBOLearner.Rd':
  ‘[mlr]{regr.randomForest}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    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 24.3Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  19.3Mb
Namespace in Imports field not imported from: ‘plotrix’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘matlib’
  All declared Imports should be used.
Found the following significant warnings:
  fdf.cpp:127:21: warning: 'ptr_fun<double, double>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/mmpca.Rcheck/00install.out’ for details.
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
Namespace in Imports field not imported from: ‘gmp’
  All declared Imports should be used.
File ‘mmpca/libs/mmpca.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
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.
Error(s) in re-building vignettes:
--- re-building ‘MODIStsp.Rmd’ using rmarkdown
[WARNING] Note with key '1^' defined at line 939 column 1 but not used.
[WARNING] Note with key '2^' defined at line 941 column 1 but not used.
[WARNING] Note with key '3^' defined at line 943 column 1 but not used.
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'MODIStsp.Rmd' failed with diagnostics:
Failed to compile MODIStsp.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See MODIStsp.log for more info.
--- failed re-building ‘MODIStsp.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘BioStatR’ ‘ggplot2’
  All declared Imports should be used.
Found the following files/directories:
  ‘example.result.csv’
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    1.8Mb
    libs   3.4Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
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.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   8.5Mb
Error(s) in re-building vignettes:
--- re-building ‘Installation.Rmd’ using rmarkdown
--- finished re-building ‘Installation.Rmd’

--- re-building ‘Intro.Rmd’ using rmarkdown

HINT: Most of the functions work well with 'poissonL', however for complex mortality laws like Heligman-Pollard (HP) one can obtain a better fit using other loss functions (e.g. 'LF2'). You are strongly encouraged to test different option before deciding on the final version. The results might be slightly different.

! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'Intro.Rmd' failed with diagnostics:
Failed to compile Intro.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See Intro.log for more info.
--- failed re-building ‘Intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.1Mb
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.
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 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
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 16.9Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  14.9Mb
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  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
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.
Found the following significant warnings:
  ./matrix.h:4365:3: warning: 'bind1st<std::__1::minus<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./matrix.h:4365:3: warning: 'bind2nd<std::__1::minus<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./matrix.h:4330:3: warning: 'bind1st<std::__1::plus<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./matrix.h:4330:3: warning: 'bind2nd<std::__1::plus<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./matrix.h:4436:3: warning: 'bind1st<std::__1::divides<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./matrix.h:4436:3: warning: 'bind2nd<std::__1::divides<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./matrix.h:4401:3: warning: 'bind1st<std::__1::multiplies<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./matrix.h:4401:3: warning: 'bind2nd<std::__1::multiplies<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./matrix.h:4690:3: warning: 'bind1st<std::__1::equal_to<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./matrix.h:4690:3: warning: 'bind2nd<std::__1::equal_to<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./smath.h:762:3: warning: 'ptr_fun<double, double, double>' is deprecated [-Wdeprecated-declarations]
  ./smath.h:762:3: warning: 'bind1st<std::__1::pointer_to_binary_function<double, double, double>, double>' is deprecated [-Wdeprecated-declarations]
  ./smath.h:762:3: warning: 'bind2nd<std::__1::pointer_to_binary_function<double, double, double>, double>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/mRm.Rcheck/00install.out’ for details.
File ‘mRm/libs/mRm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 29.9Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.0Mb
    libs  27.2Mb
installed size is 46.7Mb
  sub-directories of 1Mb or more:
    libs  46.2Mb
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 18.1Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs  17.0Mb
Running examples in ‘mstate-Ex.R’ failed
The error most likely occurred in:

> ### Name: crprep
> ### Title: Function to create weighted data set for competing risks
> ###   analyses
> ### Aliases: crprep crprep.default
> ### Keywords: datagen survival
> 
> ### ** Examples
> 
> data(aidssi)
> aidssi.w <- crprep("time", "cause", data=aidssi, trans=c("AIDS","SI"),
+                    cens="event-free", id="patnr", keep="ccr5")
> 
> # calculate cause-specific cumulative incidence, no truncation,
> # compare with Cuminc (also from mstate)
> ci <- Cuminc(aidssi$time, aidssi$status)
> sf <- survfit(Surv(Tstart,Tstop,status=="AIDS")~1, data=aidssi.w,
+               weight=weight.cens, subset=failcode=="AIDS")
> plot(sf, fun="event", mark.time=FALSE)
> lines(CI.1~time,data=ci,type="s",col="red")
> sf <- survfit(Surv(Tstart,Tstop,status=="SI")~1, data=aidssi.w,
+               weight=weight.cens, subset=failcode=="SI")
> plot(sf, fun="event", mark.time=FALSE)
> lines(CI.2~time,data=ci,type="s",col="red")
Error in eval(predvars, data, env) : object 'CI.2' not found
Calls: lines ... lines.formula -> eval -> eval -> <Anonymous> -> eval -> eval
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Tutorial.Rnw’ using Sweave
Loading required package: survival
Warning in max(ci$CI.2[idx0]) :
  no non-missing arguments to max; returning -Inf

Error: processing vignette 'Tutorial.Rnw' failed with diagnostics:
 chunk 59 (label = fig3do) 
Error in xy.coords(x, y) : 'x' and 'y' lengths differ

--- failed re-building ‘Tutorial.Rnw’

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

Error: Vignette re-building failed.
Execution halted
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.
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.
File ‘multicool/libs/multicool.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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’ ‘doRNG’ ‘foreach’
  All declared Imports should be used.
installed size is 76.1Mb
  sub-directories of 1Mb or more:
    libs  75.8Mb
Namespace in Imports field not imported from: ‘igraphdata’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
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 27.9Mb
  sub-directories of 1Mb or more:
    libs  27.7Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
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.
Error(s) in re-building vignettes:
--- re-building ‘mvp.Rmd’ using rmarkdown

Attaching package: 'mvp'

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

    trunc


Attaching package: 'spray'

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

    aderiv, constant, constant<-, homog, is.zero, knight, linear,
    nterms, ooom, product, subs, xyz

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

    pmax, pmin


Attaching package: 'mpoly'

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

    is.constant, vars

! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'mvp.Rmd' failed with diagnostics:
Failed to compile mvp.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See mvp.log for more info.
--- failed re-building ‘mvp.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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  5.6Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.4Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
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  7.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
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.
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  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.7Mb
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.
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rlang’ ‘tidyselect’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘igraph’
  All declared Imports should be used.
File ‘netcoh/libs/netcoh.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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 11.6Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   7.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
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  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   6.2Mb
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.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
installed size is  6.7Mb
  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  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
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.
Namespaces in Imports field not imported from:
  ‘ProjectTemplate’ ‘devtools’ ‘plyr’ ‘survival’
  All declared Imports should be used.
installed size is 33.4Mb
  sub-directories of 1Mb or more:
    CppCode        1.1Mb
    R              5.8Mb
    classic-bugs   1.6Mb
    include        5.7Mb
    libs          16.9Mb
    tests          1.5Mb
Error(s) in re-building vignettes:
--- re-building ‘nipals_algorithm.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'nipals_algorithm.Rmd' failed with diagnostics:
Failed to compile nipals_algorithm.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See nipals_algorithm.log for more info.
--- failed re-building ‘nipals_algorithm.Rmd’

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

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
  'config' variable 'CXXCPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/nloptr.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘nloptr.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'nloptr.Rmd' failed with diagnostics:
Failed to compile nloptr.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See nloptr.log for more info.
--- failed re-building ‘nloptr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [7s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.unsetenv("R_TESTS")
  > 
  > library(testthat)
  > library(nlrx)
  > 
  > test_check("nlrx")
  /usr/local/bin/pandoc +RTS -K512m -RTS nldoc.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output nldoc.html --email-obfuscation none --self-contained --standalone --section-divs --table-of-contents --toc-depth 3 --template /data/gannet/ripley/R/test-clang/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --number-sections --variable 'theme:cosmo' --include-in-header /tmp/RtmptMxV8a/working_dir/RtmpA2a1sG/rmarkdown-str3192230bc60d.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /data/gannet/ripley/R/test-clang/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /data/gannet/ripley/R/test-clang/rmarkdown/rmd/lua/latex-div.lua 
  [1] "File successfully compiled!"
  ── 1. Failure: nldoc (@test_nldoc.R#30)  ───────────────────────────────────────
  length(nldoc_readin) not equal to 8.
  1/1 mismatches
  [1] 27 - 8 == 19
  
  /usr/local/bin/pandoc +RTS -K512m -RTS nldoc.utf8.md --to docx --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output nldoc.docx --table-of-contents --toc-depth 3 --highlight-style tango --lua-filter /data/gannet/ripley/R/test-clang/rmarkdown/rmd/lua/pagebreak.lua 
  [1] "File successfully compiled!"
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 138 | SKIPPED: 8 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: nldoc (@test_nldoc.R#30) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘FixedParameters.Rmd’ using rmarkdown
--- finished re-building ‘FixedParameters.Rmd’

--- re-building ‘nlsr-derivs.Rmd’ using rmarkdown
Loading required package: Ryacas

Attaching package: 'Ryacas'

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

    integrate

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

    %*%, diag, diag<-, lower.tri, upper.tri

! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'nlsr-derivs.Rmd' failed with diagnostics:
Failed to compile nlsr-derivs.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See nlsr-derivs.log for more info.
--- failed re-building ‘nlsr-derivs.Rmd’

--- re-building ‘nlsr-devdoc.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'nlsr-devdoc.Rmd' failed with diagnostics:
Failed to compile nlsr-devdoc.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See nlsr-devdoc.log for more info.
--- failed re-building ‘nlsr-devdoc.Rmd’

SUMMARY: processing the following files failed:
  ‘nlsr-derivs.Rmd’ ‘nlsr-devdoc.Rmd’

Error: Vignette re-building failed.
Execution halted
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: ‘uroot’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘igraph’ ‘lwgeom’
  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.
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.
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.
File ‘norm2/libs/norm2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc   8.6Mb
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  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
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.
Found the following files/directories:
  ‘001509Nova Southeastern University20191123.txt’
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’ ‘tidyverse’ ‘tsibble’
  All declared Imports should be used.
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    doc    7.4Mb
    libs  18.5Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
Note: found 13172 marked Latin-1 strings
installed size is 39.0Mb
  sub-directories of 1Mb or more:
    extdata  38.9Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   8.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.1Mb
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
Found the following files/directories:
  ‘Gulf_of_Lions.pdf’ ‘Gulf_of_Lions_extended.pdf’
File ‘OceanView/libs/OceanView.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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:
    R      2.3Mb
    doc    2.6Mb
    help   2.5Mb
    libs   3.5Mb
Found the following significant warnings:
  'config' variable 'CXXCPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/odbc.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
  'config' variable 'CXXCPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/odpc.Rcheck/00install.out’ for details.
PKG_CFLAGS set in ‘src/Makevars’ without any corresponding files
   PKG_CFLAGS set in ‘src/Makevars.in’ without any corresponding files
Found the following significant warnings:
  ./DataStd.h:180:60: warning: 'bind2nd<std::__1::minus<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./DataStd.h:182:60: warning: 'bind2nd<std::__1::multiplies<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./DataStd.h:225:64: warning: 'bind2nd<std::__1::minus<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./DataStd.h:227:64: warning: 'bind2nd<std::__1::multiplies<double>, double>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/oem.Rcheck/00install.out’ for details.
installed size is 85.3Mb
  sub-directories of 1Mb or more:
    libs  84.8Mb
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 33.9Mb
  sub-directories of 1Mb or more:
    libs  32.5Mb
Namespaces in Imports field not imported from:
  ‘e1071’ ‘fs’ ‘pdp’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘safer’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.8Mb
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.
File ‘ontologySimilarity/libs/ontologySimilarity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/OpenCL.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘readxl’ ‘xml2’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘multifile_zip_resources.Rmd’ using rmarkdown
Quitting from lines 23-30 (multifile_zip_resources.Rmd) 
Error: processing vignette 'multifile_zip_resources.Rmd' failed with diagnostics:
`resource` must be a 1 row data frame or a length 1 character vector.
--- failed re-building ‘multifile_zip_resources.Rmd’

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

--- re-building ‘multisheet_resources.Rmd’ using rmarkdown
New names:
* `` -> ...2
* `` -> ...3
* `` -> ...4
* `` -> ...5
* `` -> ...6
* … and 30 more problems

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

New names:
* `` -> ...1
* `` -> ...2
* `` -> ...4
* `` -> ...5
* `` -> ...6
* … and 79 more problems
New names:
* `` -> ...1
* `` -> ...2
* `` -> ...4
* `` -> ...5
* `` -> ...6
* … and 33 more problems
--- finished re-building ‘multisheet_resources.Rmd’

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

--- re-building ‘spatial_data.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

--- finished re-building ‘spatial_data.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   5.4Mb
installed size is 199.3Mb
  sub-directories of 1Mb or more:
    R         2.5Mb
    libs    189.2Mb
    models    4.7Mb
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  7.4Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      5.5Mb
Namespaces in Imports field not imported from:
  ‘rlang’ ‘stringi’
  All declared Imports should be used.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
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.
Error(s) in re-building vignettes:
--- re-building ‘Extend-optimx.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'Extend-optimx.Rmd' failed with diagnostics:
Failed to compile Extend-optimx.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See Extend-optimx.log for more info.
--- failed re-building ‘Extend-optimx.Rmd’

--- re-building ‘Rvmmin.Rmd’ using knitr
--- finished re-building ‘Rvmmin.Rmd’

--- re-building ‘SNewton.Rmd’ using knitr
--- finished re-building ‘SNewton.Rmd’

SUMMARY: processing the following file failed:
  ‘Extend-optimx.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.4Mb
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 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
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:
    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.
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 10.9Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   6.9Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
Package suggested but not available for checking: ‘Rcplex’
Namespace in Imports field not imported from: ‘quantreg’
  All declared Imports should be used.
Found the following significant warnings:
  likelihoods.cpp:479:38: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/outbreaker2.Rcheck/00install.out’ for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   2.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
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:
  ‘jcolors’ ‘oompaBase’ ‘palr’ ‘pals’ ‘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.
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.
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 ‘pbdDEMO/libs/pbdDEMO.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    lib   9.6Mb
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  6.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    examples   1.7Mb
Error(s) in re-building vignettes:
--- re-building ‘pca3d.rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'pca3d.rmd' failed with diagnostics:
Failed to compile pca3d.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See pca3d.log for more info.
--- failed re-building ‘pca3d.rmd’

SUMMARY: processing the following file failed:
  ‘pca3d.rmd’

Error: Vignette re-building failed.
Execution halted
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  8.3Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   2.7Mb
    libs      2.9Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pander’
  All declared Imports should be used.
Found the following significant warnings:
  l1pcahp.c:82:8: warning: expression result unused [-Wunused-value]
  l1pcahp.c:92:8: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/pcaL1.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘projPointsl1pca.txt’
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   6.7Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
installed size is 140.8Mb
  sub-directories of 1Mb or more:
    doc     2.6Mb
    libs  137.8Mb
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.
File ‘PCIT/libs/PCIT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 31.4Mb
  sub-directories of 1Mb or more:
    libs  30.2Mb
Error(s) in re-building vignettes:
--- re-building ‘PCRedux.Rmd’ using rmarkdown
--- finished re-building ‘PCRedux.Rmd’

--- re-building ‘SI1.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'SI1.Rmd' failed with diagnostics:
Failed to compile SI1.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See SI1.log for more info.
--- failed re-building ‘SI1.Rmd’

SUMMARY: processing the following file failed:
  ‘SI1.Rmd’

Error: Vignette re-building failed.
Execution halted
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  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
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.
File ‘pedometrics/libs/pedometrics.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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   4.9Mb
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.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
  'config' variable 'CXXCPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/pense.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
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.
Found the following files/directories:
  ‘myTest_compHomToPep.fasta’
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.
Error(s) in re-building vignettes:
--- re-building ‘permutes.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'permutes.Rmd' failed with diagnostics:
Failed to compile permutes.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See permutes.log for more info.
--- failed re-building ‘permutes.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
Error(s) in re-building vignettes:
--- re-building ‘Introduction.Rmd’ using rmarkdown_notangle
ERROR: Duplicated records found in prim.key field
ERROR: NULL records found in prim.key field
OK: No duplicated records found in prim.key field
OK: No NULL records found in prim.key field
Fuzzy matching
Phonetic matching
Semantic matching
Fuzzy matching
Phonetic matching
Semantic matching
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
Failed to compile Introduction.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See Introduction.log for more info.
--- 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 ‘pgsc_vignette.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'pgsc_vignette.Rmd' failed with diagnostics:
Failed to compile pgsc_vignette.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See pgsc_vignette.log for more info.
--- failed re-building ‘pgsc_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
Found the following files/directories:
  ‘1’ ‘alcMat.txt’ ‘doseTrace.pdf’ ‘patData.txt’ ‘recMat.txt’
Found the following significant warnings:
  LJMA_arms.c:297:11: warning: comparison of array 'env->p' equal to a null pointer is always false [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/PhaseType.Rcheck/00install.out’ for details.
File ‘PhaseType/libs/PhaseType.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘LJMA_arms.o’
File ‘PhaseType/libs/PhaseType.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 ‘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.
Found the following files/directories:
  ‘mycross.csv’
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
Error(s) in re-building vignettes:
--- re-building ‘PhenotypeSimulator.Rmd’ using rmarkdown
--- finished re-building ‘PhenotypeSimulator.Rmd’

--- re-building ‘Sample-scripts-external-genotype-simulation.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'Sample-scripts-external-genotype-simulation.Rmd' failed with diagnostics:
Failed to compile Sample-scripts-external-genotype-simulation.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See Sample-scripts-external-genotype-simulation.log for more info.
--- failed re-building ‘Sample-scripts-external-genotype-simulation.Rmd’

--- re-building ‘Simulation-and-LinearModel.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'Simulation-and-LinearModel.Rmd' failed with diagnostics:
Failed to compile Simulation-and-LinearModel.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See Simulation-and-LinearModel.log for more info.
--- failed re-building ‘Simulation-and-LinearModel.Rmd’

--- re-building ‘SimulationBasedOnExampleData.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'SimulationBasedOnExampleData.Rmd' failed with diagnostics:
Failed to compile SimulationBasedOnExampleData.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See SimulationBasedOnExampleData.log for more info.
--- failed re-building ‘SimulationBasedOnExampleData.Rmd’

SUMMARY: processing the following files failed:
  ‘Sample-scripts-external-genotype-simulation.Rmd’
  ‘Simulation-and-LinearModel.Rmd’ ‘SimulationBasedOnExampleData.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  phreeqcpp/Parser.h:283:69: warning: 'ptr_fun<int, int>' is deprecated [-Wdeprecated-declarations]
  phreeqcpp/Parser.h:288:60: warning: 'ptr_fun<int, int>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/phreeqc.Rcheck/00install.out’ for details.
installed size is 38.5Mb
  sub-directories of 1Mb or more:
    libs  37.7Mb
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 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
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 15.4Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  12.9Mb
installed size is  5.5Mb
  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 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
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.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   2.0Mb
    doc    3.0Mb
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘stringi’
  All declared Imports should be used.
Found the following files/directories:
  ‘file4e4971cc6716.md’
installed size is 25.0Mb
  sub-directories of 1Mb or more:
    libs  24.9Mb
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.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
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.
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.
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.
Error(s) in re-building vignettes:
--- re-building ‘AncestryCheck.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'AncestryCheck.Rmd' failed with diagnostics:
Failed to compile AncestryCheck.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See AncestryCheck.log for more info.
--- failed re-building ‘AncestryCheck.Rmd’

--- re-building ‘Genomes1000.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'Genomes1000.Rmd' failed with diagnostics:
Failed to compile Genomes1000.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See Genomes1000.log for more info.
--- failed re-building ‘Genomes1000.Rmd’

--- re-building ‘HapMap.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'HapMap.Rmd' failed with diagnostics:
Failed to compile HapMap.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See HapMap.log for more info.
--- failed re-building ‘HapMap.Rmd’

--- re-building ‘plinkQC.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'plinkQC.Rmd' failed with diagnostics:
Failed to compile plinkQC.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See plinkQC.log for more info.
--- failed re-building ‘plinkQC.Rmd’

SUMMARY: processing the following files failed:
  ‘AncestryCheck.Rmd’ ‘Genomes1000.Rmd’ ‘HapMap.Rmd’ ‘plinkQC.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘PlackettLuce’ ‘StatRank’ ‘pmr’ ‘prefmod’ ‘rankdist’
  All declared Imports should be used.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   7.4Mb
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.
Found the following files/directories:
  ‘Legend3665209266b3.png’ ‘Legend36652c8b9efc.png’ ‘myMap2.htm’
Namespaces in Imports field not imported from:
  ‘hexbin’ ‘quantreg’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.6Mb
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 ‘plyr/libs/plyr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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   6.3Mb
    libs   1.9Mb
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:
  ‘htmltools’ ‘lubridate’ ‘tibble’
  All declared Imports should be used.
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  9.7Mb
  sub-directories of 1Mb or more:
    R      6.4Mb
    data   2.5Mb
Found the following files/directories:
  ‘LG1’ ‘LG2’ ‘LG3’ ‘LG3_homologue1_P1.pwd’ ‘LG4’ ‘LG5’ ‘TetraOrigin’
  ‘TetraploidSNPMap_QTLfiles’ ‘all_linkages_P1’ ‘mapping_files_MDSMap’
Error(s) in re-building vignettes:
--- re-building ‘POMDP.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'POMDP.Rmd' failed with diagnostics:
Failed to compile POMDP.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See POMDP.log for more info.
--- failed re-building ‘POMDP.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Found the following significant warnings:
  whopgenome/whoptbi_info.cpp:116:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  whopgenome/whoptbi_info.cpp:122:7: 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]
  whopgenome/whoptbi_region.cpp:80:13: warning: 'this' pointer cannot be null 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/PopGenome.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘burkina-faso-females.Rnw’ using Sweave
Loading required package: coda
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files
gdata: ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files
gdata: ENABLED.

Attaching package: ‘gdata’

The following object is masked from ‘package:stats’:

    nobs

The following object is masked from ‘package:utils’:

    object.size

The following object is masked from ‘package:base’:

    startsWith

Calculating life expectancy at birth ...
... done
Calculating net number of migrants ...
... done
Error: processing vignette 'burkina-faso-females.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'burkina-faso-females.tex' failed.
BibTeX errors:
The top-level auxiliary file: burkina-faso-females.aux
I couldn't open style file apa.bst
---line 19 of file burkina-faso-females.aux
 : \bibstyle{apa
 :              }
I'm skipping whatever remains of this command
I found no style file---while reading file burkina-faso-females.aux
--- failed re-building ‘burkina-faso-females.Rnw’

SUMMARY: processing the following file failed:
  ‘burkina-faso-females.Rnw’

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

It is 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:
    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  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
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.
Error(s) in re-building vignettes:
--- re-building ‘simulations.Rmd’ using rmarkdown
--- finished re-building ‘simulations.Rmd’

--- re-building ‘technical.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'technical.Rmd' failed with diagnostics:
Failed to compile technical.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See technical.log for more info.
--- failed re-building ‘technical.Rmd’

--- re-building ‘three-level.Rmd’ using rmarkdown
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
--- finished re-building ‘three-level.Rmd’

--- re-building ‘two-level.Rmd’ using rmarkdown
--- finished re-building ‘two-level.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    doc  11.8Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
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:
  ‘TH.data’ ‘moonBook’
  All declared Imports should be used.
Found the following files/directories:
  ‘AlleleOR.txt’ ‘GenoOR.txt’ ‘RiskscorePredRisk.txt’ ‘multiOR.txt’
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 16.2Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
Namespaces in Imports field not imported from:
  ‘datasets’ ‘dplyr’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
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.
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  14.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
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
Namespace in Imports field not imported from: ‘processmapR’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘TH.data’ ‘jtools’ ‘modelr’ ‘prediction’ ‘rlang’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘expm’ ‘mvtnorm’
  All declared Imports should be used.
File ‘profdpm/libs/profdpm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    extdata   7.4Mb
    libs      5.8Mb
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  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   2.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   2.6Mb
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.
Found the following files/directories:
  ‘intro.mod’ ‘intro2.mod’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.1Mb
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:
  ‘foreign’ ‘mitools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘forecast’ ‘knitr’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
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.
possible bashism in configure line 7 (should be >word 2>&1):
      echo &>2 R_HOME is not set, are you running R CMD INSTALL?
  possible bashism in configure line 46 (test -a/-o):
  if [ -n "$FREEBSD" -o -n "$OPENBSD" -o -n "$NETBSD" ]; then
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.7Mb
    doc   2.4Mb
Found the following files/directories:
  ‘test.ICLUST.graph.dot’
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  8.0Mb
  sub-directories of 1Mb or more:
    doc        4.6Mb
    examples   2.5Mb
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘desctable’ ‘effects’ ‘knitr’ ‘latex2exp’ ‘lme4’ ‘nlme’
  ‘nnet’ ‘ordinal’ ‘pander’ ‘papeR’
  All declared Imports should be used.
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    libs  33.5Mb
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:
  ‘R6’ ‘hms’
  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
Package required but not available: ‘dti’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘purrr’ ‘rmarkdown’
  All declared Imports should be used.
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 12.0Mb
  sub-directories of 1Mb or more:
    data  11.8Mb
File ‘QRM/libs/QRM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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:
    data  12.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘msm’
  All declared Imports should be used.
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
installed size is 11.5Mb
  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  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   1.3Mb
    libs  15.5Mb
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 10.4Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   5.2Mb
Found the following significant warnings:
  NewickParser.cpp:20:63: warning: 'ptr_fun<int, int>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/Quartet.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘Critical-distances.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'Critical-distances.Rmd' failed with diagnostics:
Failed to compile Critical-distances.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See Critical-distances.log for more info.
--- failed re-building ‘Critical-distances.Rmd’

--- re-building ‘Tree-distance-metrics.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'Tree-distance-metrics.Rmd' failed with diagnostics:
Failed to compile Tree-distance-metrics.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See Tree-distance-metrics.log for more info.
--- failed re-building ‘Tree-distance-metrics.Rmd’

SUMMARY: processing the following files failed:
  ‘Critical-distances.Rmd’ ‘Tree-distance-metrics.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
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  5.8Mb
  sub-directories of 1Mb or more:
    Output   2.2Mb
    bin      3.3Mb
File ‘R4dfp/libs/R4dfp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘RAbHIT-vignette.Rmd’ using rmarkdown
Loading required package: ggplot2
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.
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'RAbHIT-vignette.Rmd' failed with diagnostics:
Failed to compile RAbHIT-vignette.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See RAbHIT-vignette.log for more info.
--- failed re-building ‘RAbHIT-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘RAbHIT-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘scran’
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    5.9Mb
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
Running examples in ‘radiant.model-Ex.R’ failed
The error most likely occurred in:

> ### Name: predict.crtree
> ### Title: Predict method for the crtree function
> ### Aliases: predict.crtree
> 
> ### ** Examples
> 
> result <- crtree(titanic, "survived", c("pclass", "sex"), lev = "Yes")
> predict(result, pred_cmd = "pclass = levels(pclass)")
Classification and regression trees
Data                 : titanic 
Response variable    : survived 
Level(s)             : Yes in survived 
Explanatory variables: pclass, sex 
Prediction command   : pclass = levels(pclass) 

  sex pclass Prediction
 male    1st      0.205
 male    2nd      0.205
 male    3rd      0.205
> result <- crtree(titanic, "survived", "pclass", lev = "Yes")
> predict(result, pred_data = titanic) %>% head()
Classification and regression trees
Data                 : 
Response variable    : 
Explanatory variables:  
Error in if (pred_type == "cmd") { : argument is of length zero
Calls: <Anonymous> -> print.crtree.predict -> print_predict_model
Execution halted
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.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
possible bashism in configure line 30 ($(OS|MACH)TYPE):
  elif [[ "$OSTYPE" == "darwin"* ]]; then
  possible bashism in configure line 30 (alternative test command ([[ foo ]] should be [ foo ])):
  elif [[ "$OSTYPE" == "darwin"* ]]; then
  possible bashism in configure line 30 (should be 'b = a'):
  elif [[ "$OSTYPE" == "darwin"* ]]; then
  possible bashism in configure line 35 (should be '.', not 'source'):
      source tools/autobrew
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    libs  27.5Mb
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 ‘ramsvm/libs/ramsvm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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  7.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.2Mb
    libs   5.0Mb
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.
Namespaces in Imports field not imported from:
  ‘ENMeval’ ‘MASS’ ‘biomod2’ ‘dismo’ ‘dplyr’ ‘ecospat’ ‘googlesheets’
  ‘jsonlite’ ‘rgbif’ ‘rgdal’ ‘rgeos’ ‘sp’ ‘spThin’ ‘spatstat’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
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.
File ‘RANN.L1/libs/RANN.L1.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 17.4Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs  11.8Mb
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 10.4Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    libs   6.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    etc    1.9Mb
    po     1.2Mb
installed size is 32.0Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  28.2Mb
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 15.4Mb
  sub-directories of 1Mb or more:
    blp    7.1Mb
    libs   7.4Mb
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 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   2.9Mb
    po    2.2Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    corpora   7.6Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    include   5.9Mb
    libs      1.6Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
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.
‘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 32.2Mb
  sub-directories of 1Mb or more:
    include   7.9Mb
    libs     23.6Mb
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  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 57.3Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib      43.3Mb
    libs     11.9Mb
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 10.0Mb
  sub-directories of 1Mb or more:
    include   7.0Mb
    libs      2.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib       2.8Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    include   6.4Mb
    libs      4.8Mb
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  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
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.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/Rcsdp.Rcheck/00install.out’ for details.
File ‘Rcsdp/libs/Rcsdp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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:
    libs   9.5Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘smcure’
  All declared Imports should be used.
File ‘rDEA/libs/rDEA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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:
    libs  13.2Mb
Found the following significant warnings:
  dist.cpp:19:33: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
  dist.cpp:65:33: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
  dist.cpp:111:36: warning: explicitly assigning value of variable of type 'float' 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.
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
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 10.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   8.3Mb
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  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Note: found 1 marked Latin-1 string
  Note: found 1 marked UTF-8 string
  Note: found 7 strings marked as "bytes"
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
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  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   3.2Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
Found the following significant warnings:
  RecurseCalculator.cpp:417:17: warning: 'bind1st<std::__1::multiplies<double>, double>' is deprecated [-Wdeprecated-declarations]
  RecurseCalculator.cpp:422:18: warning: 'bind1st<std::__1::multiplies<double>, double>' is deprecated [-Wdeprecated-declarations]
  RecurseCalculator.cpp:424:18: warning: 'bind1st<std::__1::multiplies<double>, double>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/recurse.Rcheck/00install.out’ for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.2Mb
Namespaces in Imports field not imported from:
  ‘DBI’ ‘readr’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   5.2Mb
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs  16.5Mb
Found the following files/directories:
  ‘delta_t_mat_allmk_list_test.Rdata’ ‘gt_opt_test.Rdata’
  ‘t_mat0_test.Rdata’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.2Mb
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:
  ‘rlang’ ‘spatstat’
  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 11.4Mb
  sub-directories of 1Mb or more:
    doc    8.6Mb
    libs   2.1Mb
Namespace in Imports field not imported from: ‘data.tree’
  All declared Imports should be used.
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 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
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.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
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.
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.
Namespace in Imports field not imported from: ‘SnowballC’
  All declared Imports should be used.
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
installed size is 53.2Mb
  sub-directories of 1Mb or more:
    libs  51.9Mb
File ‘RFgroove/libs/RFgroove.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘Rfit/libs/Rfit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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:
    java   5.3Mb
Namespaces in Imports field not imported from:
  ‘prob’ ‘titanic’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘vignette_RGCCA.Rmd’ using rmarkdown
tlmgr search --file --global '/tikzlibrarytopaths.code.tex'
tlmgr search --file --global '/tikzlibraryarrows.code.tex'
tlmgr search --file --global '/tikzlibraryplotmarks.code.tex'
Trying to automatically install missing LaTeX packages...
tlmgr install pgf
tlmgr: package repository http://mirror.ox.ac.uk/sites/ctan.org/systems/texlive/tlnet (verified)
tlmgr install: package already present: pgf
tlmgr path add
add_link_dir_dir: /usr/local/share/info/dir exists; not making symlink.
tlmgr search --file --global '/tikzlibrarytopaths.code.tex'
tlmgr search --file --global '/tikzlibraryarrows.code.tex'
tlmgr search --file --global '/tikzlibraryplotmarks.code.tex'
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'vignette_RGCCA.Rmd' failed with diagnostics:
Failed to compile vignette_RGCCA.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See vignette_RGCCA.log for more info.
--- failed re-building ‘vignette_RGCCA.Rmd’

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

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

> ### Name: CCGamma
> ### Title: This function extends 'continuity_ratio' and adds the
> ###   corresponding gaussian correlation matrix for no-precipitation
> ###   occurence.
> ### Aliases: CCGamma
> 
> ### ** Examples
> 
> 
> data(trentino)
> 
> year_min <- 1961
> year_max <- 1990
> origin <- paste(year_min,1,1,sep="-")
> 
> period <- PRECIPITATION$year>=year_min & PRECIPITATION$year<=year_max
> station <- names(PRECIPITATION)[!(names(PRECIPITATION) %in% c("day","month","year"))]
> prec_mes <- PRECIPITATION[period,station]  
> 
> ## removing nonworking stations (e.g. time series with NA)
> accepted <- array(TRUE,length(names(prec_mes)))
> names(accepted) <- names(prec_mes)
> for (it in names(prec_mes)) {
+ 		 accepted[it]  <- (length(which(!is.na(prec_mes[,it])))==length(prec_mes[,it]))
+ }
> 
> prec_mes <- prec_mes[,accepted]
> ## the dateset is reduced!!! 
> prec_mes <- prec_mes[,1:2]
> 
> CCGamma <- CCGamma(data=prec_mes,lag=0,tolerance=0.001,only.matrix=FALSE)
lag
0
Error in 1:nrow(out$nooccurence_correlation) : argument of length 0
Calls: CCGamma
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.7Mb
Namespaces in Imports field not imported from:
  ‘leaflet’ ‘pals’ ‘raster’ ‘sp’
  All declared Imports should be used.
File ‘rgexf/libs/rgexf.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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/rgl.Rcheck/00install.out’ for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc     3.6Mb
    fonts   1.5Mb
    libs    2.6Mb
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 23.9Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  10.5Mb
    libs   7.9Mb
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.
Error(s) in re-building vignettes:
--- re-building ‘rich_introduction.Rmd’ using rmarkdown

rich version 1.0.1 is loaded
You can access the package vignette by typing vignette('rich_introduction') in the R console

Attaching package: 'gplots'

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

    lowess

! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'rich_introduction.Rmd' failed with diagnostics:
Failed to compile rich_introduction.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See rich_introduction.log for more info.
--- failed re-building ‘rich_introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
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 24.0Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  22.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
File ‘RJaCGH/libs/RJaCGH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: 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 22.3Mb
  sub-directories of 1Mb or more:
    libs  22.1Mb
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  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is 53.8Mb
  sub-directories of 1Mb or more:
    libs  53.3Mb
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  22.6Mb
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  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Found the following significant warnings:
  DbResult.cpp:19:8: warning: 'auto_ptr<DbResult>' is deprecated [-Wdeprecated-declarations]
  connection.cpp:23:8: warning: 'auto_ptr<DbConnection>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/RMariaDB.Rcheck/00install.out’ for details.
installed size is  9.2Mb
  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 56.3Mb
  sub-directories of 1Mb or more:
    libs  55.6Mb
Namespaces in Imports field not imported from:
  ‘blogdown’ ‘bookdown’ ‘bookdownplus’ ‘citr’ ‘pagedown’ ‘rticles’
  ‘tinytex’ ‘xaringan’
  All declared Imports should be used.
Found the following files/directories:
  ‘exampleland.genepop’
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   6.3Mb
installed size is 38.7Mb
  sub-directories of 1Mb or more:
    libs  37.8Mb
installed size is 33.8Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  32.1Mb
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.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/Rmpfr.Rcheck/00install.out’ for details.
Running examples in ‘RMRAINGEN-Ex.R’ failed
The error most likely occurred in:

> ### Name: CCGamma
> ### Title: This function extends 'continuity_ratio' and adds the
> ###   corresponding gaussian correlation matrix for no-precipitation
> ###   occurence.
> ### Aliases: CCGamma
> 
> ### ** Examples
> 
> library(RMAWGEN)
> data(trentino)
> 
> year_min <- 1961
> year_max <- 1990
> origin <- paste(year_min,1,1,sep="-")
> 
> period <- PRECIPITATION$year>=year_min & PRECIPITATION$year<=year_max
> station <- names(PRECIPITATION)[!(names(PRECIPITATION) %in% c("day","month","year"))]
> prec_mes <- PRECIPITATION[period,station]
> 
> ## removing nonworking stations (e.g. time series with NA)
> accepted <- array(TRUE,length(names(prec_mes)))
> names(accepted) <- names(prec_mes)
> for (it in names(prec_mes)) {
+ 		 accepted[it]  <- (length(which(!is.na(prec_mes[,it])))==length(prec_mes[,it]))
+ }
> 
> prec_mes <- prec_mes[,accepted]
> ## the dateset is reduced!!!
> prec_mes <- prec_mes[,1:2]
> 
> CCGamma <- CCGamma(data=prec_mes,lag=0,tolerance=0.001,only.matrix=FALSE)
[1] "lag"
[1] 0
Error in if (is.na(p0_v2)) { : argument is of length zero
Calls: CCGamma -> omega_inv -> omega
Execution halted
Namespace in Imports field not imported from: ‘statmod’
  All declared Imports should be used.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    libs  21.0Mb
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  5.8Mb
  sub-directories of 1Mb or more:
    doxygen   1.6Mb
    libs      3.2Mb
installed size is 90.5Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     88.4Mb
Namespace in Imports field not imported from: ‘impute’
  All declared Imports should be used.
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
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
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 14.6Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
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 23.4Mb
  sub-directories of 1Mb or more:
    libs  23.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
File ‘robustHD/libs/robustHD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    libs  31.6Mb
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.
o.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
p.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
o.rocc: no visible global function definition for ‘prediction’
o.rocc: no visible global function definition for ‘performance’
o.rocc: no visible global function definition for ‘binom.test’
tr.rocc: no visible global function definition for ‘prediction’
tr.rocc: no visible global function definition for ‘performance’
Undefined global functions or variables:
  binom.test performance prediction
Consider adding
  importFrom("stats", "binom.test")
to your NAMESPACE file.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/RODBCext.Rcheck/00install.out’ for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
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 20.0Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘rstudioapi’ ‘tinytex’
  All declared Imports should be used.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.3Mb
    libs   6.0Mb
File ‘rotations/libs/rotations.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘RoughSets/libs/RoughSets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘httpuv’ ‘utils’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    libs    2.2Mb
    tests   1.2Mb
File ‘RPANDA/libs/RPANDA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      4.0Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   4.9Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘testthat’
  All declared Imports should be used.
Found the following significant warnings:
  DbDataFrame.cpp:52:77: warning: 'mem_fun_ref<DATA_TYPE, DbColumn>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/RPostgres.Rcheck/00install.out’ for details.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.6Mb
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 42.1Mb
  sub-directories of 1Mb or more:
    libs  41.4Mb
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.
Namespaces in Imports field not imported from:
  ‘data.tree’ ‘penalized’
  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  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
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.
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
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 14.0Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
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  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 44.1Mb
  sub-directories of 1Mb or more:
    libs  43.4Mb
Found the following significant warnings:
  DbDataFrame.cpp:52:77: warning: 'mem_fun_ref<DATA_TYPE, DbColumn>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/RSQLite.Rcheck/00install.out’ for details.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
Namespace in Imports field not imported from: ‘pkgconfig’
  All declared Imports should be used.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/Rssa.Rcheck/00install.out’ for details.
installed size is 191.7Mb
  sub-directories of 1Mb or more:
    R       1.5Mb
    doc     1.2Mb
    libs  188.4Mb
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    libs  25.7Mb
installed size is 172.6Mb
  sub-directories of 1Mb or more:
    libs  169.8Mb
installed size is 92.0Mb
  sub-directories of 1Mb or more:
    libs  90.8Mb
Namespace in Imports field not imported from: ‘loo’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  13.4Mb
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.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rworldmap’
  All declared Imports should be used.
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.
Found the following files/directories:
  ‘input.fas’ ‘pwm.meme’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       2.5Mb
    projects   2.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
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 28.3Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  19.5Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   2.2Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   7.0Mb
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.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/Runuran.Rcheck/00install.out’ for details.
installed size is 39.8Mb
  sub-directories of 1Mb or more:
    libs  39.1Mb
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 55.7Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs     51.3Mb
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.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs    7.8Mb
    yacas   1.5Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs    8.5Mb
    yacas   1.6Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
Found the following significant warnings:
  'config' variable 'CXXCPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/rzmq.Rcheck/00install.out’ for details.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
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.
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 15.6Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  12.4Mb
Namespaces in Imports field not imported from:
  ‘gdistance’ ‘methods’
  All declared Imports should be used.
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
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 21.0Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   3.4Mb
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.
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.
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.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
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.
Error(s) in re-building vignettes:
--- re-building ‘scbursts.Rmd’ using rmarkdown
tlmgr search --file --global '/tikzlibrarytopaths.code.tex'
tlmgr search --file --global '/tikzlibraryshapes.code.tex'
tlmgr search --file --global '/tikzlibraryarrows.code.tex'
Trying to automatically install missing LaTeX packages...
tlmgr install pgf
tlmgr: package repository http://mirror.ox.ac.uk/sites/ctan.org/systems/texlive/tlnet (verified)
tlmgr install: package already present: pgf
tlmgr path add
add_link_dir_dir: /usr/local/share/info/dir exists; not making symlink.
tlmgr search --file --global '/tikzlibrarytopaths.code.tex'
tlmgr search --file --global '/tikzlibraryshapes.code.tex'
tlmgr search --file --global '/tikzlibraryarrows.code.tex'
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'scbursts.Rmd' failed with diagnostics:
Failed to compile scbursts.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See scbursts.log for more info.
--- failed re-building ‘scbursts.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
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.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘future’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘gbm’
  All declared Imports should be used.
File ‘SDMTools/libs/SDMTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.
Found the following significant warnings:
  Warning: ‘__var_1_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/sdwd.Rcheck/00install.out’ for details.
File ‘sdwd/libs/sdwd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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:
    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 10.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   7.1Mb
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: ‘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  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
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:
  ‘RColorBrewer’ ‘SemNetCleaner’ ‘grid’ ‘purrr’
  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  7.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.5Mb
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs  13.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
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 25.9Mb
  sub-directories of 1Mb or more:
    libs  24.5Mb
installed size is  8.2Mb
  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.
Error(s) in re-building vignettes:
--- re-building ‘cover.Rmd’ using rmarkdown
--- finished re-building ‘cover.Rmd’

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

--- re-building ‘methodology.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'methodology.Rmd' failed with diagnostics:
Failed to compile methodology.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See methodology.log for more info.
--- failed re-building ‘methodology.Rmd’

--- re-building ‘tutorial.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
Failed to compile tutorial.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See tutorial.log for more info.
--- failed re-building ‘tutorial.Rmd’

SUMMARY: processing the following files failed:
  ‘methodology.Rmd’ ‘tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
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', 'MAST', 'monocle'
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 24.4Mb
  sub-directories of 1Mb or more:
    doc     12.0Mb
    libs     8.3Mb
    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 10.8Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.0Mb
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.
File ‘sharpeRratio/libs/sharpeRratio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘sharpshootR-Ex.R’ failed
The error most likely occurred in:

> ### Name: PCP_plot
> ### Title: Percentiles of Cumulative Precipitation
> ### Aliases: PCP_plot
> ### Keywords: hplots
> 
> ### ** Examples
> 
> ## get data from CDEC
> 
> # define station of interest
> s <- 'SPW'
> # get metadata
> s.info <- CDEC_StationInfo(s)
Error in open.connection(x, "rb") : 
  Timeout was reached: [cdec.water.ca.gov] Connection timed out after 10005 milliseconds
Calls: CDEC_StationInfo -> <Anonymous> -> read_html.default
Execution halted
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.
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.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
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  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  11.7Mb
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’
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.
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.
Namespaces in Imports field not imported from:
  ‘BB’ ‘MASS’ ‘ggplot2’ ‘grid’ ‘triangle’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  21.1Mb
Namespace in Imports field not imported from: ‘pracma’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘pagedown’ ‘rosr’
  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 11.2Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   7.3Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
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.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.2Mb
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 40.2Mb
  sub-directories of 1Mb or more:
    libs  38.7Mb
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.
Error(s) in re-building vignettes:
--- re-building ‘slim.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'slim.Rmd' failed with diagnostics:
Failed to compile slim.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See slim.log for more info.
--- failed re-building ‘slim.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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
File ‘smac/libs/smac.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘Amelia’ ‘Boruta’ ‘DMwR’ ‘MVN’ ‘NoiseFiltersR’ ‘VIM’ ‘adaptiveGPCA’
  ‘class’ ‘clusterSim’ ‘denoiseR’ ‘discretization’ ‘imbalance’ ‘lle’
  ‘missForest’ ‘missMDA’ ‘outliers’ ‘unbalanced’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ISLR’
  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.
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.
Found the following files/directories:
  ‘results_2019-11-23.txt’ ‘results_2019-11-23_1.txt’
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs  10.3Mb
Found the following significant warnings:
  createPosDef.cpp:84:12: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/smoothSurv.Rcheck/00install.out’ for details.
File ‘sna/libs/sna.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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’ ‘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  6.0Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.6Mb
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.
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  9.8Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.6Mb
    libs   5.9Mb
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 ‘soobench/libs/soobench.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.9Mb
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 ‘spacejam/libs/spacejam.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.
Found the following files/directories:
  ‘spacodi.formatted.txt’
Namespaces in Imports field not imported from:
  ‘devtools’ ‘rstudioapi’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘spaero-introduction.Rmd’ using rmarkdown_notangle
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'spaero-introduction.Rmd' failed with diagnostics:
Failed to compile spaero-introduction.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See spaero-introduction.log for more info.
--- failed re-building ‘spaero-introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘spaero-introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  32.1Mb
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 16.4Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
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.
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:
  ‘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  5.8Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Note: found 25 marked Latin-1 strings
  Note: found 658 marked UTF-8 strings
File ‘spatialTailDep/libs/spatialTailDep.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  17.2Mb
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 18.3Mb
  sub-directories of 1Mb or more:
    R      5.2Mb
    doc    4.9Mb
    help   5.2Mb
    libs   2.1Mb
installed size is 31.9Mb
  sub-directories of 1Mb or more:
    libs  30.1Mb
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
    libs  10.4Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
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 ‘SpeciesMix/libs/SpeciesMix.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   2.6Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘usethis’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘Spectrum_vignette.Rmd’ using rmarkdown
tlmgr search --file --global '/framed.sty'
Trying to automatically install missing LaTeX packages...
tlmgr install framed
tlmgr: package repository http://mirror.ox.ac.uk/sites/ctan.org/systems/texlive/tlnet (verified)
tlmgr install: package already present: framed
tlmgr path add
add_link_dir_dir: /usr/local/share/info/dir exists; not making symlink.
tlmgr search --file --global '/framed.sty'
! LaTeX Error: File `framed.sty' not found.

! Emergency stop.
<read *> 

Error: processing vignette 'Spectrum_vignette.Rmd' failed with diagnostics:
Failed to compile Spectrum_vignette.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See Spectrum_vignette.log for more info.
--- failed re-building ‘Spectrum_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
Found the following files/directories:
  ‘test9285-270.rData’ ‘test9285-35.rData’ ‘test9285-48.rData’
  ‘test9285-92.rData’
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’
  All declared Imports should be used.
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
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  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Namespaces in Imports field not imported from:
  ‘GGally’ ‘tibble’ ‘webshot’
  All declared Imports should be used.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
  'config' variable 'CXXCPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/SplitReg.Rcheck/00install.out’ for details.
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.
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 15.3Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   9.2Mb
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘ggplot2’
  All declared Imports should be used.
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs  13.2Mb
Namespaces in Imports field not imported from:
  ‘BayesX’ ‘BayesXsrc’ ‘automap’ ‘plyr’ ‘rgdal’ ‘splines’
  All declared Imports should be used.
Running ‘testthat.R’ [16s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("SqlRender")
  Loading required package: SqlRender
  Reading SQL from package folder: /data/gannet/ripley/R/packages/tests-clang/SqlRender.Rcheck/SqlRender/sql/sql_server/test.sql
  Writing R function to: /tmp/RtmpWpZjlh/working_dir/RtmpzCmICu/file1897551bd6e1
  ── 1. Error: If-then-else: error on bad boolean logic syntax (@test-renderSql.R#
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(render("{true = true} ? {true} : {false}"))
   13. rlang::cnd_entrace(cnd)
   16. rJava:::`$.Throwable`(cnd, "trace")
   17. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ── 2. Error: translate sql server throws error when invalid target is given (@te
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(translate("iSELECT * FROM a;", targetDialect = "pwd"))
   13. rlang::cnd_entrace(cnd)
   16. rJava:::`$.Throwable`(cnd, "trace")
   17. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ── 3. Error: translateSingleStatement sql server -> oracle throw error if > 1 st
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(...)
   13. rlang::cnd_entrace(cnd)
   16. rJava:::`$.Throwable`(cnd, "trace")
   17. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 448 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Error: If-then-else: error on bad boolean logic syntax (@test-renderSql.R#155) 
  2. Error: translate sql server throws error when invalid target is given (@test-translateSql.R#394) 
  3. Error: translateSingleStatement sql server -> oracle throw error if > 1 statement (@test-translateSql.R#2338) 
  
  Error: testthat unit tests failed
  Execution halted
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 73.2Mb
  sub-directories of 1Mb or more:
    libs  72.8Mb
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
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 13.3Mb
  sub-directories of 1Mb or more:
    include  10.3Mb
    lib       2.8Mb
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
Running ‘testthat.R’ [60s/120s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(stationaRy)
  > 
  > test_check("stationaRy")
  trying URL 'https://www1.ncdc.noaa.gov/pub/data/noaa/isd-inventory.csv'
  ── 1. Error: The `get_inventory_tbl()` fcn provides the expected table (@test-ge
  cannot open URL 'https://www1.ncdc.noaa.gov/pub/data/noaa/isd-inventory.csv'
  Backtrace:
   1. stationaRy:::get_inventory_tbl()
   2. downloader::download(url = file_location, destfile = temp_file)
   3. utils::download.file(url, method = method, ...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 39 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: The `get_inventory_tbl()` fcn provides the expected table (@test-get_met_station_data.R#227) 
  
  Error: testthat unit tests failed
  Execution halted
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’ ‘multigroup’ ‘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  7.2Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   4.5Mb
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.
Found the following files/directories:
  ‘plot1.pdf’
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
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.
Found the following significant warnings:
  equalizeImageHist.cpp:14:7: warning: 'pointer_to_unary_function<double, double>' is deprecated [-Wdeprecated-declarations]
  equalizeImageHist.cpp:17:59: warning: 'bind1st<std::__1::multiplies<double>, int>' is deprecated [-Wdeprecated-declarations]
  equalizeImageHist.cpp:53:59: warning: 'bind1st<std::__1::multiplies<double>, double>' is deprecated [-Wdeprecated-declarations]
  findCornerSubPix.cpp:62:62: warning: 'bind1st<std::__1::plus<int>, int>' is deprecated [-Wdeprecated-declarations]
  findCornerSubPix.cpp:66:62: warning: 'bind1st<std::__1::plus<int>, int>' is deprecated [-Wdeprecated-declarations]
  thresholdImageMatrix.cpp:19:7: warning: 'pointer_to_unary_function<double, double>' is deprecated [-Wdeprecated-declarations]
  thresholdImageMatrix.cpp:29:71: warning: 'bind1st<std::__1::multiplies<double>, int>' is deprecated [-Wdeprecated-declarations]
  thresholdImageMatrix.cpp:32:80: warning: 'bind1st<std::__1::multiplies<double>, int>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/StereoMorph.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘Mug_2D.tps’ ‘Owl_3D.tps’ ‘Shapes_2D.tps’ ‘Shapes_3D.tps’
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  7.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   4.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R          2.1Mb
    datasets   2.6Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.4Mb
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘readr’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Namespace in Imports field not imported from: ‘knitcitations’
  All declared Imports should be used.
Package suggested but not available for checking: ‘BSgenome.Ptroglodytes.UCSC.panTro5’
Namespaces in Imports field not imported from:
  ‘BSgenome’ ‘BiocManager’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘boot’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
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.
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 13.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  10.6Mb
Found the following significant warnings:
  'config' variable 'CXXCPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/stringi.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘broom’ ‘car’ ‘lmerTest’ ‘pbkrtest’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
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:
  ‘UpSetR’ ‘alluvial’ ‘geoR’ ‘gridBase’
  All declared Imports should be used.
Found the following significant warnings:
  sub-linux.cc:362:28: warning: designated initializers are a C99 feature [-Wc99-extensions]
  sub-linux.cc:362:42: warning: designated initializers are a C99 feature [-Wc99-extensions]
See ‘/data/gannet/ripley/R/packages/tests-clang/subprocess.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘DT’ ‘V8’ ‘bsplus’ ‘colourpicker’ ‘dplyr’ ‘grDevices’ ‘graphics’
  ‘jsonlite’ ‘shinyjs’
  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.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/SuperGauss.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘R.matlab’ ‘fBasics’ ‘spls’
  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/SuppDists.Rcheck/00install.out’ for details.
File ‘SuppDists/libs/SuppDists.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘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  8.3Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    libs   1.7Mb
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 142.2Mb
  sub-directories of 1Mb or more:
    libs  140.7Mb
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.
Namespace in Imports field not imported from: ‘cowplot’
  All declared Imports should be used.
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.
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.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Different type kinds at (1)
  Warning: GNU Extension: initialization of common block variable ‘iset’ in DATA statement at (1)
  Warning: GNU Extension: Variable ‘iset’ at (1) is in COMMON but only in BLOCK DATA initialization is allowed
  Warning: GNU Extension: Missing comma at (1)
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1) [-Wcharacter-truncation]
  Warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘cnop’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1) [-Wcharacter-truncation]
  Warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/SWATmodel.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘lazyeval’ ‘lubridate’ ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘spatstat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘magrittr’
  All declared Imports should be used.
Running ‘winpath.R’
Running the tests in ‘tests/winpath.R’ failed.
Complete output:
  > library(switchr)
  > if(getOption("repos")["CRAN"] == "@CRAN@")
  +     chooseCRANmirror(ind=2)
  > checkUrlRoundtrip = function(pth) {
  +     pth = switchr:::normalizePath2(pth)
  +     furl = switchr:::makeFileURL(pth)
  +     pth2 = switchr:::fileFromFileURL(furl)
  +     if(pth != pth2)
  +         stop("Round trip result (", pth2, ") does not match original (", pth, ") when creating file URLs")
  + }
  > 
  > ## regression test to ensure that the roundtrip
  > ## between path and file url is working properly
  > checkUrlRoundtrip(getwd())
  > checkUrlRoundtrip(tempdir())
  > if(switchr:::isWindows())
  +     checkUrlRoundtrip("\\\\laptop\\My Documents\\")
  > 
  > ## regreossion test to ensure that package dependencies
  > ## are added to the dontunload list when a package
  > ## is specified
  > bef = switchrDontUnload()
  > af = switchrDontUnload("knitr")
  Warning: unable to access index for repository https://cran.usthb.dz/src/contrib:
    cannot open URL 'https://cran.usthb.dz/src/contrib/PACKAGES'
  Error in av[pkg, c("Depends", "Imports")] : subscript out of bounds
  Calls: switchrDontUnload -> .dodepsourselves -> .innerdodeps
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
Found the following files/directories:
  ‘moment_20191124_0131.lp’
Found the following files/directories:
  ‘cfFVA1_cnd_det.csv’ ‘cfFVA1_cnd_res.csv’
  ‘glpk_llFBA_20191124_0131.lp’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
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
Running ‘testthat.R’ [112s/77s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("tabulizer")
  > 
  > stop_logging()
  > test_check("tabulizer")
  WARNING: An illegal reflective access operation has occurred
  WARNING: Illegal reflective access by RJavaTools to method java.util.ArrayList$Itr.hasNext()
  WARNING: Please consider reporting this to the maintainers of RJavaTools
  WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
  WARNING: All illegal access operations will be denied in a future release
  ── 1. Error: Extract from encrypted PDF (@test_extract_tables.R#64)  ───────────
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(extract_tables(f6, password = "wrongpassword"))
   14. rlang::cnd_entrace(cnd)
   17. rJava:::`$.Throwable`(cnd, "trace")
   18. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 86 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Extract from encrypted PDF (@test_extract_tables.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
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.
File ‘tailDepFun/libs/tailDepFun.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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  7.0Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   4.8Mb
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  6.8Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.9Mb
Found the following significant warnings:
  ./topology/simplex.hpp:36:63: warning: 'bind2nd<std::__1::not_equal_to<unsigned int>, unsigned int>' is deprecated [-Wdeprecated-declarations]
  ./topology/simplex.hpp:37:63: warning: 'bind2nd<std::__1::not_equal_to<unsigned int>, unsigned int>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/TDA.Rcheck/00install.out’ for details.
installed size is 31.8Mb
  sub-directories of 1Mb or more:
    libs  30.5Mb
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.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    apps   2.8Mb
    libs   7.9Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘tidyr’
  All declared Imports should be used.
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  16.0Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
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.
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  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Namespace in Imports field not imported from: ‘details’
  All declared Imports should be used.
Running examples in ‘texPreview-Ex.R’ failed
The error most likely occurred in:

> ### Name: as.kable
> ### Title: Try to coerce an object into a knitr_kable object
> ### Aliases: as.kable
> 
> ### ** Examples
> 
> 
> tex <- '\\begin{tabular}{llr}
+ \\hline
+ \\multicolumn{2}{c}{Item} \\\\
+ \\cline{1-2}
+ Animal    & Description & Price (\\$) \\\\
+ \\hline
+ Gnat      & per gram    & 13.65      \\\\
+ & each        & 0.01       \\\\
+ Gnu       & stuffed     & 92.50      \\\\
+ Emu       & stuffed     & 33.33      \\\\
+ Armadillo & frozen      & 8.99       \\\\
+ \\hline
+ \\end{tabular}'
> 
> ktex <- as.kable(tex)
> 
> class(ktex)
[1] "knitr_kable"
> 
> attributes(ktex)
$class
[1] "knitr_kable"

$format
[1] "latex"

> 
> ktex
\begin{tabular}{llr}
\hline
\multicolumn{2}{c}{Item} \\
\cline{1-2}
Animal    & Description & Price (\$) \\
\hline
Gnat      & per gram    & 13.65      \\
& each        & 0.01       \\
Gnu       & stuffed     & 92.50      \\
Emu       & stuffed     & 33.33      \\
Armadillo & frozen      & 8.99       \\
\hline
\end{tabular}
> 
> # using an input call
> 
> x <- tex_preview(tex,returnType = 'input')
Error in tex_preview.default(obj, tex_lines, stem, overwrite, keep_pdf,  : 
   
! LaTeX Error: File `/tmp/Rtmplmv6ms/working_dir/RtmpSeGuYV/tex_temp.tex ' not 
found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: tex )

Enter file name: 
! Emergency stop.
<read *> 
 
l.17 ...v6ms/working_dir/RtmpSeGuYV/tex_temp.tex }
 ^^M 
!  ==> Fatal error occurred, no output PDF file produced!
Calls: tex_preview -> tex_preview.character -> tex_preview.default
Execution halted
Found the following significant warnings:
  GloveFitter.cpp:80:7: warning: explicitly assigning value of variable of type 'GloveFit' to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/text2vec.Rcheck/00install.out’ for details.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.6Mb
    libs   5.4Mb
Namespace in Imports field not imported from: ‘irlba’
  All declared Imports should be used.
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  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
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 16.3Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
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.
Namespace in Imports field not imported from: ‘tiff’
  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 29.5Mb
  sub-directories of 1Mb or more:
    libs  29.3Mb
Namespace in Imports field not imported from: ‘mix’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘stringr’
  All declared Imports should be used.
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 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
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.
Running examples in ‘TITAN2-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot_taxa_ridges
> ### Title: Taxon change point ridge plots
> ### Aliases: plot_taxa_ridges
> 
> ### ** Examples
> 
> 
> data(glades.titan)
> 
> 
> # basic usage
> plot_taxa_ridges(glades.titan)
There are 90 indicator taxa of 90 possible for plotting
Number of Decreasers = 41
Number of Increasers = 49
Error in stats::approxfun(x_in, lab_in[, 1]) : 
  need at least two non-NA values to interpolate
Calls: plot_taxa_ridges ... seq_gradient_pal -> gradient_n_pal -> colour_ramp -> <Anonymous>
Execution halted
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 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    examples  14.2Mb
    include    3.0Mb
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
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.
Error(s) in re-building vignettes:
--- re-building ‘tmod.rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'tmod.rmd' failed with diagnostics:
Failed to compile tmod.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See tmod.log for more info.
--- failed re-building ‘tmod.rmd’

SUMMARY: processing the following file failed:
  ‘tmod.rmd’

Error: Vignette re-building failed.
Execution halted
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.
Found the following files/directories:
  ‘tnet_ucinet_network-2019-11-24_015546.dl’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
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
Namespaces in Imports field not imported from:
  ‘R6’ ‘jmvcore’
  All declared Imports should be used.
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
Namespaces in Imports field not imported from:
  ‘animation’ ‘ggplot2’ ‘jpeg’ ‘pastecs’ ‘plyr’ ‘raster’ ‘wesanderson’
  All declared Imports should be used.
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 13.6Mb
  sub-directories of 1Mb or more:
    extdata   1.4Mb
    libs     12.0Mb
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  5.3Mb
  sub-directories of 1Mb or more:
    doc   3.5Mb
installed size is 116.3Mb
  sub-directories of 1Mb or more:
    doc     4.1Mb
    libs  111.3Mb
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.
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  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
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  8.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   7.5Mb
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  5.7Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
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.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
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.
Error(s) in re-building vignettes:
--- re-building ‘tsvrvignette.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'tsvrvignette.Rmd' failed with diagnostics:
Failed to compile tsvrvignette.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See tsvrvignette.log for more info.
--- failed re-building ‘tsvrvignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘shinyAce’ ‘shinyjs’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
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  9.2Mb
  sub-directories of 1Mb or more:
    doc     6.3Mb
    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 30.7Mb
  sub-directories of 1Mb or more:
    doc         6.9Mb
    dummydata   1.4Mb
    libs       21.0Mb
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.
Namespace in Imports field not imported from: ‘viridis’
  All declared Imports should be used.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    8.4Mb
Namespaces in Imports field not imported from:
  ‘numDeriv’ ‘sfsmisc’
  All declared Imports should be used.
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
Error(s) in re-building vignettes:
--- re-building ‘Intro.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'Intro.Rmd' failed with diagnostics:
Failed to compile Intro.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See Intro.log for more info.
--- failed re-building ‘Intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.6Mb
    libs   8.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
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
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
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.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/uuid.Rcheck/00install.out’ for details.
File ‘uuid/libs/uuid.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘gen_uuid.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘gen_uuid.o’
File ‘uuid/libs/uuid.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:
  'config' variable 'CXXCPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/V8.Rcheck/00install.out’ for details.
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  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
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 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
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 ‘VBLPCM/libs/VBLPCM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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  8.0Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
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.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘maptools’ ‘rgeos’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘vdmR-vignette.Rnw’ using knitr
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Quitting from lines 189-193 (vdmR-vignette.Rnw) 
Error: processing vignette 'vdmR-vignette.Rnw' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘vdmR-vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘vdmR-vignette.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R   2.5Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
Found the following significant warnings:
  ./DataStd.h:149:60: warning: 'bind2nd<std::__1::minus<double>, double>' is deprecated [-Wdeprecated-declarations]
  ./DataStd.h:151:60: warning: 'bind2nd<std::__1::multiplies<double>, double>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/vennLasso.Rcheck/00install.out’ for details.
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
Error(s) in re-building vignettes:
--- re-building ‘using_the_vennLasso_package.Rmd’ using rmarkdown
tlmgr search --file --global '/tikzlibrarytopaths.code.tex'
tlmgr search --file --global '/tikzlibraryshapes.code.tex'
tlmgr search --file --global '/tikzlibrarybackgrounds.code.tex'
tlmgr search --file --global '/tikzlibrarypositioning.code.tex'
tlmgr search --file --global '/tikzlibraryarrows.code.tex'
tlmgr search --file --global '/tikzlibrarymatrix.code.tex'
tlmgr search --file --global '/tikzlibraryfit.code.tex'
tlmgr search --file --global '/tikzlibrarycalc.code.tex'
tlmgr search --file --global '/tikzlibrarytrees.code.tex'
Trying to automatically install missing LaTeX packages...
tlmgr install pgf
tlmgr: package repository http://mirror.ox.ac.uk/sites/ctan.org/systems/texlive/tlnet (verified)
tlmgr install: package already present: pgf
tlmgr path add
add_link_dir_dir: /usr/local/share/info/dir exists; not making symlink.
tlmgr search --file --global '/tikzlibrarytopaths.code.tex'
tlmgr search --file --global '/tikzlibraryshapes.code.tex'
tlmgr search --file --global '/tikzlibrarybackgrounds.code.tex'
tlmgr search --file --global '/tikzlibrarypositioning.code.tex'
tlmgr search --file --global '/tikzlibraryarrows.code.tex'
tlmgr search --file --global '/tikzlibrarymatrix.code.tex'
tlmgr search --file --global '/tikzlibraryfit.code.tex'
tlmgr search --file --global '/tikzlibrarycalc.code.tex'
tlmgr search --file --global '/tikzlibrarytrees.code.tex'
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'using_the_vennLasso_package.Rmd' failed with diagnostics:
Failed to compile using_the_vennLasso_package.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See using_the_vennLasso_package.log for more info.
--- failed re-building ‘using_the_vennLasso_package.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    doc    1.2Mb
    help   2.9Mb
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.
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.
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    libs  24.9Mb
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
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
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 43.8Mb
  sub-directories of 1Mb or more:
    libs  43.4Mb
Namespaces in Imports field not imported from:
  ‘iterators’ ‘knitr’ ‘purrr’ ‘testthat’
  All declared Imports should be used.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
Found the following files/directories:
  ‘ccchart1.png’ ‘ccchart2.png’ ‘cchart1.png’ ‘cchart6.png’
  ‘colplot.png’ ‘div_divorced.png’ ‘div_married.png’ ‘div_widowed.png’
  ‘divp_divorced.png’ ‘divp_divorced_wing.png’ ‘divp_married.png’
  ‘divp_married_wing.png’ ‘divp_single.png’ ‘divp_widowed.png’
  ‘divp_widowed_wing.png’ ‘iris2_contributions2.png’ ‘iris2_lps.png’
  ‘iris2_outcomes.png’ ‘iris_contributions2.png’ ‘iris_lps.png’
  ‘iris_outcomes.png’ ‘multinom_ccchart_divorced_ccchart.png’
  ‘multinom_ccchart_married_ccchart.png’
  ‘multinom_ccchart_widowed_ccchart.png’
  ‘multinom_ccchartp_divorced_ccchart.png’
  ‘multinom_ccchartp_married_ccchart.png’
  ‘multinom_ccchartp_single_ccchart.png’
  ‘multinom_ccchartp_widowed_ccchart.png’ ‘multinom_divorced.png’
  ‘multinom_divorced_cchart.png’ ‘multinom_married.png’
  ‘multinom_married_cchart.png’ ‘multinom_patientsummary.png’
  ‘multinom_patientsummary2.png’ ‘multinom_widowed.png’
  ‘multinom_widowed_cchart.png’ ‘multinomp_divorced.png’
  ‘multinomp_divorced_cchart.png’ ‘multinomp_divorced_wing.png’
  ‘multinomp_married.png’ ‘multinomp_married_cchart.png’
  ‘multinomp_married_wing.png’ ‘multinomp_single.png’
  ‘multinomp_single_cchart.png’ ‘multinomp_widowed.png’
  ‘multinomp_widowed_cchart.png’ ‘multinomp_widowed_wing.png’
  ‘mysummary.Rnw’ ‘mysummary.html’ ‘mysummary1.Rnw’ ‘mysummary1.html’
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 57.6Mb
  sub-directories of 1Mb or more:
    libs  56.4Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ENMeval’ ‘RColorBrewer’ ‘XML’ ‘dismo’ ‘dplyr’ ‘leaflet.extras’
  ‘maptools’ ‘raster’ ‘rgdal’ ‘rgeos’ ‘rmarkdown’ ‘shinyjs’
  ‘shinythemes’ ‘spThin’ ‘spocc’ ‘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  7.2Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   5.6Mb
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.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
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.
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.
Namespace in Imports field not imported from: ‘moonBook’
  All declared Imports should be used.
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘later’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    doc   11.9Mb
    libs   1.3Mb
File ‘weightedScores/libs/weightedScores.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.0Mb
  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 15.0Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
File ‘widals/libs/widals.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘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  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
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
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
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.
Error(s) in re-building vignettes:
--- re-building ‘wsynvignette.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'wsynvignette.Rmd' failed with diagnostics:
Failed to compile wsynvignette.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See wsynvignette.log for more info.
--- failed re-building ‘wsynvignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
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 21.8Mb
  sub-directories of 1Mb or more:
    libs  21.0Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    java  19.0Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    java   9.8Mb
Found the following files/directories:
  ‘myXLfile.xlsx’ ‘myXLfile_2019_11_24_024035.xlsx’
  ‘myXLfile_2019_11_24_024038.xlsx’ ‘myXLfile_2019_11_24_024040.xlsx’
possible bashism in configure line 31 ($(OS|MACH)TYPE):
      if echo $OSTYPE | grep -q '^darwin1[567]'; then
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    exampleData   1.6Mb
    examples      4.6Mb
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.
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  5.3Mb
  sub-directories of 1Mb or more:
    include   3.5Mb
    libs      1.7Mb
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 38.9Mb
  sub-directories of 1Mb or more:
    libs  38.6Mb
Namespace in Imports field not imported from: ‘ghyp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Amelia’ ‘MatchIt’ ‘WhatIf’
  All declared Imports should be used.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘testthat’
  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:
  ADAPTgdwm.c:136:73: warning: statement with no effect [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/AMORE.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘ORdensity_2019-11-24.jpeg’ ‘discordanceDelta_2019-11-24.txt’
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/apcf.Rcheck/00install.out’ for details.
Found the following significant warnings:
  code.c:1148:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  code.c:1162:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  code.c:1086:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/ARTP.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:
  'config' variable 'CXXCPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/av.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘mzR’
Found the following significant warnings:
  Blasso.cpp:451:53: warning: ‘*<unknown>.Blasso::icept’ is used uninitialized in this function [-Wuninitialized]
  LogitWrapper.cpp:417:8: 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/bayesCL.Rcheck/00install.out’ for details.
Running examples in ‘bayesCL-Ex.R’ failed
The error most likely occurred in:

> ### Name: lasso
> ### Title: Bayesian Lasso
> ### Aliases: lasso
> ### Keywords: regression
> 
> ### ** Examples
> 
> 
> set.seed(0)
> n_samples  <- 500
> n_features <- 40
> X <- matrix(rnorm(n_features * n_samples), nrow = n_samples)
> y <- 2 * X[,1] - 3 * X[,2] + rnorm(n_samples) # only features 1 & 2 are relevant
> 
> X_train <- X[1:400,]
> y_train <- y[1:400]
> X_test  <- X[401:500,]
> y_test  <- y[401:500]
> 
> 
> # START ------------------------------------------------------------------------
> 
> # first, standardize data !!!
> X_train <- scale(X_train)
> 
> tmp00 <- bayesCL::lasso(X = X_train, 
+                           y = y_train, 
+                           T = 500,  # number of Gibbs sampling iterations
+                           icept = T,
+                           device=0  ) # use constant term (intercept), we do
------------------------------
Platform and device selection

 *** caught segfault ***
address 0x12298e10, cause 'memory not mapped'

Traceback:
 1: prepare(precision = 0, device = device, parameters = parameters)
 2: bayesCL::lasso(X = X_train, y = y_train, T = 500, icept = T,     device = 0)
An irrecoverable exception occurred. R is aborting now ...
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/BayHap.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘outhaplo241119102823585YDGABKNRWJ.txt’
  ‘outhaplo241119102827019XNBMRYFAHT.txt’
  ‘outhaplo241119102830514LOATCFJWUY.txt’
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 files/directories:
  ‘lambda-20191124-170421.txt’
Running ‘test-all.R’ [37s/38s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > test_check("broom.mixed")
  Loading required package: broom.mixed
  Registered S3 methods overwritten by 'broom.mixed':
    method         from 
    augment.lme    broom
    augment.merMod broom
    glance.lme     broom
    glance.merMod  broom
    glance.stanreg broom
    tidy.brmsfit   broom
    tidy.gamlss    broom
    tidy.lme       broom
    tidy.merMod    broom
    tidy.rjags     broom
    tidy.stanfit   broom
    tidy.stanreg   broom
  ── 1. Error: (unknown) (@test-alltibbles.R#53)  ────────────────────────────────
  object 'Days' not found
  Backtrace:
    1. broom.mixed:::testf("augment", z)
    6. broom.mixed:::augment.glmmTMB(obj)
    7. broom::augment_columns(x, data, newdata, ...)
   10. glmmTMB:::fitted.glmmTMB(...)
   12. glmmTMB:::predict.glmmTMB(object, type = "response")
   15. glmmTMB:::mkTMBStruc(...)
   16. glmmTMB:::getXReTrms(formula, mf, fr, contrasts = contrasts)
   17. glmmTMB::splitForm(formula)
   18. glmmTMB:::fbx(formula, debug, specials)
   19. glmmTMB:::fbx(term[[2]], debug, specials)
   20. glmmTMB:::fbx(term[[3]], debug, specials)
   22. utils:::head.default(term)
   23. base::do.call(`[`, c(list(x), indvecs, if (!is.null(dim(x))) list(drop = FALSE)))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 184 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 1 ]
  1. Error: (unknown) (@test-alltibbles.R#53) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 2048 equals destination size [-Wstringop-truncation]
  rulebasedmodels.c:65:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:75:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:76:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:115:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:128:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:143:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:151:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:161:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:162:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:178:3: warning: statement with no effect [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/C50.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:
  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:
  'config' variable 'CXXCPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/cld3.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/clpAPI.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.
Running ‘test.R’ [167s/159s]
Running the tests in ‘tests/test.R’ failed.
Complete output:
  > library(testthat)
  > library(mockr)
  
  Attaching package: 'mockr'
  
  The following object is masked from 'package:testthat':
  
      with_mock
  
  > library(corehunter)
  Loading required package: rJava
  > 
  > test_check("corehunter")
  ── 1. Error: arguments are checked (@testAnalysis.R#12)  ───────────────────────
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(...)
   14. rlang::cnd_entrace(cnd)
   17. rJava:::`$.Throwable`(cnd, "trace")
   18. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ── 2. Error: arguments are checked (@testData.R#532)  ──────────────────────────
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(...)
   13. rlang::cnd_entrace(cnd)
   16. rJava:::`$.Throwable`(cnd, "trace")
   17. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 2416 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: arguments are checked (@testAnalysis.R#12) 
  2. Error: arguments are checked (@testData.R#532) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 2048 equals destination size [-Wstringop-truncation]
  rulebasedmodels.c:95:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:105:3: warning: statement with no effect [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/Cubist.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.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dbplyr)
  > 
  > test_check("dbplyr")
  Registering testing src: df OK
  Registering testing src: sqlite OK
  Registering testing src: mysql OK
  Registering testing src: MariaDB 
   *** caught segfault ***
  address 0x161, cause 'memory not mapped'
  
  Traceback:
   1: result_release(res@ptr)
   2: dbClearResult(rs)
   3: dbClearResult(rs)
   4: dbExecute(con, "SET time_zone = '+00:00'")
   5: dbExecute(con, "SET time_zone = '+00:00'")
   6: .local(drv, ...)
   7: DBI::dbConnect(...)
   8: DBI::dbConnect(...)
   9: paste0("src_", class(con)[[1]])
  10: src_dbi(DBI::dbConnect(...), auto_disconnect = TRUE)
  11: test_srcs$add(name, src)
  12: doTryCatch(return(expr), name, parentenv, handler)
  13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  14: tryCatchList(expr, classes, parentenv, handlers)
  15: tryCatch({    test_srcs$add(name, src)    message("OK")}, error = function(e) message("\n* ", conditionMessage(e)))
  16: test_register_src(name, src_dbi(DBI::dbConnect(...), auto_disconnect = TRUE))
  17: test_register_con("MariaDB", RMariaDB::MariaDB(), dbname = "test",     host = "localhost", user = Sys.getenv("USER"))
  18: eval(exprs, env)
  19: eval(exprs, env)
  20: FUN(X[[i]], ...)
  21: lapply(files, source_file, env = env, chdir = chdir, wrap = wrap)
  22: source_dir(path, "^helper.*\\.[rR]$", env = env, wrap = FALSE)
  23: source_test_helpers(path, env)
  24: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,     ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     wrap = wrap)
  25: test_package_dir(package = package, test_path = test_path, filter = filter,     reporter = reporter, ..., stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  26: test_check("dbplyr")
  An irrecoverable exception occurred. R is aborting now ...
Error(s) in re-building vignettes:
--- re-building ‘chytrid_dede_example.Rmd’ using rmarkdown
Loading required package: deSolve
Order of initial conditions is  C, S, Z
initial posterior probability = -13968.8205931737
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'chytrid_dede_example.Rmd' failed with diagnostics:
Failed to compile chytrid_dede_example.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See chytrid_dede_example.log for more info.
--- failed re-building ‘chytrid_dede_example.Rmd’

--- re-building ‘logistic_ode_example.Rmd’ using rmarkdown
Loading required package: deSolve
Order of initial conditions is  N
initial posterior probability = -7868.61983481059
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'logistic_ode_example.Rmd' failed with diagnostics:
Failed to compile logistic_ode_example.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See logistic_ode_example.log for more info.
--- failed re-building ‘logistic_ode_example.Rmd’

--- re-building ‘deBInfer_compiled_code.pdf.asis’ using asis
--- finished re-building ‘deBInfer_compiled_code.pdf.asis’

SUMMARY: processing the following files failed:
  ‘chytrid_dede_example.Rmd’ ‘logistic_ode_example.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘Example.t.H.values.txt’ ‘Example.t.Hest_loci.values.txt’
  ‘Example.t.Hest_mean.values.txt’
  ‘Example.t.allelefreq.2019-11-24.txt’
  ‘Example.t.overall.Dest.loci.2019-11-24.txt’
  ‘Example.t.overall.Dest.loci.ci2019-11-24.txt’
  ‘Example.t.overall.Dest.loci.p.2019-11-24.txt’
  ‘Example.t.overall.Dest.mean.2019-11-24.txt’
  ‘Example.t.overall.Dest.mean.ci2019-11-24.txt’
  ‘Example.t.overall.Dest.mean.p.2019-11-24.txt’
  ‘Example.t.sample.sizes.2019-11-24.txt’ ‘Example.u.H.values.txt’
  ‘Example.u.Hest_loci.values.txt’ ‘Example.u.Hest_mean.values.txt’
  ‘Example.u.allelefreq.2019-11-24.txt’
  ‘Example.u.pairwise.Gst.loci.2019-11-24.txt’
  ‘Example.u.pairwise.Gst.mean.2019-11-24.txt’
  ‘Example.u.sample.sizes.2019-11-24.txt’ ‘Output-Inputformat.txt’
Running ‘test-all.R’ [33s/35s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > 
  > library(dendextend)
  
  ---------------------
  Welcome to dendextend version 1.12.0
  Type citation('dendextend') for how to cite the package.
  
  Type browseVignettes(package = 'dendextend') for the package vignette.
  The github page is: https://github.com/talgalili/dendextend/
  
  Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
  Or contact: <tal.galili@gmail.com>
  
  	To suppress this message use:  suppressPackageStartupMessages(library(dendextend))
  ---------------------
  
  
  Attaching package: 'dendextend'
  
  The following object is masked from 'package:stats':
  
      cutree
  
  > test_check("dendextend")
  Bootstrap (r = 0.4)... Done.
  Bootstrap (r = 0.6)... Done.
  Bootstrap (r = 0.8)... Done.
  Bootstrap (r = 1.0)... Done.
  Bootstrap (r = 1.2)... Done.
  Bootstrap (r = 1.4)... Done.
  ── 1. Failure: extract au (@test-pvclust_extract.R#12)  ────────────────────────
  round(pvclust_edges(dend)[, 3], digits = 2) not identical to c(0.97, 1, 1).
  2/3 mismatches (average diff: 0.11)
  [1] 0.76 - 0.97 == -0.21
  [2] 0.99 - 1.00 == -0.01
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 409 | SKIPPED: 0 | WARNINGS: 10 | FAILED: 1 ]
  1. Failure: extract au (@test-pvclust_extract.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
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:
  GetData.c:70:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  GetData.c:72:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  GetData.c:74:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  GetData.c:77:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  GetData.c:79:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  SimulDiv.c:210:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  SimulDiv.c:212:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  SimulDiv.c:214:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  SimulDiv.c:217:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  SimulDiv.c:219:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  SimulDiv.c:222:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  SimulDiv.c:224:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  SimulDiv.c:227:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/DetSel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CXXCPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/dfmta.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:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/diversitree.Rcheck/00install.out’ for details.
Found the following significant warnings:
  /usr/include/bits/string_fortified.h:128:33: warning: ‘char* __builtin___strcat_chk(char*, const char*, long unsigned int)’ accessing 4097 or more bytes at offsets 0 and 4096 may overlap 1 byte at offset 4096 [-Wrestrict]
See ‘/data/gannet/ripley/R/packages/tests-devel/divest.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 files/directories:
  ‘iris2_2019-11-24.tsv’
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:
  eiutil.c:132:5: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/eiPack.Rcheck/00install.out’ for details.
Found the following significant warnings:
  emmix.cpp:351:195: warning: value computed is not used [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/EMMIXgene.Rcheck/00install.out’ for details.
Found the following significant warnings:
  epanet.c:2472:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  epanet.c:2474:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  output.c:597:13: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  report.c:448:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  report.c:453:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/epanet2toolkit.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 files/directories:
  ‘descriptive_statistics2019-11-24_20.13.42.txt’
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/fftw.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [166s/179s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > if (require(testthat)) {
  +   test_check("forecast")
  + }
  Loading required package: testthat
  Loading required package: forecast
  Registered S3 methods overwritten by 'forecast':
    method             from    
    fitted.fracdiff    fracdiff
    residuals.fracdiff fracdiff
  ── 1. Error: tests for autoplot/gg functions (@test-ggplot.R#64)  ──────────────
  need at least two non-NA values to interpolate
  Backtrace:
   1. forecast::ggseasonplot(...)
   2. ggplot2::scale_color_gradientn(colours = col)
   5. scales::gradient_n_pal(colours, values, space)
   6. scales::colour_ramp(colours)
   7. stats::approxfun(x_in, lab_in[, 1])
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 774 | SKIPPED: 5 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: tests for autoplot/gg functions (@test-ggplot.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  testcpp_rec6.cpp:197:37: warning: value computed is not used [-Wunused-value]
  testcpp_rec6.cpp:551:37: warning: value computed is not used [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/forestFloor.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:
  'config' variable 'CXXCPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/gaselect.Rcheck/00install.out’ for details.
Found the following significant warnings:
  NNLS_Double.cpp:930:7: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
  Gdmlib.cpp:2352:13: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  Gdmlib.cpp:1738:8: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
  Gdmlib.cpp:2352:23: warning: ‘%lf’ directive writing between 3 and 317 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
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: ‘__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:
  Converter.cpp:154:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  Converter.cpp:157:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  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:193:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  Sequence.cpp:197:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  Sequence.cpp:230:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  Sequence.cpp:292:7: 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/gkmSVM.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/glpkAPI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  dftcf.c:31:9: warning: array subscript -1 is outside array bounds of ‘int[15]’ [-Warray-bounds]
See ‘/data/gannet/ripley/R/packages/tests-devel/GPB.Rcheck/00install.out’ for details.
Found the following significant warnings:
  gpc.c:1036:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  gpc.c:1043:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  gpc.c:1046:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  gpc.c:1053:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/gpclib.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [87s/95s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(gqlr)
  > 
  > test_check("gqlr")
  ── 1. Failure: pryr fails (@test-aaa-pryr-unenclose.R#25)  ─────────────────────
  ans$A() == "A" isn't false.
  
  ── 2. Failure: pryr fails (@test-aaa-pryr-unenclose.R#26)  ─────────────────────
  ans$B() == "B" isn't false.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 541 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 2 ]
  1. Failure: pryr fails (@test-aaa-pryr-unenclose.R#25) 
  2. Failure: pryr fails (@test-aaa-pryr-unenclose.R#26) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following files/directories:
  ‘cat.expressions.dir.2019-11-24.1.1’
  ‘cat.expressions.dir.2019-11-24.1.2’
  ‘cat.expressions.dir.2019-11-24.1.3’
  ‘cat.expressions.dir.2019-11-24.1.4’
  ‘cat.expressions.dir.2019-11-24.1.5’
  ‘cat.expressions.dir.2019-11-24.1.6’
  ‘cat.expressions.dir.2019-11-24.1.7’
  ‘cat.expressions.dir.2019-11-24.1.8’
  ‘cat.expressions.dir.2019-11-24.1.9’
  ‘cat.expressions.dir.2019-11-24.2’
  ‘cat.expressions.dir.2019-11-24.2.1’
  ‘cat.expressions.dir.2019-11-24.2.2’
  ‘cat.expressions.dir.2019-11-24.2.3’
  ‘cat.expressions.dir.2019-11-24.2.4’
  ‘cat.expressions.dir.2019-11-24.2.5’
  ‘cat.expressions.dir.2019-11-24.2.6’
  ‘cat.expressions.dir.2019-11-24.2.7’ ‘graphfactorD - 10-08-2016 -
  Function Viz1.png’ ‘graphfactorD - 10-08-2016 - Function Viz10.png’
  ‘graphfactorD - 10-08-2016 - Function Viz11.png’ ‘graphfactorD -
  10-08-2016 - Function Viz12.png’ ‘graphfactorD - 10-08-2016 -
  Function Viz2.png’ ‘graphfactorD - 10-08-2016 - Function Viz3.png’
  ‘graphfactorD - 10-08-2016 - Function Viz4.png’ ‘graphfactorD -
  10-08-2016 - Function Viz5.png’ ‘graphfactorD - 10-08-2016 - Function
  Viz6.png’
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(GSODR)
  > 
  > test_check("GSODR")
  ── 1. Failure: The 'max_missing' parameter filters out improper stations (@test-
  `get_GSOD(years = 1929, max_missing = 1)` threw an error with unexpected message.
  Expected match: "There were no stations that had a max of."
  Actual message: "attempt to set an attribute on NULL"
  Backtrace:
   1. testthat::expect_error(...)
   6. GSODR::get_GSOD(years = 1929, max_missing = 1)
   7. GSODR:::.validate_missing_days(max_missing, file_list)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 31 | SKIPPED: 9 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: The 'max_missing' parameter filters out improper stations (@test-get_GSOD.R#128) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/gwsem.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: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/hier.part.Rcheck/00install.out’ for details.
Found the following significant warnings:
  codegenerator.cpp:464:4: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  codegenerator.cpp:1742:4: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  codegenerator.cpp:1743:4: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  languagedefinition.cpp:100:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-devel/highlight.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:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/icd.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘1-Reasonableness_ID_var_check_errors_20191124.xlsx’
  ‘1-Reasonableness_Var2_check_errors_20191124.xlsx’
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:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/JavaGD.Rcheck/00install.out’ for details.
Found the following significant warnings:
  keypress-unix.c:196:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
  keypress-unix.c:199:2: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
  keypress-unix.c:203:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
  keypress-unix.c:213:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
  keypress-unix.c:215:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
  keypress-unix.c:217:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/keypress.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:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/KSgeneral.Rcheck/00install.out’ for details.
File ‘logconcens/libs/logconcens.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  /data/gannet/ripley/R/test-3.7/BH/include/boost/container/detail/copy_move_algo.hpp:183:19: 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-3.7/BH/include/boost/container/detail/copy_move_algo.hpp:897:16: 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-3.7/BH/include/boost/container/detail/copy_move_algo.hpp:197:19: 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:
  ../../inst/include/lpkit.h:32:99: warning: right-hand operand of comma expression has no effect [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/lpSolveAPI.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 ‘/data/gannet/ripley/R/packages/tests-devel/lpSolve.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/lwgeom.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CXXCPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/magick.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:
  cuts.c:24:2: warning: statement with no effect [-Wunused-value]
  cuts.c:24:5: warning: statement with no effect [-Wunused-value]
  cuts.c:24:9: warning: statement with no effect [-Wunused-value]
  cuts.c:32:2: warning: statement with no effect [-Wunused-value]
  cuts.c:32:6: warning: statement with no effect [-Wunused-value]
  cuts.c:32:10: warning: statement with no effect [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/mapproj.Rcheck/00install.out’ for details.
Found the following significant warnings:
  migrate.c:179:30: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:186:26: warning: ‘.asc’ directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:199:28: warning: ‘.asc’ directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:286:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:312:29: warning: ‘%d’ directive writing between 1 and 8 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:559:31: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:595:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:603:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/MigClim.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘..md’ ‘NA.R’ ‘NA.mm’ ‘md-2019-11-24-23-33-08.mm’ ‘md.R’ ‘md.mm’
  ‘mindr.md’ ‘mindr.mm’ ‘mm.md’ ‘outline-2019-11-24-23-33-08.md’
  ‘outline.md’ ‘r.R’ ‘r.Rmd’
Found the following significant warnings:
  GLMM_Deviance.cpp:153:8: warning: statement has no effect [-Wunused-value]
  GLMM_Deviance.cpp:708:10: warning: statement has no effect [-Wunused-value]
  GLMM_Deviance2.cpp:173:8: warning: statement has no effect [-Wunused-value]
  GLMM_Deviance2.cpp:780:10: warning: statement has no effect [-Wunused-value]
  GLMM_newData.cpp:183:8: warning: statement has no effect [-Wunused-value]
  GLMM_updateRanEf.cpp:161:8: warning: statement has no effect [-Wunused-value]
  GLMM_updateRanEf.cpp:626:6: warning: statement has no effect [-Wunused-value]
  GLMM_updateRanEf_QR.cpp:124:8: warning: statement has no effect [-Wunused-value]
  GLMM_updateRanEf_QR.cpp:328:10: warning: statement has no effect [-Wunused-value]
  MCMC_Moments_NormalApprox_QR.cpp:104:10: warning: statement has no effect [-Wunused-value]
  MCMC_Moments_NormalApprox_QR.cpp:209:10: warning: statement has no effect [-Wunused-value]
  NMix_updateMeansVars.cpp:516:9: warning: statement has no effect [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/mixAK.Rcheck/00install.out’ for details.
listGenoToTable: no visible binding for global variable ‘dummy’
Undefined global functions or variables:
  dummy
Found the following significant warnings:
  abc_R.c:188:16: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  abc_R.c:287:17: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/networkABC.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
  'config' variable 'CXXCPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/nloptr.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [7s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.unsetenv("R_TESTS")
  > 
  > library(testthat)
  > library(nlrx)
  > 
  > test_check("nlrx")
  /usr/local/bin/pandoc +RTS -K512m -RTS nldoc.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output nldoc.html --email-obfuscation none --self-contained --standalone --section-divs --table-of-contents --toc-depth 3 --template /data/gannet/ripley/R/test-3.7/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --number-sections --variable 'theme:cosmo' --include-in-header /tmp/RtmpPFMJXT/working_dir/RtmpPWDpf9/rmarkdown-str9add7ad3a31b.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /data/gannet/ripley/R/test-3.7/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /data/gannet/ripley/R/test-3.7/rmarkdown/rmd/lua/latex-div.lua 
  [1] "File successfully compiled!"
  ── 1. Failure: nldoc (@test_nldoc.R#30)  ───────────────────────────────────────
  length(nldoc_readin) not equal to 8.
  1/1 mismatches
  [1] 27 - 8 == 19
  
  /usr/local/bin/pandoc +RTS -K512m -RTS nldoc.utf8.md --to docx --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output nldoc.docx --table-of-contents --toc-depth 3 --highlight-style tango --lua-filter /data/gannet/ripley/R/test-3.7/rmarkdown/rmd/lua/pagebreak.lua 
  [1] "File successfully compiled!"
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 138 | SKIPPED: 8 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: nldoc (@test_nldoc.R#30) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following files/directories:
  ‘001509Nova Southeastern University20191125.txt’
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:
  'config' variable 'CXXCPP' is deprecated
  connection.cpp:67:36: warning: catching polymorphic type ‘class nanodbc::database_error’ by value [-Wcatch-value=]
  odbc_connection.cpp:37:36: warning: catching polymorphic type ‘class nanodbc::database_error’ by value [-Wcatch-value=]
  odbc_connection.cpp:75:36: warning: catching polymorphic type ‘class nanodbc::database_error’ by value [-Wcatch-value=]
See ‘/data/gannet/ripley/R/packages/tests-devel/odbc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
  'config' variable 'CXXCPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/odpc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  oem_dense.h:10:36: warning: statement has no effect [-Wunused-value]
  oem_logistic_dense.h:10:36: warning: statement has no effect [-Wunused-value]
  oem_sparse.h:10:36: warning: statement has no effect [-Wunused-value]
  oem_logistic_sparse.h:10:36: warning: statement has no effect [-Wunused-value]
  oem_xval_dense.h:10:36: warning: statement has no effect [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/oem.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.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/OpenCL.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:
  opus_miner.cpp:90:15: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
See ‘/data/gannet/ripley/R/packages/tests-devel/opusminer.Rcheck/00install.out’ for details.
Found the following significant warnings:
  likelihoods.cpp:479:38: warning: value computed is not used [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/outbreaker2.Rcheck/00install.out’ for details.
Found the following significant warnings:
  l1pcahp.c:82:3: warning: statement with no effect [-Wunused-value]
  l1pcahp.c:92:3: warning: statement with no effect [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/pcaL1.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
  'config' variable 'CXXCPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/pense.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:
  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 files/directories:
  ‘filea26e740ee20f.md’
Found the following files/directories:
  ‘Legend929416d9e94e.png’ ‘Legend9294180ebd78.png’ ‘myMap2.htm’
Found the following significant warnings:
  dftcf.c:31:9: warning: array subscript -1 is outside array bounds of ‘int[15]’ [-Warray-bounds]
See ‘/data/gannet/ripley/R/packages/tests-devel/poibin.Rcheck/00install.out’ for details.
Found the following significant warnings:
  /usr/include/bits/string_fortified.h:90:10: warning: ‘__builtin_strcpy’ accessing 1 byte at offsets [-4611686018427387904, 4611686018427387903] and [-4611686018427387904, 4611686018427387903] may overlap 1 byte at offset -4611686018427387904 [-Wrestrict]
See ‘/data/gannet/ripley/R/packages/tests-devel/pomdp.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.
Found the following significant warnings:
  pts2polys.cpp:1560:8: 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/pts2polys.Rcheck/00install.out’ for details.
Found the following significant warnings:
  projectend.c:378:16: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
  projectend.c:391:16: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
  projectend.c:403:16: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/PwrGSD.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:
  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:
  /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/R4dfp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Machine.h:227:42: warning: array subscript 1 is above array bounds of ‘Systems_type’ {aka ‘system_type [1]’} [-Warray-bounds]
  MachineOthers.h:54:38: warning: array subscript 1 is above array bounds of ‘Systems_type’ {aka ‘system_type [1]’} [-Warray-bounds]
  MachineOthers.h:53:33: warning: array subscript 1 is above array bounds of ‘Systems_type’ {aka ‘system_type [1]’} [-Warray-bounds]
See ‘/data/gannet/ripley/R/packages/tests-devel/RandomFields.Rcheck/00install.out’ for details.
.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 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:
  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:
  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:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/rgl.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:
  DbResult.cpp:19:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  DbResult.cpp:81:41: warning: catching polymorphic type ‘class MariaResultPrep::UnsupportedPS’ by value [-Wcatch-value=]
  connection.cpp:23:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-devel/RMariaDB.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/Rmpfr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  nxsreader.cpp:659:22: warning: catching polymorphic type ‘class NxsException’ by value [-Wcatch-value=]
  nxsreader.cpp:709:25: warning: catching polymorphic type ‘class NxsException’ by value [-Wcatch-value=]
See ‘/data/gannet/ripley/R/packages/tests-devel/rncl.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/RODBCext.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:
  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:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/Rssa.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ssl.cpp:1134:10: 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/RSSL.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/rstream.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:
  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/rtfbs.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ClStr2Mat.cpp:12:8: 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/rtk.Rcheck/00install.out’ for details.
Found the following significant warnings:
  global.h:108:26: warning: statement with no effect [-Wunused-value]
  global.h:109:28: warning: statement with no effect [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/Rttf2pt1.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/Runuran.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:
  'config' variable 'CXXCPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/rzmq.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:
  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: ‘__var_1_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/sdwd.Rcheck/00install.out’ for details.
Running examples in ‘sharpshootR-Ex.R’ failed
The error most likely occurred in:

> ### Name: PCP_plot
> ### Title: Percentiles of Cumulative Precipitation
> ### Aliases: PCP_plot
> ### Keywords: hplots
> 
> ### ** Examples
> 
> ## get data from CDEC
> 
> # define station of interest
> s <- 'SPW'
> # get metadata
> s.info <- CDEC_StationInfo(s)
Error in open.connection(x, "rb") : 
  Timeout was reached: [cdec.water.ca.gov] Connection timed out after 10001 milliseconds
Calls: CDEC_StationInfo -> <Anonymous> -> read_html.default
Execution halted
Found the following significant warnings:
  /data/gannet/ripley/R/test-3.7/BH/include/boost/graph/detail/adjacency_list.hpp:2240:43: 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:
  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 files/directories:
  ‘results_2019-11-24.txt’ ‘results_2019-11-24_1.txt’
Found the following significant warnings:
  createPosDef.cpp:84:12: warning: statement has no effect [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/smoothSurv.Rcheck/00install.out’ for details.
Found the following significant warnings:
  fft.c:138:9: warning: array subscript -1 is outside array bounds of ‘int[15]’ [-Warray-bounds]
See ‘/data/gannet/ripley/R/packages/tests-devel/SpatialExtremes.Rcheck/00install.out’ for details.
Found the following significant warnings:
  gpc.c:1039:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  gpc.c:1046:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  gpc.c:1049:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  gpc.c:1056:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/spatialkernel.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘test25499-270.rData’ ‘test25499-35.rData’ ‘test25499-48.rData’
  ‘test25499-92.rData’
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
  'config' variable 'CXXCPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/SplitReg.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [15s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("SqlRender")
  Loading required package: SqlRender
  Reading SQL from package folder: /data/gannet/ripley/R/packages/tests-devel/SqlRender.Rcheck/SqlRender/sql/sql_server/test.sql
  Writing R function to: /tmp/RtmpAURBhX/working_dir/RtmpwFE4oK/file94f016f4b343
  ── 1. Error: If-then-else: error on bad boolean logic syntax (@test-renderSql.R#
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(render("{true = true} ? {true} : {false}"))
   13. rlang::cnd_entrace(cnd)
   16. rJava:::`$.Throwable`(cnd, "trace")
   17. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ── 2. Error: translate sql server throws error when invalid target is given (@te
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(translate("iSELECT * FROM a;", targetDialect = "pwd"))
   13. rlang::cnd_entrace(cnd)
   16. rJava:::`$.Throwable`(cnd, "trace")
   17. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ── 3. Error: translateSingleStatement sql server -> oracle throw error if > 1 st
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(...)
   13. rlang::cnd_entrace(cnd)
   16. rJava:::`$.Throwable`(cnd, "trace")
   17. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 448 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Error: If-then-else: error on bad boolean logic syntax (@test-renderSql.R#155) 
  2. Error: translate sql server throws error when invalid target is given (@test-translateSql.R#394) 
  3. Error: translateSingleStatement sql server -> oracle throw error if > 1 statement (@test-translateSql.R#2338) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  /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]
See ‘/data/gannet/ripley/R/packages/tests-devel/SSN.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [47s/48s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(stationaRy)
  > 
  > test_check("stationaRy")
  trying URL 'https://www1.ncdc.noaa.gov/pub/data/noaa/isd-inventory.csv'
  ── 1. Error: The `get_inventory_tbl()` fcn provides the expected table (@test-ge
  cannot open URL 'https://www1.ncdc.noaa.gov/pub/data/noaa/isd-inventory.csv'
  Backtrace:
   1. stationaRy:::get_inventory_tbl()
   2. downloader::download(url = file_location, destfile = temp_file)
   3. utils::download.file(url, method = method, ...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 39 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: The `get_inventory_tbl()` fcn provides the expected table (@test-get_met_station_data.R#227) 
  
  Error: testthat unit tests failed
  Execution halted
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:
  'config' variable 'CXXCPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/stringi.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:
  rapi.cc:191:12: warning: catching polymorphic type ‘struct subprocess::subprocess_exception’ by value [-Wcatch-value=]
  sub-linux.cc:362:28: warning: C++ designated initializers only available with ‘-std=c++2a’ or ‘-std=gnu++2a’ [-Wpedantic]
  sub-linux.cc:362:42: warning: C++ designated initializers only available with ‘-std=c++2a’ or ‘-std=gnu++2a’ [-Wpedantic]
See ‘/data/gannet/ripley/R/packages/tests-devel/subprocess.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/SuperGauss.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: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Different type kinds at (1)
  Warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  Warning: GNU Extension: initialization of common block variable ‘iset’ in DATA statement at (1)
  Warning: GNU Extension: Variable ‘iset’ at (1) is in COMMON but only in BLOCK DATA initialization is allowed
  Warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘cnop’ is used uninitialized in this function [-Wuninitialized]
  Warning: GNU Extension: Missing comma at (1)
  Warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1) [-Wcharacter-truncation]
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1) [-Wcharacter-truncation]
  Warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/SWATmodel.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘moment_20191125_0434.lp’
Found the following files/directories:
  ‘cfFVA1_cnd_det.csv’ ‘cfFVA1_cnd_res.csv’
  ‘glpk_llFBA_20191125_0434.lp’
Running ‘testthat.R’ [84s/69s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("tabulizer")
  > 
  > stop_logging()
  > test_check("tabulizer")
  ── 1. Error: Extract from encrypted PDF (@test_extract_tables.R#64)  ───────────
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(extract_tables(f6, password = "wrongpassword"))
   14. rlang::cnd_entrace(cnd)
   17. rJava:::`$.Throwable`(cnd, "trace")
   18. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 86 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Extract from encrypted PDF (@test_extract_tables.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘texPreview-Ex.R’ failed
The error most likely occurred in:

> ### Name: as.kable
> ### Title: Try to coerce an object into a knitr_kable object
> ### Aliases: as.kable
> 
> ### ** Examples
> 
> 
> tex <- '\\begin{tabular}{llr}
+ \\hline
+ \\multicolumn{2}{c}{Item} \\\\
+ \\cline{1-2}
+ Animal    & Description & Price (\\$) \\\\
+ \\hline
+ Gnat      & per gram    & 13.65      \\\\
+ & each        & 0.01       \\\\
+ Gnu       & stuffed     & 92.50      \\\\
+ Emu       & stuffed     & 33.33      \\\\
+ Armadillo & frozen      & 8.99       \\\\
+ \\hline
+ \\end{tabular}'
> 
> ktex <- as.kable(tex)
> 
> class(ktex)
[1] "knitr_kable"
> 
> attributes(ktex)
$class
[1] "knitr_kable"

$format
[1] "latex"

> 
> ktex
\begin{tabular}{llr}
\hline
\multicolumn{2}{c}{Item} \\
\cline{1-2}
Animal    & Description & Price (\$) \\
\hline
Gnat      & per gram    & 13.65      \\
& each        & 0.01       \\
Gnu       & stuffed     & 92.50      \\
Emu       & stuffed     & 33.33      \\
Armadillo & frozen      & 8.99       \\
\hline
\end{tabular}
> 
> # using an input call
> 
> x <- tex_preview(tex,returnType = 'input')
Error in tex_preview.default(obj, tex_lines, stem, overwrite, keep_pdf,  : 
   
! LaTeX Error: File `/tmp/Rtmpx32Atf/working_dir/Rtmpt9l9Kj/tex_temp.tex ' not 
found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: tex )

Enter file name: 
! Emergency stop.
<read *> 
 
l.17 ...2Atf/working_dir/Rtmpt9l9Kj/tex_temp.tex }
 ^^M 
!  ==> Fatal error occurred, no output PDF file produced!
Calls: tex_preview -> tex_preview.character -> tex_preview.default
Execution halted
Found the following significant warnings:
  /data/gannet/ripley/R/test-3.7/sparsepp/include/sparsepp/spp_utils.h:422:44: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair<const std::pair<unsigned int, unsigned int>, int>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess]
  /data/gannet/ripley/R/test-3.7/sparsepp/include/sparsepp/spp_utils.h:422:44: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair<const std::pair<unsigned int, unsigned int>, float>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess]
See ‘/data/gannet/ripley/R/packages/tests-devel/text2vec.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘tnet_ucinet_network-2019-11-25_045821.dl’
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:
  /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:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/uuid.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CXXCPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/V8.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.
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 significant warnings:
  assp/dsputils.c:414:13: warning: value computed is not used [-Wunused-value]
  assp/labelobj.c:165:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/wrassp.Rcheck/00install.out’ for details.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-devel/x13binary.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘myXLfile.xlsx’ ‘myXLfile_2019_11_25_054240.xlsx’
  ‘myXLfile_2019_11_25_054243.xlsx’ ‘myXLfile_2019_11_25_054245.xlsx’
Found the following significant warnings:
  emitter.c:28:6: warning: value computed is not used [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/yaml.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
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
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
Found the following significant warnings:
  ADAPTgdwm.c:136:13: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/AMORE.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/AntAngioCOOL.Rcheck/00install.out' for details.
installed size is 73.0Mb
  sub-directories of 1Mb or more:
    gdal   3.8Mb
    libs  68.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   1.1Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs  12.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/arulesNBMiner.Rcheck/00install.out' for details.
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    bin   12.0Mb
    misc   2.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/aslib.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/AtelieR.Rcheck/00install.out' for details.
Package which this enhances but not available for checking: 'rPython'
installed size is 46.8Mb
  sub-directories of 1Mb or more:
    libs  46.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/AWR.Athena.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/AWR.Kinesis.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/AWR.KMS.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/AWR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/awsjavasdk.Rcheck/00install.out' for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/BACA.Rcheck/00install.out' for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   1.8Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   2.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/bartMachineJARs.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/bartMachine.Rcheck/00install.out' for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.1Mb
    libs   2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/BASiNET.Rcheck/00install.out' for details.
Packages which this enhances but not available for checking:
  'doMC', 'rPython'
Running examples in 'BatchMap-Ex.R' failed
The error most likely occurred in:

> ### Name: add.marker
> ### Title: Creates a new sequence by adding markers.
> ### Aliases: add.marker
> 
> ### ** Examples
> 
> data(example.out)
> twopt <- rf.2pts(example.out)
Error in est_rf_out(geno = input.obj$geno, seg_type = input.obj$segr.type.num,  : 
  function 'dataptr' not provided by package 'Rcpp'
Calls: rf.2pts -> est_rf_out
Execution halted
Package suggested but not available for checking: 'doMC'
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.7/bayesCL.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/bayesDem.Rcheck/00install.out' for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Running examples in 'bayesDP-Ex.R' failed
The error most likely occurred in:

> ### Name: bdplm
> ### Title: Bayesian Discount Prior: Two-Arm Linear Regression
> ### Aliases: bdplm bdplm,ANY-method
> 
> ### ** Examples
> 
> # Set sample sizes
> n_t  <- 30     # Current treatment sample size
> n_c  <- 30     # Current control sample size
> n_t0 <- 80     # Historical treatment sample size
> n_c0 <- 80     # Historical control sample size
> 
> # Treatment group vectors for current and historical data
> treatment   <- c(rep(1,n_t), rep(0,n_c))
> treatment0  <- c(rep(1,n_t0), rep(0,n_c0))
> 
> # Simulate a covariate effect for current and historical data
> x  <- rnorm(n_t+n_c, 1, 5)
> x0 <- rnorm(n_t0+n_c0, 1, 5)
> 
> # Simulate outcome:
> # - Intercept of 10 for current and historical data
> # - Treatment effect of 31 for current data
> # - Treatment effect of 30 for historical data
> # - Covariate effect of 3 for current and historical data
> Y  <- 10 + 31*treatment  + x*3 + rnorm(n_t+n_c,0,5)
> Y0 <- 10 + 30*treatment0 + x0*3 + rnorm(n_t0+n_c0,0,5)
> 
> # Place data into separate treatment and control data frames and
> # assign historical = 0 (current) or historical = 1 (historical)
> df_ <- data.frame(Y=Y, treatment=treatment, x=x)
> df0 <- data.frame(Y=Y0, treatment=treatment0, x=x0)
> 
> # Fit model using default settings
> fit <- bdplm(formula=Y ~ treatment+x, data=df_, data0=df0,
+              method="fixed")
Error in sigma2marginal(n = number_mcmc_sigmagrid, grid = grid_sigma2,  : 
  function 'enterRNGScope' not provided by package 'Rcpp'
Calls: bdplm -> bdplm -> sigma2marginal
Execution halted
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 23.8Mb
  sub-directories of 1Mb or more:
    libs  23.7Mb
File 'BayHap/libs/i386/BayHap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'mcmc.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'mcmc.o'
File 'BayHap/libs/x64/BayHap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'mcmc.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'mcmc.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  5.0Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.3Mb
Packages suggested but not available for checking: 'bcmapsdata', 'doMC'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/bdl.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/BEACH.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/beadarrayMSV.Rcheck/00install.out' for details.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is 149.6Mb
  sub-directories of 1Mb or more:
    include  148.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/BiBitR.Rcheck/00install.out' for details.
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/bigalgebra.Rcheck/00install.out' for details.
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  5.7Mb
  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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Biocomb.Rcheck/00install.out' for details.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   8.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/BioMedR.Rcheck/00install.out' for details.
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.
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  6.7Mb
  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
Running examples in 'BNPmix-Ex.R' failed
The error most likely occurred in:

> ### Name: BNPdens
> ### Title: BNPdens class constructor
> ### Aliases: BNPdens
> 
> ### ** Examples
> 
> data_toy <- c(rnorm(100, -3, 1), rnorm(100, 3, 1))
> grid <- seq(-7, 7, length.out = 50)
> est_model <- PYdensity(y = data_toy, mcmc = list(niter = 100,
+                       nburn = 10, nupd = 100), output = list(grid = grid))
Error in cICS(y, grid_use, niter, nburn, m0, k0, a0, b0, m1, s21, tau1,  : 
  function 'enterRNGScope' not provided by package 'Rcpp'
Calls: PYdensity -> cICS
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/boilerpipeR.Rcheck/00install.out' for details.
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/BPEC.Rcheck/00install.out' for details.
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.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     2.9Mb
    doc   2.6Mb
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    1.6Mb
    libs   6.0Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Found the following significant warnings:
  rulebasedmodels.c:65:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:75:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:76:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:115:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:128:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:143:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:151:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:161:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:162:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:178:3: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/C50.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/CADStat.Rcheck/00install.out' for details.
Package which this enhances but not available for checking: 'FastRWeb'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R        1.1Mb
    data     1.5Mb
    models   2.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/causalMGM.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/ChoR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/CITAN.Rcheck/00install.out' for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/clusterfly.Rcheck/00install.out' for details.
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.
Running examples in 'codebook-Ex.R' failed
The error most likely occurred in:

> ### Name: codebook
> ### Title: Generate rmarkdown codebook
> ### Aliases: codebook
> 
> ### ** Examples
> 
> # will generate figures in a temporary directory
> old_base_dir <- knitr::opts_knit$get("base.dir")
> knitr::opts_knit$set(base.dir = tempdir())
> on.exit(knitr::opts_knit$set(base.dir = old_base_dir))
> data("bfi")
> bfi <- bfi[, c("BFIK_open_1", "BFIK_open_1")]
> md <- codebook(bfi, survey_repetition = "single", metadata_table = FALSE)
No missing values.
Warning: 'skimr::skim_to_wide' is deprecated.
Use 'skim()' instead.
See help("Deprecated")
Error: 'skim_with_defaults' is not an exported object from 'namespace:skimr'
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/CollapsABEL.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/collUtils.Rcheck/00install.out' for details.
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
Error(s) in re-building vignettes:
--- re-building 'chamber.Rmd' using rmarkdown
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 'chamber.Rmd'

--- re-building 'senate.Rmd' using rmarkdown
Quitting from lines 93-94 (senate.Rmd) 
Error: processing vignette 'senate.Rmd' failed with diagnostics:
Request failed. Please check the validity of the information you requested.
--- failed re-building 'senate.Rmd'

SUMMARY: processing the following file failed:
  'senate.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   5.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/corehunter.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/coreNLP.Rcheck/00install.out' for details.
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/CovSelHigh.Rcheck/00install.out' for details.
Running examples in 'coxrt-Ex.R' failed
The error most likely occurred in:

> ### Name: coxph.RT
> ### Title: Fits Cox Regression Model Using Right Truncated Data
> ### Aliases: coxph.RT
> 
> ### ** Examples
> 
> # loading AIDS data set
> library(gss)
> data(aids)
> all <- data.frame(age=aids$age, ageg=as.numeric(aids$age<=59), T=aids$incu,
+ R=aids$infe, hiv.mon =102-aids$infe)
> all$T[all$T==0] <- 0.5 # as in Kalbfeisch and Lawless (1989)
> s <- all[all$hiv.mon>60,] # select those who were infected in 1983 or later
> # analysis assuming positivity
> # we request bootstrap SE estimate as well:
> sol <- coxph.RT(T~ageg, right=R, data=s, bs=FALSE)
Error in getVar(exp.bZ, X, T, Z, sol$w) : 
  function 'enterRNGScope' not provided by package 'Rcpp'
Calls: coxph.RT -> getVar
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.7/cplexAPI.Rcheck/00install.out' for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Crossover.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/CRPClustering.Rcheck/00install.out' for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   5.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/CrypticIBDcheck.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/CSFA.Rcheck/00install.out' for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    shp   7.8Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   4.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.9Mb
Found the following significant warnings:
  rulebasedmodels.c:95:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:105:3: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/Cubist.Rcheck/00install.out' for details.
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  5.6Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    libs   1.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/CytobankAPIstats.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/DatabaseConnectorJars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/DatabaseConnector.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/DataClean.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/DataEntry.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/DataLoader.Rcheck/00install.out' for details.
.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
browse: no visible global function definition for 'slot'
browse: no visible global function definition for 'page'
default.options: no visible binding for global variable 'object.size'
heat.view: no visible global function definition for 'head'
heat.view: no visible global function definition for 'tail'
whos: no visible global function definition for 'slotNames'
whos : <anonymous> : <anonymous>: no visible global function definition
  for 'slot'
Undefined global functions or variables:
  head object.size page slot slotNames tail
Consider adding
  importFrom("methods", "slot", "slotNames")
  importFrom("utils", "head", "object.size", "page", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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:11281 (sockconn)
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/DecorateR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/DeducerPlugInExample.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/DeducerPlugInScaling.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Deducer.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/DeducerSpatial.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/DeducerSurvival.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/DeducerText.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/deisotoper.Rcheck/00install.out' for details.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Bootstrapping.CI: no visible global function definition for 'quantile'
D.Jost: no visible global function definition for 'read.table'
D.Jost: no visible global function definition for 'write.table'
Dv.locis.corrected.calc: no visible global function definition for
  'p.adjust'
Gst.Nei: no visible global function definition for 'read.table'
Gst.Nei: no visible global function definition for 'write.table'
H.out: no visible global function definition for 'write.table'
Hardy.calc: no visible global function definition for 'chisq.test'
critical.ci.values: no visible global function definition for
  'quantile'
inputformat: no visible global function definition for 'read.table'
inputformat: no visible global function definition for 'write.table'
over.all.pops: no visible global function definition for 'write.table'
p.value.correcture: no visible global function definition for
  'p.adjust'
pair.pops: no visible global function definition for 'write.table'
Undefined global functions or variables:
  chisq.test p.adjust quantile read.table write.table
Consider adding
  importFrom("stats", "chisq.test", "p.adjust", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
DEMIPathway: no visible global function definition for 'dhyper'
DEMIPathway: no visible global function definition for 'p.adjust'
calcHypergeoExon: no visible global function definition for 'dhyper'
calcHypergeoProb: no visible global function definition for 'dhyper'
demi: no visible global function definition for 'write.table'
demi.t.test: no visible global function definition for 't.test'
demi.wilcox.test: no visible global function definition for
  'wilcox.test'
demi.wilcox.test.fast: no visible global function definition for
  'wilcox.test'
demiequal: no visible global function definition for 'wilcox.test'
wprob: no visible global function definition for 'combn'
diffexp,DEMIDiff: no visible global function definition for 'median'
diffexp,DEMIDiff: no visible global function definition for 'p.adjust'
loadAnnotation,DEMIExperiment-environment: no visible global function
  definition for 'data'
loadBlat,DEMIExperiment-environment: no visible global function
  definition for 'data'
loadCytoband,DEMIExperiment-environment: no visible global function
  definition for 'data'
loadPathway,DEMIExperiment-environment: no visible global function
  definition for 'data'
Undefined global functions or variables:
  combn data dhyper median p.adjust t.test wilcox.test write.table
Consider adding
  importFrom("stats", "dhyper", "median", "p.adjust", "t.test",
             "wilcox.test")
  importFrom("utils", "combn", "data", "write.table")
to your NAMESPACE file.
Running 'test-all.R' [32s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > 
  > library(dendextend)
  
  ---------------------
  Welcome to dendextend version 1.12.0
  Type citation('dendextend') for how to cite the package.
  
  Type browseVignettes(package = 'dendextend') for the package vignette.
  The github page is: https://github.com/talgalili/dendextend/
  
  Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
  Or contact: <tal.galili@gmail.com>
  
  	To suppress this message use:  suppressPackageStartupMessages(library(dendextend))
  ---------------------
  
  
  Attaching package: 'dendextend'
  
  The following object is masked from 'package:stats':
  
      cutree
  
  > test_check("dendextend")
  Bootstrap (r = 0.4)... Done.
  Bootstrap (r = 0.6)... Done.
  Bootstrap (r = 0.8)... Done.
  Bootstrap (r = 1.0)... Done.
  Bootstrap (r = 1.2)... Done.
  Bootstrap (r = 1.4)... Done.
  -- 1. Failure: extract au (@test-pvclust_extract.R#12)  ------------------------
  round(pvclust_edges(dend)[, 3], digits = 2) not identical to c(0.97, 1, 1).
  2/3 mismatches (average diff: 0.11)
  [1] 0.76 - 0.97 == -0.21
  [2] 0.99 - 1.00 == -0.01
  
  == testthat results  ===========================================================
  [ OK: 409 | SKIPPED: 0 | WARNINGS: 10 | FAILED: 1 ]
  1. Failure: extract au (@test-pvclust_extract.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.8Mb
    help   1.4Mb
    libs   1.8Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.2Mb
installed size is  7.9Mb
  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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/dialrjars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/dialr.Rcheck/00install.out' for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/diffMeanVar.Rcheck/00install.out' for details.
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:11227 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11227 (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:11715 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11715 (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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/digest.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'concepts.Rmd' using rmarkdown
--- finished re-building 'concepts.Rmd'

--- re-building 'convenience-features.Rmd' using rmarkdown
--- finished re-building 'convenience-features.Rmd'

--- re-building 'data-table-syntax.Rmd' using rmarkdown
--- finished re-building 'data-table-syntax.Rmd'

--- re-building 'glm.Rmd' using rmarkdown
--- finished re-building 'glm.Rmd'

--- re-building 'ingesting-data.Rmd' using rmarkdown
--- finished re-building 'ingesting-data.Rmd'

Warning in file(con, "r") :
  cannot open file 'D:\temp\RtmpaYODG3\file2b8b463af6b42': Permission denied
Error in file(con, "r") : cannot open the connection
Calls: <Anonymous> -> readLines -> file
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/DiversityOccupancy.Rcheck/00install.out' for details.
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    include  15.9Mb
    libs      1.3Mb
installed size is  6.7Mb
  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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Dominance.Rcheck/00install.out' for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Error(s) in re-building vignettes:
--- re-building 'using_drtmle.Rmd' using rmarkdown
drtmle: TMLE with doubly robust inference
Version: 1.0.4
Loading required package: nnls
Super Learner
Version: 2.0-25
Package created on 2019-08-05

Quitting from lines 1049-1062 (using_drtmle.Rmd) 
Error: processing vignette 'using_drtmle.Rmd' failed with diagnostics:
there is no package called 'snow'
--- failed re-building 'using_drtmle.Rmd'

SUMMARY: processing the following file failed:
  'using_drtmle.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    appinformation   3.5Mb
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  6.8Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.5Mb
    libs   1.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/e1071.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    hac    4.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/edeR.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'edgarWebR.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

Quitting from lines 71-85 (edgarWebR.Rmd) 
Error: processing vignette 'edgarWebR.Rmd' failed with diagnostics:
Service Unavailable (HTTP 503).
--- failed re-building 'edgarWebR.Rmd'

--- re-building 'parsing.Rmd' using rmarkdown
Quitting from lines 50-60 (parsing.Rmd) 
Error: processing vignette 'parsing.Rmd' failed with diagnostics:
Service Unavailable (HTTP 503).
--- failed re-building 'parsing.Rmd'

SUMMARY: processing the following files failed:
  'edgarWebR.Rmd' 'parsing.Rmd'

Error: Vignette re-building failed.
Execution halted
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 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data  11.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/ELT.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.3Mb
Found the following significant warnings:
  emmix.cpp:351:195: warning: value computed is not used [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/EMMIXgene.Rcheck/00install.out' for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/EnsembleBase.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/EnsembleCV.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/EnsemblePCReg.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/EnsemblePenReg.Rcheck/00install.out' for details.
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' [3s]
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
Running examples in 'erhcv-Ex.R' failed
The error most likely occurred in:

> ### Name: VerifyTree
> ### Title: Verify tree structure
> ### Aliases: VerifyTree
> 
> ### ** Examples
> 
> require(HAC)
Loading required package: HAC
Loading required package: copula
> str <- hac(type = 1, tree = list(list(list("X4", "X5", 6),
+                                       "X6", 3), "X1", list("X2", "X3", 10), 1))
> 
> set.seed(2018)
> U.. <- rHAC(1000, str)
Warning in hac2nacopula(hac) : NAs introduced by coercion
[1] "X4 <-> 1"
[1] "X5 <-> 2"
[1] "X6 <-> 3"
[1] "X1 <-> 4"
[1] "X2 <-> 5"
[1] "X3 <-> 6"
> U.. <- U..[,c(4, 5, 6, 1, 2, 3)]
> 
> ## Tree via hclust
> spear <- cor(U.., method = "sp")
> clust <- hclust(dist(spear, method = "maximum"),
+                 method = "complete")
> tree1 <- hclust2tree(clust)
> 
> ## Tree after verification
> tree2 <- VerifyTree(U.., alpha = 0.95,
+                     distance.method = "maximum",
+                     hclust.method = "complete")$Tree
> 
> ## Comparison
> par(mfrow = c(1, 3))
> tree2plot(tree1)
Error in plot.Node(e1$O) : 
  Package "DiagrammeR" is required to plot a `data.tree::Node`object. Please install it.
Calls: tree2plot -> plot -> plot.Node
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/evoper.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/expands.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/extraTrees.Rcheck/00install.out' for details.
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.
Running 'tinytest.R' [1s]
Running the tests in 'tests/tinytest.R' failed.
Complete output:
  > 
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  +   home <- length(unclass(packageVersion("fastshap"))[[1L]]) == 4
  +   tinytest::test_package("fastshap", at_home = home)
  + }
  Loading required package: Formula
  Loading required package: plotmo
  Loading required package: plotrix
  Loading required package: TeachingDemos
  
  Running test_fastshap.R...............    0 tests    
  Running test_fastshap.R...............    0 tests    
  Running test_fastshap.R...............    0 tests    
  Running test_fastshap.R...............    0 tests    
  Running test_fastshap.R...............    0 tests    
  Running test_fastshap.R...............    0 tests    Error in fastshap:::genOMat(num_rows, num_cols) : 
    function 'enterRNGScope' not provided by package 'Rcpp'
  Calls: <Anonymous> ... run_test_dir -> lapply -> FUN -> eval -> eval -> <Anonymous>
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.7Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/fdq.Rcheck/00install.out' for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
    libs   1.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/fit4NM.Rcheck/00install.out' for details.
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
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R   6.3Mb
opc : <anonymous>: no visible global function definition for
  'parseWorkspace'
opc : <anonymous>: no visible global function definition for
  'closeWorkspace'
Undefined global functions or variables:
  closeWorkspace parseWorkspace
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
Package which this enhances but not available for checking: 'doMC'
Running 'testthat.R' [223s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > if (require(testthat)) {
  +   test_check("forecast")
  + }
  Loading required package: testthat
  Loading required package: forecast
  Registered S3 methods overwritten by 'forecast':
    method             from    
    fitted.fracdiff    fracdiff
    residuals.fracdiff fracdiff
  -- 1. Error: tests for autoplot/gg functions (@test-ggplot.R#64)  --------------
  need at least two non-NA values to interpolate
  Backtrace:
   1. forecast::ggseasonplot(...)
   2. ggplot2::scale_color_gradientn(colours = col)
   5. scales::gradient_n_pal(colours, values, space)
   6. scales::colour_ramp(colours)
   7. stats::approxfun(x_in, lab_in[, 1])
  
  == testthat results  ===========================================================
  [ OK: 774 | SKIPPED: 5 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: tests for autoplot/gg functions (@test-ggplot.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [192s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > if (require(testthat)) {
  +   test_check("forecast")
  + }
  Loading required package: testthat
  Loading required package: forecast
  Registered S3 methods overwritten by 'forecast':
    method             from    
    fitted.fracdiff    fracdiff
    residuals.fracdiff fracdiff
  -- 1. Error: tests for autoplot/gg functions (@test-ggplot.R#64)  --------------
  need at least two non-NA values to interpolate
  Backtrace:
   1. forecast::ggseasonplot(...)
   2. ggplot2::scale_color_gradientn(colours = col)
   5. scales::gradient_n_pal(colours, values, space)
   6. scales::colour_ramp(colours)
   7. stats::approxfun(x_in, lab_in[, 1])
  
  == testthat results  ===========================================================
  [ OK: 774 | SKIPPED: 5 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: tests for autoplot/gg functions (@test-ggplot.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
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 896-920 (Vignette.Rmd) 
Error: processing vignette 'Vignette.Rmd' failed with diagnostics:
could not find function "doColorRamp"
--- failed re-building 'Vignette.Rmd'

SUMMARY: processing the following file failed:
  'Vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  testcpp_rec6.cpp:197:37: warning: value computed is not used [-Wunused-value]
  testcpp_rec6.cpp:551:37: warning: value computed is not used [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/forestFloor.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'pcl-vignette.Rmd' using rmarkdown
Quitting from lines 43-49 (pcl-vignette.Rmd) 
Error: processing vignette 'pcl-vignette.Rmd' failed with diagnostics:
need at least two non-NA values to interpolate
--- failed re-building 'pcl-vignette.Rmd'

SUMMARY: processing the following file failed:
  'pcl-vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   5.0Mb
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/fsdaR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/FSelector.Rcheck/00install.out' for details.
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/G2Sd.Rcheck/00install.out' for details.
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').
Running examples in 'gamreg-Ex.R' failed
The error most likely occurred in:

> ### Name: cv.gam
> ### Title: Robust Cross-Validation
> ### Aliases: cv.gam
> 
> ### ** Examples
> 
>   ## generate data
>   library(mvtnorm)
>   n <- 30                      # number of observations
>   p <- 10                      # number of expalanatory variables
> 
>   epsilon <- 0.1               # contamination ratio
> 
>   beta0 <- 0.0                 # intercept
>   beta <- c(numeric(p))        # regression coefficients
>   beta[1] <- 1
>   beta[2] <- 2
>   beta[3] <- 3
>   beta[4] <- 4
> 
>   Sigma <- 0.2^t(sapply(1:p, function(i, j) abs(i-j), 1:p))
>   X <- rmvnorm(n, sigma=Sigma) # explanatory variables
>   e <- rnorm(n) # error terms
> 
>   i <- 1:ceiling(epsilon*n)    # index of outliers
>   e[i] <- e[i] + 20            # vertical outliers
>   Y <- beta0*(numeric(n)+1) + X%*%beta
> 
> 
>   res <- cv.gam(X,Y,nlambda = 5, nlambda.LTS=20 ,init.mode="sLTS")
Error in winsorize.matrix(cbind(x[, j], y), const = const, prob = prob,  : 
  function 'dataptr' not provided by package 'Rcpp'
Calls: cv.gam ... sapply -> lapply -> FUN -> winsorize -> winsorize.matrix
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   2.7Mb
installed size is 10.8Mb
  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  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
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
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  5.2Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R         2.4Mb
    extdata   2.2Mb
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  9.2Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/GGUM.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
installed size is 23.5Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  21.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/glmnet.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/glmulti.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'cplexAPI'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/gMCP.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.
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.
installed size is 30.9Mb
  sub-directories of 1Mb or more:
    R  30.8Mb
Running 'testthat.R' [117s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(gqlr)
  > 
  > test_check("gqlr")
  -- 1. Failure: pryr fails (@test-aaa-pryr-unenclose.R#25)  ---------------------
  ans$A() == "A" isn't false.
  
  -- 2. Failure: pryr fails (@test-aaa-pryr-unenclose.R#26)  ---------------------
  ans$B() == "B" isn't false.
  
  == testthat results  ===========================================================
  [ OK: 541 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 2 ]
  1. Failure: pryr fails (@test-aaa-pryr-unenclose.R#25) 
  2. Failure: pryr fails (@test-aaa-pryr-unenclose.R#26) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/GrammR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/GreedyExperimentalDesignJARs.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/GreedyExperimentalDesign.Rcheck/00install.out' for details.
Running examples in 'groupedSurv-Ex.R' failed
The error most likely occurred in:

> ### Name: groupedSurvFam
> ### Title: Compute the Efficient Score Statistic for the Frailty Model
> ### Aliases: groupedSurvFam
> 
> ### ** Examples
> 
> # Generate dummy data
> set.seed(111)
> n <- 24
> 
> # effect size
> beta <- 0.3
> 
> # covariate parameters
> theta <- c(0.2, 0.2)
> 
> # variable of interest
> MAF <- 0.05
> x <- matrix(rbinom(n, 2, MAF), ncol = 1)
> 
> # covariate data (centered at 0)
> z1 <- rnorm(n)
> z2 <- rbinom(n, 1, 0.5) - 0.5
> Z  <- matrix(cbind(z1, z2), ncol = 2)
> 
> # continuous survival time
> lam0 <- 1
> cmax <- 3
> lami <- lam0 * exp(x*beta + Z[,1]*theta[1]+Z[,2]*theta[2])
> stime <- rexp(n, lami)
> ctime <- runif(n, 0, cmax)
> delta <- stime < ctime
> otime <- pmin(stime, ctime)
> 
> # number of observation times
> ntps <- 5
> 
> # number of intervals
> r <- ntps + 1
> 
> # last observation time
> maxbreakq <- 0.85
> maxbreak <- qexp(maxbreakq, lam0)
> 
> # grouped failure times
> breaks <- (1:ntps) * (maxbreak/ntps)
> gtime <- findInterval(otime, breaks) + 1
> delta[gtime == r] <- FALSE
> dctime <- findInterval(ctime, breaks) + 1
> delta[gtime == dctime] <- FALSE
> delta <- as.numeric(delta)
> 
> # family-specific information
> m <- n/3
> fam_role <- rep(c("o","f","m"),m)
> fam_group <- as.character(rep(1:m,rep(3,m)))
> 
> # nuisance parameters
> alpha <- thetaEst(Z, gtime,delta)$alpha
> var <- 0.2
> 
> # compute efficient score statistics
> res   <- groupedSurvFam(x, fam_group, fam_role, alpha, var, gtime, delta) 
> res
            [,1]
[1,] -0.09108599
[2,] -0.03535880
[3,] -0.05805514
[4,] -0.07539618
[5,]  0.09537326
[6,]  0.50679716
[7,] -0.01163486
[8,] -0.02150784
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11102 (sockconn)
Execution halted
Running examples in 'groupedSurv-Ex.R' failed
The error most likely occurred in:

> ### Name: groupedSurvFam
> ### Title: Compute the Efficient Score Statistic for the Frailty Model
> ### Aliases: groupedSurvFam
> 
> ### ** Examples
> 
> # Generate dummy data
> set.seed(111)
> n <- 24
> 
> # effect size
> beta <- 0.3
> 
> # covariate parameters
> theta <- c(0.2, 0.2)
> 
> # variable of interest
> MAF <- 0.05
> x <- matrix(rbinom(n, 2, MAF), ncol = 1)
> 
> # covariate data (centered at 0)
> z1 <- rnorm(n)
> z2 <- rbinom(n, 1, 0.5) - 0.5
> Z  <- matrix(cbind(z1, z2), ncol = 2)
> 
> # continuous survival time
> lam0 <- 1
> cmax <- 3
> lami <- lam0 * exp(x*beta + Z[,1]*theta[1]+Z[,2]*theta[2])
> stime <- rexp(n, lami)
> ctime <- runif(n, 0, cmax)
> delta <- stime < ctime
> otime <- pmin(stime, ctime)
> 
> # number of observation times
> ntps <- 5
> 
> # number of intervals
> r <- ntps + 1
> 
> # last observation time
> maxbreakq <- 0.85
> maxbreak <- qexp(maxbreakq, lam0)
> 
> # grouped failure times
> breaks <- (1:ntps) * (maxbreak/ntps)
> gtime <- findInterval(otime, breaks) + 1
> delta[gtime == r] <- FALSE
> dctime <- findInterval(ctime, breaks) + 1
> delta[gtime == dctime] <- FALSE
> delta <- as.numeric(delta)
> 
> # family-specific information
> m <- n/3
> fam_role <- rep(c("o","f","m"),m)
> fam_group <- as.character(rep(1:m,rep(3,m)))
> 
> # nuisance parameters
> alpha <- thetaEst(Z, gtime,delta)$alpha
> var <- 0.2
> 
> # compute efficient score statistics
> res   <- groupedSurvFam(x, fam_group, fam_role, alpha, var, gtime, delta) 
> res
            [,1]
[1,] -0.09108599
[2,] -0.03535880
[3,] -0.05805514
[4,] -0.07539618
[5,]  0.09537326
[6,]  0.50679716
[7,] -0.01163486
[8,] -0.02150784
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11381 (sockconn)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/growthPheno.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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/gWidgets2RGtk2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/gWidgetsRGtk2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/gwsem.Rcheck/00install.out' for details.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/helloJavaWorld.Rcheck/00install.out' for details.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs   4.0Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc           3.7Mb
    htmlwidgets   4.0Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
    libs   1.5Mb
Found the following significant warnings:
  codegenerator.cpp:1743:26: warning: 'auto_ptr' is deprecated (declared at D:/Compiler/gcc-4.9.3/mingw_32/i686-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
  codegenerator.cpp:1743:26: warning: 'auto_ptr' is deprecated (declared at D:/Compiler/gcc-4.9.3/mingw_64/x86_64-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
See 'd:/Rcompile/CRANpkg/local/4.0/highlight.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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/hive.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.9Mb
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(hmstimer)
  > 
  > test_check("hmstimer")
  -- 1. Failure: tmr_elapsed (@test-timer.R#106)  --------------------------------
  as.numeric(tmr) is not more than 1. Difference: -0.0135
  
  == testthat results  ===========================================================
  [ OK: 48 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: tmr_elapsed (@test-timer.R#106) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.5Mb
    libs   1.5Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
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  5.2Mb
  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
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      1.8Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   7.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/ie2misc.Rcheck/00install.out' for details.
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/imageData.Rcheck/00install.out' for details.
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       5.3Mb
    include   2.8Mb
    libs     12.9Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/ImportExport.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/InSilicoVA.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/intamapInteractive.Rcheck/00install.out' for details.
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/InterfaceqPCR.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.
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/iplots.Rcheck/00install.out' for details.
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:11642 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11642 (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:11857 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11857 (sockconn)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/ISM.Rcheck/00install.out' for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs           4.3Mb
Package unavailable to check Rd xrefs: 'doMC'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/jdx.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/JGR.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'joineRML.Rmd' using rmarkdown
Quitting from lines 79-89 (joineRML.Rmd) 
Error: processing vignette 'joineRML.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building 'joineRML.Rmd'

--- re-building 'technical.Rnw' using Sweave
--- finished re-building 'technical.Rnw'

SUMMARY: processing the following file failed:
  'joineRML.Rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'competing-risks.Rmd' using rmarkdown
Quitting from lines 130-135 (competing-risks.Rmd) 
Error: processing vignette 'competing-risks.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building 'competing-risks.Rmd'

--- re-building 'joineR.Rmd' using rmarkdown
Quitting from lines 289-300 (joineR.Rmd) 
Error: processing vignette 'joineR.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building 'joineR.Rmd'

SUMMARY: processing the following files failed:
  'competing-risks.Rmd' 'joineR.Rmd'

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/joinXL.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/jsr223.Rcheck/00install.out' for details.
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/KoNLP.Rcheck/00install.out' for details.
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/lar.Rcheck/00install.out' for details.
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  5.1Mb
  sub-directories of 1Mb or more:
    libs   2.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
    libs   1.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/lilikoi.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/llama.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/LLM.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/LLSR.Rcheck/00install.out' for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs       2.1Mb
    testdata   1.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      1.5Mb
Found the following significant warnings:
  ../../inst/include/lpkit.h:32:99: warning: right-hand operand of comma expression has no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/lpSolveAPI.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/lpSolve.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.6Mb
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 10.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
    proj   5.0Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    TS_files     5.8Mb
    base_files   6.3Mb
installed size is 41.3Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs  34.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/maGUI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/mailR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/mallet.Rcheck/00install.out' for details.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc           1.2Mb
    htmlwidgets   1.4Mb
    libs          7.7Mb
Found the following significant warnings:
  cuts.c:24:2: warning: statement with no effect [-Wunused-value]
  cuts.c:24:5: warning: statement with no effect [-Wunused-value]
  cuts.c:24:9: warning: statement with no effect [-Wunused-value]
  cuts.c:32:2: warning: statement with no effect [-Wunused-value]
  cuts.c:32:6: warning: statement with no effect [-Wunused-value]
  cuts.c:32:10: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/mapproj.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/matchingMarkets.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'my-vignette.Rmd' using rmarkdown
Loading required package: MASS
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
Error writing to connection:  No space left on device
--- failed re-building 'my-vignette.Rmd'

SUMMARY: processing the following file failed:
  'my-vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
Rd conversion errors:
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in file(out, "wt") :
  cannot open file 'D:\temp\RtmpysgnT9\ltx2e8d471957c5e/prop_01.tex': No space left on device
Error in file(out, "wt") : cannot open the connection
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/mbgraphic.Rcheck/00install.out' for details.
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/mdendro.Rcheck/00install.out' for details.
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/mdsOpt.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      1.5Mb
Error(s) in re-building vignettes:
--- re-building 'data_input.Rmd' using rmarkdown
--- finished re-building 'data_input.Rmd'

--- re-building 'meaRtoolsGeneralUsage.Rmd' using rmarkdown
Quitting from lines 182-195 (meaRtoolsGeneralUsage.Rmd) 
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Error: processing vignette 'meaRtoolsGeneralUsage.Rmd' failed with diagnostics:
Error writing to connection
--- failed re-building 'meaRtoolsGeneralUsage.Rmd'

--- re-building 'sttc.Rmd' using rmarkdown
Warning in file(datafile, "wb") :
  cannot open file 'sttc_cache/html/unnamed-chunk-1_7e6c0a67e342b16774bd1ff92b263690.rdb': No space left on device
Quitting from lines 38-39 (sttc.Rmd) 
Error: processing vignette 'sttc.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'sttc.Rmd'

SUMMARY: processing the following files failed:
  'meaRtoolsGeneralUsage.Rmd' 'sttc.Rmd'

Error: Vignette re-building failed.
Execution halted
Rd conversion errors:
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in file(out, "wt") :
  cannot open file 'D:\temp\Rtmp23oLk5\ltx22a582fa82142/plateinfo.tex': No space left on device
Error in file(out, "wt") : cannot open the connection
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
SFM_metric.Rd: Sections \title, and \name must exist and be unique in Rd files
Error writing to connection:  No space left on device
VerticalProfiles.Rd: Sections \title, and \name must exist and be unique in Rd files
biophysics.Rd: Sections \title, and \name must exist and be unique in Rd files
Error writing to connection:  No space left on device
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connecti* checking Rd metadata ... OK
Warning in file(out, "wt") :
  cannot open file 'D:\temp\Rtmpae6tJW\fileec783a745e28/VerticalProfiles.R': No space left on device
Error in file(out, "wt") : cannot open the connection
Execution halted
Error(s) in re-building vignettes:
Warning in file(con, "r") :
  cannot open file 'D:\temp\RtmpgJrdND\file2983c3a347e11': No such file or directory
Error in file(con, "r") : cannot open the connection
Calls: <Anonymous> -> cat -> readLines -> file
Execution halted
Rd conversion errors:
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Error in writeLines(x, con, useBytes = TRUE, ...) : 
  Error writing to connection:  No space left on device
Rd conversion errors:
Error in writeLines(x, con, useBytes = TRUE, ...) : 
  Error writing to connection:  No space left on device
meltt_duplicates.Rd: Sections \title, and \name must exist and be unique in Rd files
meltt_inspect.Rd: Sections \title, and \name must exist and be unique in Rd files
mplot.Rd: Sections \title, and \name must exist and be unique in Rd files
plot.meltt.Rd: Sections \title, and \name must exist and be unique in Rd files
print.meltt.Rd: Sections \title, and \name must exist and be unique in Rd files
summary.meltt.Rd: Sections \title, and \name must exist and be unique in Rd files
tplot.Rd: Sections \title, and \name must exist and be unique in Rd files
problems found in 'meltt_duplicates.Rd', 'meltt_inspect.Rd', 'mplot.Rd', 'plot.meltt.Rd', 'print.meltt.Rd', 'summary.meltt.Rd', 'tplot.Rd'
Warning in file(out, "wt") :
  cannot open file 'D:\temp\RtmpAhrUU6\file1c4c05a595d8a/meltt_data.R': No space left on device
Error in file(out, "wt") : cannot open the connection
Execution halted
Running massageExamples to create 'meltt-Ex.R' failed

 NONE
Rd conversion errors:
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/melviewr.Rcheck/00install.out' for details.
Error: package or namespace load failed for 'meme':
 .onLoad failed in loadNamespace() for 'showtext', details:
  call: sysfonts::font_add("wqy-microhei", out_file)
  error: freetype: unknown file format, error code 2
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   })
1: library(pack
Execution halted
Error in file(open = "w+", encoding = "UTF-8") : 
  cannot open the connection
Calls: <Anonymous> -> .load_package_quietly -> .try_quietly
Execution halted
Error in file(open = "w+", encoding = "UTF-8") : 
  cannot open the connection
Calls: <Anonymous> -> .load_package_quietly -> .try_quietly
Execution halted
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.
Running examples in 'meme-Ex.R' failed
The error occurred in:


R Under development (unstable) (2019-11-21 r77446) -- "Unsuffered Consequences"
Copyright (C) 2019 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 <- "meme"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> library('meme')
Warning in utils::unzip(font_file, exdir = out_dir, overwrite = FALSE) :
  write error in extracting from zip file
Error: package or namespace load failed for 'meme':
 .onLoad failed in loadNamespace() for 'showtext', details:
  call: sysfonts::font_add("wqy-microhei", out_file)
  error: freetype: unknown file format, error code 2
Execution halted
Running 'testthat.R' [23s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(memery)
  Loading required package: showtext
  Loading required package: sysfonts
  Loading required package: showtextdb
  > 
  > test_check("memery")
Warning in file(out, "wt") :
  cannot open file 'D:\temp\RtmpuWmPqS\file2cf5c5d1d7c04/mgForward.R': No space left on device
Error in file(out, "wt") : cannot open the connection
Execution halted
Running massageExamples to create 'memgene-Ex.R' failed
Error in file(out, "wt") : cannot open the connection
Calls: <Anonymous> -> Rd2ex -> file
In addition: Warning message:
In file(out, "wt") :
  cannot open file 'D:\temp\RtmpI7NrKb\file2eae04ccc1fe7/mgForward.R': No space left on device
Execution halted
 NONE
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   3.1Mb
Warning in file(out, "wt") :
  cannot open file 'D:\temp\Rtmp8KmBm1\file1acec49565e6f/common_subgraphs.R': No space left on device
Error in file(out, "wt") : cannot open the connection
Execution halted
unable to create examples directory
** DONE
Running massageExamples to create 'memoise-Ex.R' failed
Error in file(out, "wt") : cannot open the connection
Calls: <Anonymous> -> Rd2ex -> file
In addition: Warning message:
In file(out, "wt") :
  cannot open file 'D:\temp\RtmpMFeUZ5\file20d583a31b05/has_cache.R': No space left on device
Execution halted
 NONE
Rd conversion errors:
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in file(out, "wt") :
  cannot open file 'D:\temp\Rtmp8OAh2p\ltx2891c69d72014/cache_s3.tex': No space left on device
Error in file(out, "wt") : cannot open the connection
Error(s) in re-building vignettes:
--- re-building 'README.Rmd' using rmarkdown
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in file(con, "w") :
  cannot open file 'README.knit.md': No space left on device
Error: processing vignette 'README.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'README.Rmd'

SUMMARY: processing the following file failed:
  'README.Rmd'

Error: Vignette re-building failed.
Execution halted
Rd conversion errors:
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in file(out, "wt") :
  cannot open file 'D:\temp\Rtmp2ZyQXy\ltxb23019d46325/strategies.tex': No space left on device
Error in file(out, "wt") : cannot open the connection
climate.Rd: Sections \title, and \name must exist and be unique in Rd files
Error writing to connection:  No space left on device
experimentToTable.Rd: Sections \title, and \name must exist and be unique in Rd files
Error writing to connection:  No space left on device
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
problems found in 'climate.Rd', 'computeMemory.Rd', 'experimentToTable.Rd', 'extractMemoryFeatures.Rd', 'mergePalaeoData.Rd', 'palaeodata.Rd', 'palaeodataLagged.Rd', 'palaeodataMemory.Rd', 'plotExperiment.Rd', 'plotInteraction.Rd', 'plotMemory.Rd', 'pollen.Rd', 'prepareLaggedData.Rd', 'runExperiment.Rd'
Warning in file(out, "wt") :
  cannot open file 'D:\temp\RtmpM7PBTb\file1f92c66983226/mergePalaeoData.R': No space left on device
Error in file(out, "wt") : cannot open the connection
Execution halted
Running massageExamples to create 'memoria-Ex.R' failed
Error in file(out, "wt") : cannot open the connection
Calls: <Anonymous> -> Rd2ex -> file
In addition: Warning messages:
1: In close.connection(con) :
  Problem closing connection:  No space left on device
2: In file(out, "wt") :
  cannot open file 'D:\temp\RtmpEDfx5j\file205b074dc74f4/mergePalaeoData.R': No space left on device
Execution halted
 NONE
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/MergeGUI.Rcheck/00install.out' for details.
mergeTrees.Rd: Sections \title, and \name must exist and be unique in Rd files
problem found in 'mergeTrees.Rd'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.1Mb
Installation failed.
See  for details.
*
Error(s) in re-building vignettes:
--- re-building 'MetaLonDA.Rmd' using rmarkdown
Quitting from lines 28-43 (MetaLonDA.Rmd) 
Error: processing vignette 'MetaLonDA.Rmd' failed with diagnostics:
non-numeric argument to binary operator
--- failed re-building 'MetaLonDA.Rmd'

SUMMARY: processing the following file failed:
  'MetaLonDA.Rmd'

Error: Vignette re-building failed.
Execution halted
*
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 ?) ========
Packages suggested but not available for checking: 'doMC', 'doSMP'
Installation failed.
See * DONE

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 ?) ========
allmetap.Rd: Sections \title, and \name must exist and be unique in Rd files
invchisq.Rd: Sections \title, and \name must exist and be unique in Rd files
invt.Rd: Sections \title, and \name must exist and be unique in Rd files
logitp.Rd: Sections \title, and \name must exist and be unique in Rd files
meanp.Rd: Sections \title, and \name must exist and be unique in Rd files
meanz.Rd: Sections \title, and \name must exist and be unique in Rd files
metap-package.Rd: Sections \title, and \name must exist and be unique in Rd files
package-data.Rd: Sections \title, and \name must exist and be unique in Rd files
plotp.Rd: Sections \title, and \name must exist and be unique in Rd files
schweder.Rd: Sections \title, and \name must exist and be unique in Rd files
sumlog.Rd: Sections \title, and \name must exist and be unique in Rd files
sump.Rd: Sections \title, and \name must exist and be unique in Rd files
sumz.Rd: Sections \title, and \name must exist and be unique in Rd files
two2one.Rd: Sections \title, and \name must exist and be unique in Rd files
votep.Rd: Sections \title, and \name must exist and be unique in Rd files
wilkinsonp.Rd: Sections \title, and \name must exist and be unique in Rd files
problems found in 'allmetap.Rd', 'invchisq.Rd', 'invt.Rd', 'logitp.Rd', 'meanp.Rd', 'meanz.Rd', 'metap-package.Rd', 'package-data.Rd', 'plotp.Rd', 'schweder.Rd', 'sumlog.Rd', 'sump.Rd', 'sumz.Rd', 'two2one.Rd', 'votep.Rd', 'wilkinsonp.Rd'
Warning in file(out, "wt") :
  cannot open file 'D:\temp\RtmpKCoWZ9\file98743a7119/meanz.R': No space left on device
Error in file(out, "wt") : cannot open the connection
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/metapro.Rcheck/00install.out' for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    help   2.0Mb
    libs   1.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/MetSizeR.Rcheck/00install.out' for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    1.1Mb
    libs   4.1Mb
    misc   1.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/MicroStrategyR.Rcheck/00install.out' for details.
File 'MigClim/libs/i386/MigClim.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'genclust.o', 'migrate.o', 'src_cell.o', 'validate.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'genclust.o', 'migrate.o'
File 'MigClim/libs/x64/MigClim.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'genclust.o', 'migrate.o', 'src_cell.o', 'validate.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'genclust.o', 'migrate.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.
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.
Found the following significant warnings:
  Warning: namespace 'flexmix' is not available and has been replaced
  Warning: namespace 'modeltools' is not available and has been replaced
  Warning: namespace 'kernlab' is not available and has been replaced
  Warning: namespace 'robustbase' is not available and has been replaced
See 'd:/Rcompile/CRANpkg/local/4.0/miRtest.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/MissingDataGUI.Rcheck/00install.out' for details.
Found the following significant warnings:
  GLMM_Deviance.cpp:153:9: warning: statement has no effect [-Wunused-value]
  GLMM_Deviance.cpp:708:11: warning: statement has no effect [-Wunused-value]
  GLMM_Deviance2.cpp:173:9: warning: statement has no effect [-Wunused-value]
  GLMM_Deviance2.cpp:780:11: warning: statement has no effect [-Wunused-value]
  GLMM_newData.cpp:183:9: warning: statement has no effect [-Wunused-value]
  GLMM_updateRanEf.cpp:161:9: warning: statement has no effect [-Wunused-value]
  GLMM_updateRanEf.cpp:626:11: warning: statement has no effect [-Wunused-value]
  GLMM_updateRanEf_QR.cpp:124:9: warning: statement has no effect [-Wunused-value]
  GLMM_updateRanEf_QR.cpp:328:11: warning: statement has no effect [-Wunused-value]
  MCMC_Moments_NormalApprox_QR.cpp:104:11: warning: statement has no effect [-Wunused-value]
  MCMC_Moments_NormalApprox_QR.cpp:209:11: warning: statement has no effect [-Wunused-value]
  NMix_updateMeansVars.cpp:516:16: warning: statement has no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/mixAK.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/mlDNA.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/mleap.Rcheck/00install.out' for details.
listGenoToTable: no visible binding for global variable 'dummy'
Undefined global functions or variables:
  dummy
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
Found a 'configure.in' file: 'configure.ac' has long been preferred.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/MODIStsp.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    1.8Mb
    libs   1.9Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   1.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   1.6Mb
    libs   1.4Mb
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 23.6Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.0Mb
    libs  20.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/MSIseq.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Running examples in 'mstate-Ex.R' failed
The error most likely occurred in:

> ### Name: crprep
> ### Title: Function to create weighted data set for competing risks
> ###   analyses
> ### Aliases: crprep crprep.default
> ### Keywords: datagen survival
> 
> ### ** Examples
> 
> data(aidssi)
> aidssi.w <- crprep("time", "cause", data=aidssi, trans=c("AIDS","SI"),
+                    cens="event-free", id="patnr", keep="ccr5")
> 
> # calculate cause-specific cumulative incidence, no truncation,
> # compare with Cuminc (also from mstate)
> ci <- Cuminc(aidssi$time, aidssi$status)
> sf <- survfit(Surv(Tstart,Tstop,status=="AIDS")~1, data=aidssi.w,
+               weight=weight.cens, subset=failcode=="AIDS")
> plot(sf, fun="event", mark.time=FALSE)
> lines(CI.1~time,data=ci,type="s",col="red")
> sf <- survfit(Surv(Tstart,Tstop,status=="SI")~1, data=aidssi.w,
+               weight=weight.cens, subset=failcode=="SI")
> plot(sf, fun="event", mark.time=FALSE)
> lines(CI.2~time,data=ci,type="s",col="red")
Error in eval(predvars, data, env) : object 'CI.2' not found
Calls: lines ... lines.formula -> eval -> eval -> <Anonymous> -> eval -> eval
Execution halted
Error(s) in re-building vignettes:
--- re-building 'Tutorial.Rnw' using Sweave
Loading required package: survival
Warning in max(ci$CI.2[idx0]) :
  no non-missing arguments to max; returning -Inf

Error: processing vignette 'Tutorial.Rnw' failed with diagnostics:
 chunk 59 (label = fig3do) 
Error in xy.coords(x, y) : 'x' and 'y' lengths differ

--- failed re-building 'Tutorial.Rnw'

SUMMARY: processing the following file failed:
  'Tutorial.Rnw'

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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/mutossGUI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/mwa.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Myrrixjars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Myrrix.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.4Mb
    libs   1.5Mb
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
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    CppCode   2.6Mb
    R         5.8Mb
    include   5.6Mb
    libs      1.8Mb
    tests     1.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
Running examples in 'NLMR-Ex.R' failed
The error most likely occurred in:

> ### Name: nlm_randomcluster
> ### Title: nlm_randomcluster
> ### Aliases: nlm_randomcluster
> 
> ### ** Examples
> 
> # simulate random clustering
> random_cluster <- nlm_randomcluster(ncol = 30, nrow = 30,
+                                      p = 0.4,
+                                      ai = c(0.25, 0.25, 0.5))
Loading required namespace: igraph
Failed with error:  'there is no package called 'igraph''
Error in .local(x, ...) : 
  you need to install the igraph package to be able to use this function
Calls: nlm_randomcluster -> <Anonymous> -> <Anonymous> -> .local
Execution halted
Running 'testthat.R' [38s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(NLMR)
  > 
  > test_check("NLMR")
  Failed with error:  'there is no package called 'igraph''
  -- 1. Error: (unknown) (@test_randomcluster.R#4)  ------------------------------
  you need to install the igraph package to be able to use this function
  Backtrace:
   1. base::suppressWarnings(...)
   3. NLMR::nlm_randomcluster(...)
   5. raster::clump(ranclumap, direction = neighbourhood, gaps = FALSE)
   6. raster:::.local(x, ...)
  
  == testthat results  ===========================================================
  [ OK: 63 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 1 ]
  1. Error: (unknown) (@test_randomcluster.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [45s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(NLMR)
  > 
  > test_check("NLMR")
  Failed with error:  'there is no package called 'igraph''
  -- 1. Error: (unknown) (@test_randomcluster.R#4)  ------------------------------
  you need to install the igraph package to be able to use this function
  Backtrace:
   1. base::suppressWarnings(...)
   3. NLMR::nlm_randomcluster(...)
   5. raster::clump(ranclumap, direction = neighbourhood, gaps = FALSE)
   6. raster:::.local(x, ...)
  
  == testthat results  ===========================================================
  [ OK: 63 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 1 ]
  1. Error: (unknown) (@test_randomcluster.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/nloptr.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/NLPutils.Rcheck/00install.out' for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.2Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    7.4Mb
    libs   2.7Mb
installed size is 38.9Mb
  sub-directories of 1Mb or more:
    extdata  38.9Mb
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 10.9Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    doc    2.6Mb
    help   2.5Mb
    libs   2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/ODB.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.
installed size is  5.4Mb
  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.
Package suggested but not available for checking: 'unix'
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    libs   20.0Mb
    share   9.7Mb
Error(s) in re-building vignettes:
--- re-building 'multifile_zip_resources.Rmd' using rmarkdown
Quitting from lines 23-30 (multifile_zip_resources.Rmd) 
Error: processing vignette 'multifile_zip_resources.Rmd' failed with diagnostics:
`resource` must be a 1 row data frame or a length 1 character vector.
--- failed re-building 'multifile_zip_resources.Rmd'

--- re-building 'multiple_resources_purrr.Rmd' using rmarkdown
--- finished re-building 'multiple_resources_purrr.Rmd'

--- re-building 'multisheet_resources.Rmd' using rmarkdown
New names:
* `` -> ...2
* `` -> ...3
* `` -> ...4
* `` -> ...5
* `` -> ...6
* ... and 30 more problems

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

New names:
* `` -> ...1
* `` -> ...2
* `` -> ...4
* `` -> ...5
* `` -> ...6
* ... and 79 more problems
New names:
* `` -> ...1
* `` -> ...2
* `` -> ...4
* `` -> ...5
* `` -> ...6
* ... and 33 more problems
--- finished re-building 'multisheet_resources.Rmd'

--- re-building 'opendatatoronto.Rmd' using rmarkdown
--- finished re-building 'opendatatoronto.Rmd'

--- re-building 'spatial_data.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

--- finished re-building 'spatial_data.Rmd'

SUMMARY: processing the following file failed:
  'multifile_zip_resources.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    R        2.5Mb
    libs     7.2Mb
    models   4.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/openNLPdata.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/openNLP.Rcheck/00install.out' for details.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/OpenStreetMap.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/openVA.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  6.0Mb
  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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/OSMscale.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'Rcplex'
Found the following significant warnings:
  likelihoods.cpp:479:38: warning: value computed is not used [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/outbreaker2.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   1.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/PairwiseD.Rcheck/00install.out' for details.
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/pbdBASE.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.
===================
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  7.1Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   2.7Mb
    libs      1.8Mb
Found the following significant warnings:
  l1pcahp.c:82:3: warning: statement with no effect [-Wunused-value]
  l1pcahp.c:92:3: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/pcaL1.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.3Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    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:11632 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11632 (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/petro.One.Rcheck/00install.out' for details.
File 'PhaseType/libs/i386/PhaseType.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'LJMA_arms.o'
File 'PhaseType/libs/x64/PhaseType.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'LJMA_arms.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.
Running 'testthat.R' [83s]
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
  Loading required package: bitops
  > 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 194441 bytes (189 KB)
  ==================================================
  downloaded 189 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: 2 | 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 194441 bytes (189 KB)
==================================================
downloaded 189 KB

Quitting from lines 258-272 (getting_started_phenocam_api.Rmd) 
Error: processing vignette 'getting_started_phenocam_api.Rmd' failed with diagnostics:
'url' must be a length-one character vector
--- failed re-building 'getting_started_phenocam_api.Rmd'

--- re-building 'phenocam_data_fusion.Rmd' using rmarkdown
Loading required package: rjson
Loading required package: RCurl
Loading required package: bitops
trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
Content type 'application/octet-stream' length 194441 bytes (189 KB)
==================================================
downloaded 189 KB

trying URL 'http://phenocam.sr.unh.edu/data/archive/oregonMP/ROI/oregonMP_EN_1000_3day.csv'
Content type 'application/octet-stream' length 261490 bytes (255 KB)
==================================================
downloaded 255 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
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   2.0Mb
    doc    3.0Mb
Running 'test-async.R' [18s]
  Running 'testthat.R' [8s]
Running the tests in 'tests/test-async.R' failed.
Complete output:
  > 
  > if (file.exists("async")) {
  +   library(testthat)
  +   library(pkgcache)
  +   test <- function() {
  +     package <- "pkgcache"
  +     env_test <- asNamespace("testthat")$env_test
  +     env_test$in_test <- TRUE
  +     env_test$package <- package
  +     on.exit({
  +       env_test$in_test <- FALSE
  +       env_test$package <- NULL
  +     })
  +     test_path <- "async"
  +     asNamespace("testthat")$test_package_dir(
  +       package = package, test_path = test_path,
  +       filter = NULL, reporter = "check")
  +   }
  +   test()
  + }
  -- 1. : when_any, multiple errors (@test-when-any.R#72)  -----------------------
  conditionMessage\(reason\$errors\[\[1\]\]\) does not match "bar".
  Actual value: "foo"
  
  -- 2. Error: when_any, multiple errors (@test-when-any.R#72)  ------------------
  no 'restart' 'continue_test' found
  Backtrace:
   1. pkgcache:::synchronise(do())
   4. base::invokeRestart("continue_test")
  
  == testthat results  ===========================================================
  [ OK: 644 | SKIPPED: 27 | WARNINGS: 3 | FAILED: 2 ]
  1. : when_any, multiple errors (@test-when-any.R#72) 
  2. Error: when_any, multiple errors (@test-when-any.R#72) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/PKgraph.Rcheck/00install.out' for details.
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/plfMA.Rcheck/00install.out' for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.4Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   1.6Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      6.4Mb
    data   2.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/polyPK.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/PortfolioEffectEstim.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/PortfolioEffectHFT.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.
Running examples in 'PPtreeViz-Ex.R' failed
The error most likely occurred in:

> ### Name: ENTROPYindex1D
> ### Title: ENTROPY PPindex
> ### Aliases: ENTROPYindex1D
> ### Keywords: projection pursuit
> 
> ### ** Examples
> 
> data(iris)
> ENTROPYindex1D(iris[,5],as.matrix(iris[,1,drop=FALSE]))
Error in .ENTROPYindex1D(factor(origclass), origdata, proj) : 
  function 'enterRNGScope' not provided by package 'Rcpp'
Calls: ENTROPYindex1D -> .ENTROPYindex1D
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   2.7Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc           9.2Mb
    htmlwidgets   2.5Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! File ended while scanning use of \end.
<inserted text> 
                \par 
<*> D:/temp/RtmpMzRjwD/Rd2pdf12a18716e3b8e/Rd2.tex
                                                  
! Emergency stop.
<*> D:/temp/RtmpMzRjwD/Rd2pdf12a18716e3b8e/Rd2.tex
                                                  
*** (job aborted, no legal \end found)

!  ==> Fatal error occurred, no output PDF file produced!
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'
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(projmgr)
  > 
  > test_check("projmgr")
  Error in parse(con, n = -1, srcfile = srcfile, encoding = "UTF-8") : 
    D:\RCompile\CRANpkg\local\4.0\projmgr.Rcheck\tests\testthat\setup-parse-issue.R:80:235: unexpected INCOMPLETE_STRING
  80:                                                                                                                                                 id = 19798371L, node_id = "MDQ6VXNlcjE5Nzk4Mzcx"
                                                                                                                                                                                                                                                 ^
  Calls: test_check ... source_test_setup -> source_dir -> lapply -> FUN -> parse
  Execution halted
Loading required package: Rcpp
Loading required package: rlang
Error: package or namespace load failed for 'prophet':
 .onLoad failed in loadNamespace() for 'prophet', details:
  call: sink(type = "output")
  error: invalid connection
In addition: Warning message:
In writeBin(dso@.CXXDSOMISC$dso_bin, libLFile) :
  problem writing to connection
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
Error in file(open = "w+", encoding = "UTF-8") : 
  cannot open the connection
Execution halted
Error in file(open = "w+", encoding = "UTF-8") : 
  cannot open the connection
Calls: <Anonymous> -> .load_package_quietly -> .try_quietly
Execution halted
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Error in file(open = "w+", encoding = "UTF-8") : 
  cannot open the connection
Calls: <Anonymous> -> .load_package_quietly -> .try_quietly
Execution halted
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
Error in file(open = "w+", encoding = "UTF-8") : 
  cannot open the connection
Calls: <Anonymous> -> .load_package_quietly -> .try_quietly
Execution halted
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Error: .onLoad failed in loadNamespace() for 'prophet', details:
  call: NULL
  error: .onLoad failed in loadNamespace() for 'callr', details:
  call: saveRDS(env, file = env_file, version = 2, compress = FALSE)
  error: error writing to connection
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   1.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.3Mb
Error(s) in re-building vignettes:
--- re-building 'CreatingDecoyDB.Rmd' using rmarkdown
--- finished re-building 'CreatingDecoyDB.Rmd'

--- re-building 'PeptideAnnotationwithProzor.Rmd' using rmarkdown
--- finished re-building 'PeptideAnnotationwithProzor.Rmd'

--- re-building 'TargetDecoyFDR_Example.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

pandoc.exe: TargetDecoyFDR_Example.html: hClose: resource exhausted (No space left on device)
Error: processing vignette 'TargetDecoyFDR_Example.Rmd' failed with diagnostics:
pandoc document conversion failed with error 1
--- failed re-building 'TargetDecoyFDR_Example.Rmd'

SUMMARY: processing the following file failed:
  'TargetDecoyFDR_Example.Rmd'

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/psData.Rcheck/00install.out' for details.
Warning in file(out, "wt") :
  cannot open file 'D:\temp\Rtmp4GnOrV\file2c21c73b35d2e/composite_d_matrix.R': No space left on device
Error in file(out, "wt") : cannot open the connection
Execution halted
Running massageExamples to create 'psychmeta-Ex.R' failed
Error in file(out, "wt") : cannot open the connection
Calls: <Anonymous> -> Rd2ex -> file
In addition: Warning message:
In file(out, "wt") :
  cannot open file 'D:\temp\Rtmp8IFTw7\file2dccc8323b76/composite_d_matrix.R': No space left on device
Execution halted
 NONE
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
!pdfTeX error: pdflatex.EXE: fwrite() failed
 ==> Fatal error occurred, no output PDF file produced!
Running massageExamples to create 'psychonetrics-Ex.R' failed
Error in file(out, "wt") : cannot open the connection
Calls: <Anonymous> -> Rd2ex -> file
In addition: Warning message:
In file(out, "wt") :
  cannot open file 'D:\temp\Rtmp4kwlZK\file58d42d966d17/dlvm1_family.R': No space left on device
Execution halted
 NONE
Rd conversion errors:
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Error in writeLines(x, con, useBytes = TRUE, ...) : 
  Error writing to connection:  No space left on device
Error(s) in re-building vignettes:
--- re-building 'raschtree.Rnw' using Sweave
Loading required package: partykit
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
Loading required package: psychotools

Error: processing vignette 'raschtree.Rnw' failed with diagnostics:
 chunk 8 (label = fit_raschtree_cache) 
Error in save(my_first_raschtree, file = "raschtree-spisa.rda") : 
  error writing to connection

--- failed re-building 'raschtree.Rnw'

SUMMARY: processing the following file failed:
  'raschtree.Rnw'

Error: Vignette re-building failed.
Execution halted
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Running massageExamples to create 'psych-Ex.R' failed
Error in writeLines(x, con, useBytes = TRUE, ...) : 
  Error writing to connection:  No space left on device
Calls: <Anonymous> ... Rd2ex -> render -> of0 -> of1 -> WriteLines -> writeLines
In addition: Warning message:
In close.connection(con) :
  Problem closing connection:  No space left on device
Execution halted
 NONE
Running massageExamples to create 'psyosphere-Ex.R' failed
Error in file(out, "wt") : cannot open the connection
Calls: <Anonymous> -> Rd2ex -> file
In addition: Warning messages:
1: In close.connection(con) :
  Problem closing connection:  No space left on device
2: In file(out, "wt") :
  cannot open file 'D:\temp\RtmpWOlY4e\file2e1bc2f06f89/about_demos.R': No space left on device
Execution halted
 NONE
Running examples in 'pterrace-Ex.R' failed
The error most likely occurred in:

> ### Name: three_circle_dat
> ### Title: Point cloud of three circles of different size and point density
> ### Aliases: three_circle_dat
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> # load three circle data
> data(three_circle_dat)
> 
> # input variables
> Xlim <- c(-4,12)
> Ylim <- c(-4,9)
> lim <- cbind(Xlim, Ylim)
> by <- 0.2
> spseq <- seq(0.01,1.5,length.out = 10)
> 
> # compute persistence terrace
> three_circle_pt <- computept(three_circle_dat,sp=spseq,lim=lim,by=by)
> 
> ## Not run: 
> ##D # compute persistence terrace with parallel option
> ##D spseq <- seq(0.01,1.5,length.out = 30)
> ##D three_circle_pt <- computept(three_circle_dat,sp=spseq,lim=lim,by=by,par=TRUE)
> ## End(Not run)
> 
> # draw terrace area plot
> terracearea(three_circle_pt,dimension=1)
> # draw persistence terrace, satellite view
> plotpt(three_circle_pt,dimension=1)
Warning in file.append(to[okay], from[okay]) :
  write error during file append
Error in writeLines(html, con, useBytes = TRUE) : 
  Error writing to connection:  No space left on device
Calls: <Anonymous> ... print.htmlwidget -> html_print -> save_html -> writeLines
Execution halted
Error(s) in re-building vignettes:
--- re-building 'Introduction_to_the_ptest_package.Rmd' using rmarkdown
Warning in (function (filename = "Rplot%03d.png", width = 480, height = 480,  :
  unable to open file 'D:\temp\RtmpMhH91O\file325c445734160' for writing
Warning in (function (filename = "Rplot%03d.png", width = 480, height = 480,  :
  opening device failed
Quitting from lines 64-70 (Introduction_to_the_ptest_package.Rmd) 
Error: processing vignette 'Introduction_to_the_ptest_package.Rmd' failed with diagnostics:
unable to start png() device
--- failed re-building 'Introduction_to_the_ptest_package.Rmd'
Rd conversion errors:
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in file(out, "wt") :
  cannot open file 'D:\temp\RtmpIN1h1y\ltx24403600437/ptmixed.tex': No space left on device
Error in file(out, "wt") : cannot open the connection
Running massageExamples to create 'pts2polys-Ex.R' failed
Error in file(outFile, "wt") : cannot open the connection
Calls: <Anonymous> -> massageExamples -> file
In addition: Warning messages:
1: In close.connection(con) :
  Problem closing connection:  No space left on device
2: In file(outFile, "wt") :
  cannot open file 'pts2polys-Ex.R': No space left on device
Execution halted
 NONE
Error(s) in re-building vignettes:
--- re-building 'ptstem.Rmd' using rmarkdown
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in file(con, "w") :
  cannot open file 'ptstem.knit.md': No space left on device
Error: processing vignette 'ptstem.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'ptstem.Rmd'

SUMMARY: processing the following file failed:
  'ptstem.Rmd'

Error: Vignette re-building failed.
Execution halted
Rd conversion errors:
Warning in file(out, "wt") :
  cannot open file 'D:\temp\Rtmpe2imSP\ltx287b8b405acd/overstemming_index.tex': No space left on device
Error in file(out, "wt") : cannot open the connection
Running massageExamples to create 'ptsuite-Ex.R' failed
Error in file(out, "wt") : cannot open the connection
Calls: <Anonymous> -> Rd2ex -> file
In addition: Warning message:
In file(out, "wt") :
  cannot open file 'D:\temp\Rtmp8kya1t\file1df781cda62ab/alpha_ls.R': No space left on device
Execution halted
 NONE
Data.Rd: Sections \title, and \name must exist and be unique in Rd files
PosteriorStatistics.Rd: Sections \title, and \name must exist and be unique in Rd files
WhichCols.Rd: Sections \title, and \name must exist and be unique in Rd files
checkConvergence.Rd: Sections \title, and \name must exist and be unique in Rd files
Error writing to connection:  No space left on device
createGroupsSim.Rd: Sections \title, and \name must exist and be unique in Rd files
createOrthogonalX.Rd: Sections \title, and \name must exist and be unique in Rd files
ptycho-package.Rd: Sections \title, and \name must exist and be unique in Rd files
Error writing to connection:  No space left on device
problems found in 'Data.Rd', 'PosteriorStatistics.Rd', 'WhichCols.Rd', 'checkConvergence.Rd', 'createData.Rd', 'createGroupsSim.Rd', 'createOrthogonalX.Rd', 'ptycho-package.Rd', 'ptycho.Rd'
Running massageExamples to create 'ptycho-Ex.R' failed
Error in file(out, "wt") : cannot open the connection
Calls: <Anonymous> -> Rd2ex -> file
In addition: Warning messages:
1: In close.connection(con) :
  Problem closing connection:  No space left on device
2: In file(out, "wt") :
  cannot open file 'D:\temp\RtmpOq6Bi1\file205f85a9852c4/checkConvergence.R': No space left on device
Execution halted
 NONE
Rd conversion errors:
Error in writeLines(readLines(f), outcon) : 
  Error writing to connection:  No space left on device
pub_guess_publisher.Rd: Sections \title, and \name must exist and be unique in Rd files
pub_tabularize.Rd: Sections \title, and \name must exist and be unique in Rd files
problems found in 'pub_guess_publisher.Rd', 'pub_tabularize.Rd'
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in file(out, "wt") :
  cannot open file 'D:\temp\RtmpuutYlO\file9918556d6b92/pub_providers.R': No space left on device
Error in file(out, "wt") : cannot open the connection
Execution halted
Running massageExamples to create 'pubchunks-Ex.R' failed
Error in file(out, "wt") : cannot open the connection
Calls: <Anonymous> -> Rd2ex -> file
In addition: Warning messages:
1: In close.connection(con) :
  Problem closing connection:  No space left on device
2: In close.connection(con) :
  Problem closing connection:  No space left on device
3: In file(out, "wt") :
  cannot open file 'D:\temp\RtmpUnec3e\file2b7c44db968ce/pub_providers.R': No space left on device
Execution halted
 NONE
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/pvar.Rcheck/00install.out'* DONE
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/pwr.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/pwt8.Rcheck/00install.out'* DONE
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/pwt9.Rcheck/00install.out'* DONE
installed size is  7.3Mb
    data   7.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/qap.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    gui          1.1Mb
    staticdocs   3.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/qCBA.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/qcc.Rcheck/00install.out' for details.
*
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/qsub.Rcheck/00install.out'* DONE
Package required but not available: 'qtbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   1.3Mb
    libs   3.1Mb
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.
Error in load(p, envir = env) : 
    bad restore file magic number (file may be corrupted) -- no data loaded
  Calls: <Anonymous> ... suppressPackageStartupMessages -> withCallingHandlers -> load
  In addition: Warning messages:
  1: In file.copy(files, cpdir) :
    problem copying .\data\riboflavin.rda to D:\temp\RtmpOMeZAX\cp1fd54311a593e\riboflavin.rda: No space left on device
  2: file 'chemometrics.rda' has magic number ''
    Use of save versions prior to 2 is deprecated 
  Execution halted
Running massageExamples to create 'qut-Ex.R' failed
Error in file(out, "wt") : cannot open the connection
Calls: <Anonymous> -> Rd2ex -> file
In addition: Warning messages:
1: In close.connection(con) :
  Problem closing connection:  No space left on device
2: In file(out, "wt") :
  cannot open file 'D:\temp\RtmpIlugXN\file77dc5b5215d6/internetAd.R': No space left on device
Execution halted
 NONE
Rd conversion errors:
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in file(out, "wt") :
  cannot open file 'D:\temp\Rtmpi6p42Y\ltx27c7017d671aa/internetAd.tex': No space left on device
Error in file(out, "wt") : cannot open the connection
Running massageExamples to create 'qwraps2-Ex.R' failed
Error in file(out, "wt") : cannot open the connection
Calls: <Anonymous> -> Rd2ex -> file
In addition: Warning messages:
1: In close.connection(con) :
  Problem closing connection:  No space left on device
2: In file(out, "wt") :
  cannot open file 'D:\temp\RtmpYX68Vi\file27dc870914fd9/file_check.R': No space left on device
Execution halted
 NONE
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
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 10.2Mb
  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 11.5Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   6.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rapidraker.Rcheck/00install.out' for details.
installed size is  7.9Mb
  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  7.8Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    etc    1.9Mb
    po     1.2Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   3.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Rbgs.Rcheck/00install.out' for details.
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/4.0/Rblpapi.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rCBA.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rcdklibs.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rcdk.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rChoiceDialogs.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RcmdrPlugin.BiclustGUI.Rcheck/00install.out' for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   2.9Mb
    po    2.1Mb
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  8.8Mb
  sub-directories of 1Mb or more:
    include   6.1Mb
    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  8.7Mb
  sub-directories of 1Mb or more:
    include   1.6Mb
    lib       3.9Mb
    libs      2.9Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      1.7Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    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  6.3Mb
  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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Rdroolsjars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Rdrools.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   2.6Mb
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.
Running 'testthat.R' [51s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(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(package = "recipes")
  1 package is needed for this model and is not installed. (NMF). Start a clean R session then run: install.packages("NMF")-- 1. Error: quasiquotation (@test_slice.R#40)  --------------------------------
  `call` must be a call
  
  == testthat results  ===========================================================
  [ OK: 1394 | SKIPPED: 7 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: quasiquotation (@test_slice.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.5Mb
  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
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   2.3Mb
Package which this enhances but not available for checking: 'Rcplex'
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc    8.6Mb
    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/REPPlab.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/reshapeGUI.Rcheck/00install.out' for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RFreak.Rcheck/00install.out' for details.
installed size is 80.3Mb
  sub-directories of 1Mb or more:
    gdal       3.9Mb
    libs      68.7Mb
    pictures   1.3Mb
    proj       5.0Mb
Running examples in 'RGENERATEPREC-Ex.R' failed
The error most likely occurred in:

> ### Name: CCGamma
> ### Title: This function extends 'continuity_ratio' and adds the
> ###   corresponding gaussian correlation matrix for no-precipitation
> ###   occurence.
> ### Aliases: CCGamma
> 
> ### ** Examples
> 
> 
> data(trentino)
> 
> year_min <- 1961
> year_max <- 1990
> origin <- paste(year_min,1,1,sep="-")
> 
> period <- PRECIPITATION$year>=year_min & PRECIPITATION$year<=year_max
> station <- names(PRECIPITATION)[!(names(PRECIPITATION) %in% c("day","month","year"))]
> prec_mes <- PRECIPITATION[period,station]  
> 
> ## removing nonworking stations (e.g. time series with NA)
> accepted <- array(TRUE,length(names(prec_mes)))
> names(accepted) <- names(prec_mes)
> for (it in names(prec_mes)) {
+ 		 accepted[it]  <- (length(which(!is.na(prec_mes[,it])))==length(prec_mes[,it]))
+ }
> 
> prec_mes <- prec_mes[,accepted]
> ## the dateset is reduced!!! 
> prec_mes <- prec_mes[,1:2]
> 
> CCGamma <- CCGamma(data=prec_mes,lag=0,tolerance=0.001,only.matrix=FALSE)
lag
0
Error in 1:nrow(out$nooccurence_correlation) : argument of length 0
Calls: CCGamma
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rggobi.Rcheck/00install.out' for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc     3.6Mb
    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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rGroovy.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RGtk2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RH2.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'rinatVignette.Rmd' using rmarkdown
Quitting from lines 100-102 (rinatVignette.Rmd) 
Error: processing vignette 'rinatVignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'rinatVignette.Rmd'

SUMMARY: processing the following file failed:
  'rinatVignette.Rmd'

Error: Vignette re-building failed.
Execution halted
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RJDBC.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RJDemetra.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rjdqa.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rJPSGCS.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RJSDMX.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rJython.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rkafkajars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rkafka.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RKEAjars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RKEA.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Rknots.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rlang.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Mallows: no visible global function definition for 'runif'
Mallows: no visible global function definition for 'x11'
Mallows: no visible global function definition for 'plot'
Mallows: no visible global function definition for 'dev.off'
UpdateLambda: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  dev.off plot runif uniroot x11
Consider adding
  importFrom("grDevices", "dev.off", "x11")
  importFrom("graphics", "plot")
  importFrom("stats", "runif", "uniroot")
to your NAMESPACE file.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    rmd   8.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rmcfs.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   2.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RMOAjars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RMOA.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rMouse.Rcheck/00install.out' for details.
Running examples in 'RMRAINGEN-Ex.R' failed
The error most likely occurred in:

> ### Name: CCGamma
> ### Title: This function extends 'continuity_ratio' and adds the
> ###   corresponding gaussian correlation matrix for no-precipitation
> ###   occurence.
> ### Aliases: CCGamma
> 
> ### ** Examples
> 
> library(RMAWGEN)
> data(trentino)
> 
> year_min <- 1961
> year_max <- 1990
> origin <- paste(year_min,1,1,sep="-")
> 
> period <- PRECIPITATION$year>=year_min & PRECIPITATION$year<=year_max
> station <- names(PRECIPITATION)[!(names(PRECIPITATION) %in% c("day","month","year"))]
> prec_mes <- PRECIPITATION[period,station]
> 
> ## removing nonworking stations (e.g. time series with NA)
> accepted <- array(TRUE,length(names(prec_mes)))
> names(accepted) <- names(prec_mes)
> for (it in names(prec_mes)) {
+ 		 accepted[it]  <- (length(which(!is.na(prec_mes[,it])))==length(prec_mes[,it]))
+ }
> 
> prec_mes <- prec_mes[,accepted]
> ## the dateset is reduced!!!
> prec_mes <- prec_mes[,1:2]
> 
> CCGamma <- CCGamma(data=prec_mes,lag=0,tolerance=0.001,only.matrix=FALSE)
[1] "lag"
[1] 0
Error in if (is.na(p0_v2)) { : argument is of length zero
Calls: CCGamma -> omega_inv -> omega
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RNCBIEUtilsLibs.Rcheck/00install.out' for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RNetLogo.Rcheck/00install.out' for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      5.6Mb
'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  6.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.3Mb
    libs   2.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    libs    1.7Mb
    tests   1.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rpcdsearch.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
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  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RQDA.Rcheck/00install.out' for details.
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    libs  27.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rrepast.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'rscala.Rnw' using Sweave
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


Error: processing vignette 'rscala.Rnw' failed with diagnostics:
 chunk 7 (label = Instantiate a bridge for this document) 
Error in scalaConnect(details) : Error in scalaConfig(FALSE): 

<<<<<<<<<<
<<<<<<<<<<
<<<<<<<<<<

Scala is not found!  Please run 'rscala::scalaConfig(download="scala")'

>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>



--- failed re-building 'rscala.Rnw'

SUMMARY: processing the following file failed:
  'rscala.Rnw'

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RSCAT.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RSDA.Rcheck/00install.out' for details.
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rsgcc.Rcheck/00install.out' for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.2Mb
    libs  17.8Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rstap.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rsubgroup.Rcheck/00install.out' for details.
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  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rSymPy.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Rtextrankr.Rcheck/00install.out' for details.
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RtutoR.Rcheck/00install.out' for details.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RunuranGUI.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Package suggested but not available for checking: 'gpuR'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rviewgraph.Rcheck/00install.out' for details.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs      8.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RWekajars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RWeka.Rcheck/00install.out' for details.
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'.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RxnSim.Rcheck/00install.out' for details.
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  7.9Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.3Mb
    libs   1.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/SanzCircos.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/SBRect.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/scagnostics.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.
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  5.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   3.5Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R   7.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   2.5Mb
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
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   1.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/SeqGrapheR.Rcheck/00install.out' for details.
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.
installed size is 94.9Mb
  sub-directories of 1Mb or more:
    doc     12.0Mb
    gdal     3.9Mb
    libs    70.1Mb
    proj     5.0Mb
    sqlite   1.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.0Mb
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  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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/SimuChemPC.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   2.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/sjdbc.Rcheck/00install.out' for details.
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/smartR.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.6Mb
Found the following significant warnings:
  createPosDef.cpp:84:13: warning: statement has no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/smoothSurv.Rcheck/00install.out' for details.
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 11.7Mb
  sub-directories of 1Mb or more:
    data  11.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.6Mb
    libs   2.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/sonicscrewdriver.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
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
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    R      5.2Mb
    doc    4.9Mb
    help   5.2Mb
    libs   1.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/spatsurv.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
    libs   2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/spcosa.Rcheck/00install.out' for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   1.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/SqlRender.Rcheck/00install.out' for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/stacomiR.Rcheck/00install.out' for details.
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 10.1Mb
  sub-directories of 1Mb or more:
    include   8.9Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    doc  10.3Mb
    nc    4.5Mb
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 'ggthemes'
--- 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: 1.3-2 
 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'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/streamMOA.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.8Mb
Found the following significant warnings:
  icu61/i18n/decNumber.cpp:1524:13: warning: array subscript is above array bounds [-Warray-bounds]
  icu61/i18n/decNumber.cpp:2963:30: warning: array subscript is above array bounds [-Warray-bounds]
  icu61/i18n/decNumber.cpp:2963:43: warning: array subscript is above array bounds [-Warray-bounds]
  icu61/i18n/decNumber.cpp:2980:30: warning: array subscript is above array bounds [-Warray-bounds]
  icu61/i18n/decNumber.cpp:2980:43: warning: array subscript is above array bounds [-Warray-bounds]
See 'd:/Rcompile/CRANpkg/local/4.0/stringi.Rcheck/00install.out' for details.
installed size is 36.1Mb
  sub-directories of 1Mb or more:
    libs  35.3Mb
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(subprocess)
  > 
  > # See for more details:
  > # https://github.com/hadley/testthat/issues/144
  > # https://github.com/hadley/testthat/issues/86
  > # https://github.com/luckyrandom/cmaker/commit/b85813ac2b7aef69932eca8fbb4fa0ec225e0af0
  > #
  > # When R CMD check runs tests, it sets R_TESTS. When the tests
  > # themeselves run R CMD xxxx, as is the case with the tests in
  > # devtools, having R_TESTS set causes errors because it confuses
  > # the R subprocesses. Unsetting it here avoids those problems.
  > #
  > # We need this because we spawn child R processes and they get very
  > # confused if this variable (R_TESTS) is present in their environment.
  > Sys.setenv("R_TESTS" = "")
  > 
  > test_check("subprocess")
  Keine Instanzen verfgbar.
  -- 1. Failure: child process is terminated in Windows (@test-termination.R#33)  
  `child_id` has length 0, not length 1.
  
  -- 2. Error: child process is terminated in Windows (@test-termination.R#34)  --
  `pid` must be a single integer value
  Backtrace:
   1. testthat::expect_true(process_exists(child_id))
   4. subprocess::process_exists(child_id)
   5. base::isTRUE(.Call("C_process_exists", as.integer(x)))
  
  == testthat results  ===========================================================
  [ OK: 58 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: child process is terminated in Windows (@test-termination.R#33) 
  2. Error: child process is terminated in Windows (@test-termination.R#34) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/subspace.Rcheck/00install.out' for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    help   1.0Mb
    libs   1.7Mb
installed size is 15.7Mb
  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.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Different type kinds at (1)
  Warning: GNU Extension: initialization of common block variable 'iset' in DATA statement at (1)
  Warning: GNU Extension: Variable 'iset' at (1) is in COMMON but only in BLOCK DATA initialization is allowed
  Warning: GNU Extension: Missing comma at (1)
See 'd:/Rcompile/CRANpkg/local/4.0/SWATmodel.Rcheck/00install.out' for details.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
Warning in value[[3L]](cond) : Unable to populate the BiocDevel object
Warning in value[[3L]](cond) : Unable to populate the BiocDevel object
Warning in value[[3L]](cond) : Unable to populate the BiocDevel object
Warning in value[[3L]](cond) : Unable to populate the BiocDevel object
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Warning in value[[3L]](cond) : Unable to populate the BiocDevel object
Warning in value[[3L]](cond) : Unable to populate the BiocDevel object
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Warning in value[[3L]](cond) : Unable to populate the BiocDevel object
Warning in value[[3L]](cond) : Unable to populate the BiocDevel object
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Warning in value[[3L]](cond) : Unable to populate the BiocDevel object
Warning in value[[3L]](cond) : Unable to populate the BiocDevel object
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.
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/table1xls.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/tabulizerjars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/tabulizer.Rcheck/00install.out' for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.9Mb
    libs   1.5Mb
Error(s) in re-building vignettes:
--- re-building 'tealeaves-intermediate.Rmd' using rmarkdown
--- finished re-building 'tealeaves-intermediate.Rmd'

Warning in file(con, "r") :
  cannot open file 'D:\temp\RtmpEPNppn\file2b0050c8bc4': Permission denied
Error in file(con, "r") : cannot open the connection
Calls: <Anonymous> -> readLines -> file
Execution halted
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  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.5Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    3.6Mb
    libs   2.1Mb
Running examples in 'text2vec-Ex.R' failed
The error most likely occurred in:

> ### Name: itoken
> ### Title: Iterators (and parallel iterators) over input objects
> ### Aliases: itoken itoken.list itoken.character itoken.iterator
> ###   itoken_parallel itoken_parallel.character
> ###   itoken_parallel.ifiles_parallel itoken_parallel.list
> 
> ### ** Examples
> 
> data("movie_review")
> txt = movie_review$review[1:100]
> ids = movie_review$id[1:100]
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10)
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10, ids = ids)
> # Example of stemming tokenizer
> # stem_tokenizer =function(x) {
> #   lapply(word_tokenizer(x), SnowballC::wordStem, language="en")
> # }
> #------------------------------------------------
> # PARALLEL iterators
> #------------------------------------------------
> library(text2vec)
> 
> N_WORKERS = 1 # change 1 to number of cores in parallel backend
> if(require(doParallel)) registerDoParallel(N_WORKERS)
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> data("movie_review")
> it = itoken_parallel(movie_review$review[1:100], n_chunks = N_WORKERS)
> system.time(dtm <- create_dtm(it, hash_vectorizer(2**16), type = 'dgTMatrix'))
   user  system elapsed 
   0.01    0.00    2.01 
> 
> 
> 
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11763 (sockconn)
Execution halted
Running examples in 'text2vec-Ex.R' failed
The error most likely occurred in:

> ### Name: itoken
> ### Title: Iterators (and parallel iterators) over input objects
> ### Aliases: itoken itoken.list itoken.character itoken.iterator
> ###   itoken_parallel itoken_parallel.character
> ###   itoken_parallel.ifiles_parallel itoken_parallel.list
> 
> ### ** Examples
> 
> data("movie_review")
> txt = movie_review$review[1:100]
> ids = movie_review$id[1:100]
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10)
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10, ids = ids)
> # Example of stemming tokenizer
> # stem_tokenizer =function(x) {
> #   lapply(word_tokenizer(x), SnowballC::wordStem, language="en")
> # }
> #------------------------------------------------
> # PARALLEL iterators
> #------------------------------------------------
> library(text2vec)
> 
> N_WORKERS = 1 # change 1 to number of cores in parallel backend
> if(require(doParallel)) registerDoParallel(N_WORKERS)
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> data("movie_review")
> it = itoken_parallel(movie_review$review[1:100], n_chunks = N_WORKERS)
> system.time(dtm <- create_dtm(it, hash_vectorizer(2**16), type = 'dgTMatrix'))
   user  system elapsed 
   0.02    0.00    2.13 
> 
> 
> 
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11811 (sockconn)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/textmining.Rcheck/00install.out' for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.1Mb
Found the following significant warnings:
  lmdb/mdb.c:1734:2: warning: array subscript is above array bounds [-Warray-bounds]
See 'd:/Rcompile/CRANpkg/local/4.0/thor.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/tibble.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/tidyselect.Rcheck/00install.out' for details.
Running examples in 'TITAN2-Ex.R' failed
The error most likely occurred in:

> ### Name: plot_taxa_ridges
> ### Title: Taxon change point ridge plots
> ### Aliases: plot_taxa_ridges
> 
> ### ** Examples
> 
> 
> data(glades.titan)
> 
> 
> # basic usage
> plot_taxa_ridges(glades.titan)
There are 90 indicator taxa of 90 possible for plotting
Number of Decreasers = 41
Number of Increasers = 49
Error in stats::approxfun(x_in, lab_in[, 1]) : 
  need at least two non-NA values to interpolate
Calls: plot_taxa_ridges ... seq_gradient_pal -> gradient_n_pal -> colour_ramp -> <Anonymous>
Execution halted
Running 'mv_genz.R' [3s]
  Running 'mv_tlr.R' [5s]
Running the tests in 'tests/mv_tlr.R' failed.
Complete output:
  > library(tlrmvnmvt)
  > library(mvtnorm)
  > n = 260
  > a = rep(-10, n)
  > b = rnorm(n, 5, 2)
  > m = 16
  > gridDim = 60
  > epsl = 1e-3
  > vec1 = 1:gridDim
  > vec2 = rep(1, gridDim)
  > geom = cbind(kronecker(vec1, vec2), kronecker(vec2, vec1))
  > geom = geom / gridDim
  > geom = geom[sample(c(1:(gridDim^2)), n, FALSE), 1:2]
  > beta = 0.3
  > idx = zorder(geom)
  > geom = geom[idx, 1:2]
  > a = a[idx]
  > b = b[idx]
  > distM = as.matrix(dist(geom))
  > covM = exp(-distM / beta)
  > val1 = pmvnorm(a, b, sigma = covM)[[1]]
  > val2 = pmvn.tlr(a, b, 0, covM, NULL, NULL, NULL, FALSE, m, epsl)[[1]]
  Error in tlrmvn_internal(lower, upper, sigma, uselog2, m, epsl, N) : 
    TLR Cholesky failed. Either the original covariance matrix is not positive definite or the error in Cholesky factorization is significant
  Calls: pmvn.tlr -> tlrmvn_internal
  Execution halted
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/tm.plugin.webmining.Rcheck/00install.out' for details.
Packages suggested but not available for checking:
  'Rcampdf', 'Rpoppler', 'tm.lexicon.GeneralInquirer'
Package unavailable to check Rd xrefs: 'Rpoppler'
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  6.3Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   1.5Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs  11.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/TSsdmx.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/tweenr.Rcheck/00install.out' for details.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc     6.3Mb
    ubinc   1.9Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc         6.9Mb
    dummydata   1.4Mb
    libs        4.2Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    8.4Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.6Mb
    libs   2.3Mb
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
Found the following significant warnings:
  gen_uuid.c:309:11: warning: ordered comparison of pointer with integer zero [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0/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 24.0Mb
  sub-directories of 1Mb or more:
    libs  23.2Mb
installed size is 79.1Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    gdal      3.8Mb
    libs     68.8Mb
    proj      5.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/vctrs.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R   2.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/venneuler.Rcheck/00install.out' for details.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      3.8Mb
    doc    1.2Mb
    help   2.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/VIMGUI.Rcheck/00install.out' for details.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc           4.3Mb
    docjs         1.3Mb
    htmlwidgets   3.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/vmsbase.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/vortexR.Rcheck/00install.out' for details.
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  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   5.6Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    client   8.9Mb
    doc      1.0Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/WMCapacity.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/wordnet.Rcheck/00install.out' for details.
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 significant warnings:
  assp/dsputils.c:414:13: warning: value computed is not used [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/wrassp.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/x12GUI.Rcheck/00install.out' for details.
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  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/XLConnectJars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/XLConnect.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/xlsxjars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/xlsx.Rcheck/00install.out' for details.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    exampleData   1.4Mb
    examples      4.5Mb
    libs          4.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    include   3.4Mb
    libs      1.6Mb
Found the following significant warnings:
  emitter.c:28:6: warning: value computed is not used [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/yaml.Rcheck/00install.out' for details.
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   4.0Mb
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(AHR)
  Loading required package: survival
  >      
  > test_check("AHR")
  -- 1. Error: single stratum wkm estimate reduces to Kaplan-Meier estimator (@tes
  zero non-NA points
  Backtrace:
   1. stats::approxfun(...)
  
  == testthat results  ===========================================================
  [ OK: 12 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: single stratum wkm estimate reduces to Kaplan-Meier estimator (@test-wkm.R#32) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Found the following significant warnings:
  ADAPTgdwm.c:136:73: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/AMORE.Rcheck/00install.out' for details.
installed size is  6.8Mb
  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  6.8Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   2.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/AntAngioCOOL.Rcheck/00install.out' for details.
installed size is 73.7Mb
  sub-directories of 1Mb or more:
    gdal   3.8Mb
    libs  69.4Mb
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs  13.3Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/arulesNBMiner.Rcheck/00install.out' for details.
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    bin   22.9Mb
    misc   2.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/aslib.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/AtelieR.Rcheck/00install.out' for details.
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/AWR.Athena.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/AWR.Kinesis.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/AWR.KMS.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/AWR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/awsjavasdk.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BACA.Rcheck/00install.out' for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   2.3Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Package suggested but not available for checking: 'mzR'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BALD.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/bartMachineJARs.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/bartMachine.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   2.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BASiNET.Rcheck/00install.out' for details.
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(BatchGetSymbols)
  Loading required package: rvest
  Loading required package: xml2
  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
  
  
  > 
  > test_check("BatchGetSymbols")
  -- 1. Error: (unknown) (@test_BatchGetSymbols.R#12)  ---------------------------
  Argument 1 must have names
  Backtrace:
   1. BatchGetSymbols::BatchGetSymbols(...)
   2. dplyr::bind_rows(purrr::map(my.l, 1))
   3. dplyr:::bind_rows_(x, .id)
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test_BatchGetSymbols.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/bayesCL.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/bayesDem.Rcheck/00install.out' for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs   2.7Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   4.4Mb
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs  25.3Mb
Found the following significant warnings:
  mcmc.c:337:4: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BayHap.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/bdl.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BEACH.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/beadarrayMSV.Rcheck/00install.out' for details.
installed size is 150.1Mb
  sub-directories of 1Mb or more:
    include  149.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BiBitR.Rcheck/00install.out' for details.
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/bigalgebra.Rcheck/00install.out' for details.
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  6.1Mb
  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
Package suggested but not available for checking: 'BiocVersion'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Biocomb.Rcheck/00install.out' for details.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   8.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BioMedR.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  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/boilerpipeR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BonEV.Rcheck/00install.out' for details.
installed size is 62.1Mb
  sub-directories of 1Mb or more:
    include   8.5Mb
    lib      53.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BPEC.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Brundle.Rcheck/00install.out' for details.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   6.6Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
Found the following significant warnings:
  rulebasedmodels.c:65:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:75:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:76:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:115:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:128:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:143:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:151:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:161:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:162:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:178:3: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/C50.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/CADStat.Rcheck/00install.out' for details.
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/causalMGM.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   2.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
Running 'run.cec.tests.R' [4s]
Running the tests in 'tests/run.cec.tests.R' failed.
Complete output:
  > CEC:::run.cec.tests()
  Test: Clustering 
  ----  test.clustering.four.gaussians: OK
  Test: Covariance calculation 
  ----  test.covariances.after.point.movements.between.clusters: OK
  ----  test.covariances.before.first.iteraion: OK
  Test: Energy calculation (ball1) 
  ----  test.type.all: OK
  ----  test.type.covariance: OK
  ----  test.type.diagonal: OK
  ----  test.type.eigenvalues: OK
  ----  test.type.fixedr: OK
  ----  test.type.mean: OK
  ----  test.type.spherical: OK
  ----  test.type.spherical.cluster.removing: OK
  Test: Energy calculation (mouseset1) 
  ----  test.type.all: OK
  ----  test.type.covariance: OK
  ----  test.type.diagonal: OK
  ----  test.type.fixedr: OK
  ----  test.type.spherical: OK
  Test: energy calculation (various data sets) 
  ----  test.type.covariance: OK
  ----  test.type.diagonal.spherical.mixture: OK
  ----  test.type.eigenvalues.all.fixedr.mixture: OK
  ----  test.type.fixedr.mixture: OK
  ----  test.type.mean.two.gaussians: OK
  ----  test.type.spherical.one.cluster.removed: OK
  Test: Split method 
  ----  test.should.limit.split.to.4.cluster: OK
  ----  test.should.split.to.3.cluster.fixed.mean: FAILED
  Warning:  Numeric values are different: expected: 3 , actuall: 1 , difference: 2
  ----  test.should.split.to.4.cluster: OK
  ----  test.should.split.to.7.cluster: OK
  Test: Variable centers number 
  ----  test.should.use.1.cluster: OK
  ----  test.should.use.2.cluster: OK
  ----  test.should.use.3.cluster: OK
  Error in CEC:::run.cec.tests() : One or more tests failed.
  Execution halted
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/ChoR.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/CITAN.Rcheck/00install.out' for details.
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/clusterfly.Rcheck/00install.out' for details.
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/CollapsABEL.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/collUtils.Rcheck/00install.out' for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/corehunter.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/coreNLP.Rcheck/00install.out' for details.
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'
Error(s) in re-building vignettes:
--- re-building 'corrgram_cov2cor.Rmd' using rmarkdown
--- finished re-building 'corrgram_cov2cor.Rmd'

--- re-building 'corrgram_examples.Rmd' using rmarkdown
Quitting from lines 231-248 (corrgram_examples.Rmd) 
Error: processing vignette 'corrgram_examples.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'corrgram_examples.Rmd'

SUMMARY: processing the following file failed:
  'corrgram_examples.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/CovSelHigh.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'cowsay_tutorial.Rmd' using rmarkdown
Quitting from lines 130-135 (cowsay_tutorial.Rmd) 
Error: processing vignette 'cowsay_tutorial.Rmd' failed with diagnostics:
If you're on Windows, you can't use:
anxiouscat
fish
grumpycat
longcat
longtailcat
mushroom
shortcat
signbunny
stretchycat
--- failed re-building 'cowsay_tutorial.Rmd'

SUMMARY: processing the following file failed:
  'cowsay_tutorial.Rmd'

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/cplexAPI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Crossover.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/CRPClustering.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/CrypticIBDcheck.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/CSFA.Rcheck/00install.out' for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    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
Found the following significant warnings:
  rulebasedmodels.c:95:3: warning: statement with no effect [-Wunused-value]
  rulebasedmodels.c:105:3: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Cubist.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    libs   2.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/CytobankAPIstats.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/DatabaseConnectorJars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/DatabaseConnector.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/DataClean.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/DataEntry.Rcheck/00install.out' for details.
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/DataLoader.Rcheck/00install.out' for details.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   5.5Mb
Found the following significant warnings:
  assign.c:882:107: warning: too many arguments for format [-Wformat-extra-args]
  assign.c:889:107: warning: too many arguments for format [-Wformat-extra-args]
  assign.c:895:107: warning: too many arguments for format [-Wformat-extra-args]
  forder.c:503:10: warning: too many arguments for format [-Wformat-extra-args]
  forder.c:607:16: warning: too many arguments for format [-Wformat-extra-args]
  fread.c:418:36: warning: too many arguments for format [-Wformat-extra-args]
  fread.c:423:34: warning: too many arguments for format [-Wformat-extra-args]
  fread.c:429:30: warning: too many arguments for format [-Wformat-extra-args]
  fread.c:2217:21: warning: too many arguments for format [-Wformat-extra-args]
  froll.c:52:41: warning: too many arguments for format [-Wformat-extra-args]
  froll.c:141:41: warning: too many arguments for format [-Wformat-extra-args]
  froll.c:255:41: warning: too many arguments for format [-Wformat-extra-args]
  froll.c:339:41: warning: too many arguments for format [-Wformat-extra-args]
  frolladaptive.c:33:41: warning: too many arguments for format [-Wformat-extra-args]
  frolladaptive.c:118:41: warning: too many arguments for format [-Wformat-extra-args]
  frolladaptive.c:222:41: warning: too many arguments for format [-Wformat-extra-args]
  frolladaptive.c:302:41: warning: too many arguments for format [-Wformat-extra-args]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/data.table.Rcheck/00install.out' for details.
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:11878 (sockconn)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/DecorateR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/DeducerPlugInExample.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/DeducerPlugInScaling.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Deducer.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/DeducerSpatial.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/DeducerSurvival.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/DeducerText.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/deisotoper.Rcheck/00install.out' for details.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Running 'test-all.R' [28s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > 
  > library(dendextend)
  
  ---------------------
  Welcome to dendextend version 1.12.0
  Type citation('dendextend') for how to cite the package.
  
  Type browseVignettes(package = 'dendextend') for the package vignette.
  The github page is: https://github.com/talgalili/dendextend/
  
  Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
  Or contact: <tal.galili@gmail.com>
  
  	To suppress this message use:  suppressPackageStartupMessages(library(dendextend))
  ---------------------
  
  
  Attaching package: 'dendextend'
  
  The following object is masked from 'package:stats':
  
      cutree
  
  > test_check("dendextend")
  Bootstrap (r = 0.4)... Done.
  Bootstrap (r = 0.6)... Done.
  Bootstrap (r = 0.8)... Done.
  Bootstrap (r = 1.0)... Done.
  Bootstrap (r = 1.2)... Done.
  Bootstrap (r = 1.4)... Done.
  -- 1. Failure: extract au (@test-pvclust_extract.R#12)  ------------------------
  round(pvclust_edges(dend)[, 3], digits = 2) not identical to c(0.97, 1, 1).
  2/3 mismatches (average diff: 0.11)
  [1] 0.76 - 0.97 == -0.21
  [2] 0.99 - 1.00 == -0.01
  
  == testthat results  ===========================================================
  [ OK: 409 | SKIPPED: 0 | WARNINGS: 10 | FAILED: 1 ]
  1. Failure: extract au (@test-pvclust_extract.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.8Mb
    help   1.4Mb
    libs   2.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.8Mb
installed size is  8.1Mb
  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  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   4.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/dialrjars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/dialr.Rcheck/00install.out' for details.
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:11845 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11845 (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:11830 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11830 (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
Running examples in 'DistributionOptimization-Ex.R' failed
The error most likely occurred in:

> ### Name: DistributionOptimization
> ### Title: Distribution Fitting
> ### Aliases: DistributionOptimization
> 
> ### ** Examples
> 
> DistributionOptimization(c(rnorm(200),rnorm(200,3)), 2,Iter = 15)
Loading required namespace: parallelDist
Failed with error:  'there is no package called 'parallelDist''
Error in loadNamespace(name) : there is no package called 'parallelDist'
Calls: DistributionOptimization ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/DiversityOccupancy.Rcheck/00install.out' for details.
Found the following significant warnings:
  dcm2niix/tinydir.h:350:8: warning: 'char* strcat(char*, const char*)' accessing 4097 or more bytes at offsets 0 and 4096 may overlap 1 byte at offset 4096 [-Wrestrict]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/divest.Rcheck/00install.out' for details.
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Dominance.Rcheck/00install.out' for details.
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   5.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/edeR.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/4.0gcc8/EditImputeCont.Rcheck/00install.out' for details.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ELT.Rcheck/00install.out' for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.8Mb
Found the following significant warnings:
  emmix.cpp:351:195: warning: value computed is not used [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/EMMIXgene.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/EnsembleBase.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/EnsembleCV.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/EnsemblePCReg.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/EnsemblePenReg.Rcheck/00install.out' for details.
Found the following significant warnings:
  epanet.c:999:5: warning: 'strncpy' output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:1000:5: warning: 'strncpy' output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:1492:3: warning: 'strncpy' output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:2308:7: warning: 'strncpy' output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:2309:7: warning: 'strncpy' output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input1.c:454:7: warning: 'strncpy' output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input1.c:455:7: warning: 'strncpy' output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input3.c:604:2: warning: 'strncpy' output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/epanet2toolkit.Rcheck/00install.out' for details.
Missing or unexported object: 'glmnet::predict.coxnet'
coef,PSP: no visible global function definition for 'predict.coxnet'
Undefined global functions or variables:
  predict.coxnet
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/4.0gcc8/evoper.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/expands.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/extraTrees.Rcheck/00install.out' for details.
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      2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/FastRWeb.Rcheck/00install.out' for details.
Running 'tinytest.R' [3s]
Running the tests in 'tests/tinytest.R' failed.
Complete output:
  > 
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  +   home <- length(unclass(packageVersion("fastshap"))[[1L]]) == 4
  +   tinytest::test_package("fastshap", at_home = home)
  + }
  Loading required package: Formula
  Loading required package: plotmo
  Loading required package: plotrix
  Loading required package: TeachingDemos
  
  Running test_fastshap.R...............    0 tests    
  Running test_fastshap.R...............    0 tests    
  Running test_fastshap.R...............    0 tests    
  Running test_fastshap.R...............    0 tests    
  Running test_fastshap.R...............    0 tests    
  Running test_fastshap.R...............    0 tests    Error in fastshap:::genOMat(num_rows, num_cols) : 
    function 'enterRNGScope' not provided by package 'Rcpp'
  Calls: <Anonymous> ... run_test_dir -> lapply -> FUN -> eval -> eval -> <Anonymous>
  Execution halted
Running 'tinytest.R' [5s]
Running the tests in 'tests/tinytest.R' failed.
Complete output:
  > 
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  +   home <- length(unclass(packageVersion("fastshap"))[[1L]]) == 4
  +   tinytest::test_package("fastshap", at_home = home)
  + }
  Loading required package: Formula
  Loading required package: plotmo
  Loading required package: plotrix
  Loading required package: TeachingDemos
  
  Running test_fastshap.R...............    0 tests    
  Running test_fastshap.R...............    0 tests    
  Running test_fastshap.R...............    0 tests    
  Running test_fastshap.R...............    0 tests    
  Running test_fastshap.R...............    0 tests    
  Running test_fastshap.R...............    0 tests    Error in fastshap:::genOMat(num_rows, num_cols) : 
    function 'enterRNGScope' not provided by package 'Rcpp'
  Calls: <Anonymous> ... run_test_dir -> lapply -> FUN -> eval -> eval -> <Anonymous>
  Execution halted
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  6.1Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.6Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/fdq.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'FeatureHashing.Rmd' using rmarkdown
Quitting from lines 68-96 (FeatureHashing.Rmd) 
Error: processing vignette 'FeatureHashing.Rmd' failed with diagnostics:
could not find function "auc"
--- failed re-building 'FeatureHashing.Rmd'

--- re-building 'SentimentAnalysis.Rmd' using rmarkdown
--- finished re-building 'SentimentAnalysis.Rmd'

SUMMARY: processing the following file failed:
  'FeatureHashing.Rmd'

Error: Vignette re-building failed.
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/fit4NM.Rcheck/00install.out' for details.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   2.5Mb
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
Running 'testthat.R' [220s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > if (require(testthat)) {
  +   test_check("forecast")
  + }
  Loading required package: testthat
  Loading required package: forecast
  Registered S3 methods overwritten by 'forecast':
    method             from    
    fitted.fracdiff    fracdiff
    residuals.fracdiff fracdiff
  -- 1. Error: tests for autoplot/gg functions (@test-ggplot.R#64)  --------------
  need at least two non-NA values to interpolate
  Backtrace:
   1. forecast::ggseasonplot(...)
   2. ggplot2::scale_color_gradientn(colours = col)
   5. scales::gradient_n_pal(colours, values, space)
   6. scales::colour_ramp(colours)
   7. stats::approxfun(x_in, lab_in[, 1])
  
  == testthat results  ===========================================================
  [ OK: 774 | SKIPPED: 5 | WARNINGS: 2 | FAILED: 1 ]
  1. Error: tests for autoplot/gg functions (@test-ggplot.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [179s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > if (require(testthat)) {
  +   test_check("forecast")
  + }
  Loading required package: testthat
  Loading required package: forecast
  Registered S3 methods overwritten by 'forecast':
    method             from    
    fitted.fracdiff    fracdiff
    residuals.fracdiff fracdiff
  -- 1. Error: tests for autoplot/gg functions (@test-ggplot.R#64)  --------------
  need at least two non-NA values to interpolate
  Backtrace:
   1. forecast::ggseasonplot(...)
   2. ggplot2::scale_color_gradientn(colours = col)
   5. scales::gradient_n_pal(colours, values, space)
   6. scales::colour_ramp(colours)
   7. stats::approxfun(x_in, lab_in[, 1])
  
  == testthat results  ===========================================================
  [ OK: 774 | SKIPPED: 5 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: tests for autoplot/gg functions (@test-ggplot.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  testcpp_rec6.cpp:197:37: warning: value computed is not used [-Wunused-value]
  testcpp_rec6.cpp:551:37: warning: value computed is not used [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/forestFloor.Rcheck/00install.out' for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   5.3Mb
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  5.3Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   3.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.0Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    2.1Mb
    libs   2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/fsdaR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/FSelector.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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/G2Sd.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   3.2Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      5.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.1Mb
installed size is 85.2Mb
  sub-directories of 1Mb or more:
    L8NY18   2.2Mb
    gdal     3.8Mb
    libs    72.8Mb
    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  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
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  5.0Mb
  sub-directories of 1Mb or more:
    libs   2.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/GGUM.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
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 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  21.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/glmulti.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/gMCP.Rcheck/00install.out' for details.
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:
  dftcf.c:31:9: warning: array subscript -1 is below array bounds of 'int[15]' [-Warray-bounds]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/GPB.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/gpuR.Rcheck/00install.out' for details.
Running 'testthat.R' [103s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(gqlr)
  > 
  > test_check("gqlr")
  -- 1. Failure: pryr fails (@test-aaa-pryr-unenclose.R#25)  ---------------------
  ans$A() == "A" isn't false.
  
  -- 2. Failure: pryr fails (@test-aaa-pryr-unenclose.R#26)  ---------------------
  ans$B() == "B" isn't false.
  
  == testthat results  ===========================================================
  [ OK: 541 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 2 ]
  1. Failure: pryr fails (@test-aaa-pryr-unenclose.R#25) 
  2. Failure: pryr fails (@test-aaa-pryr-unenclose.R#26) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/GrammR.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/GreedyExperimentalDesignJARs.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/GreedyExperimentalDesign.Rcheck/00install.out' for details.
Running examples in 'groupedSurv-Ex.R' failed
The error most likely occurred in:

> ### Name: groupedSurvFam
> ### Title: Compute the Efficient Score Statistic for the Frailty Model
> ### Aliases: groupedSurvFam
> 
> ### ** Examples
> 
> # Generate dummy data
> set.seed(111)
> n <- 24
> 
> # effect size
> beta <- 0.3
> 
> # covariate parameters
> theta <- c(0.2, 0.2)
> 
> # variable of interest
> MAF <- 0.05
> x <- matrix(rbinom(n, 2, MAF), ncol = 1)
> 
> # covariate data (centered at 0)
> z1 <- rnorm(n)
> z2 <- rbinom(n, 1, 0.5) - 0.5
> Z  <- matrix(cbind(z1, z2), ncol = 2)
> 
> # continuous survival time
> lam0 <- 1
> cmax <- 3
> lami <- lam0 * exp(x*beta + Z[,1]*theta[1]+Z[,2]*theta[2])
> stime <- rexp(n, lami)
> ctime <- runif(n, 0, cmax)
> delta <- stime < ctime
> otime <- pmin(stime, ctime)
> 
> # number of observation times
> ntps <- 5
> 
> # number of intervals
> r <- ntps + 1
> 
> # last observation time
> maxbreakq <- 0.85
> maxbreak <- qexp(maxbreakq, lam0)
> 
> # grouped failure times
> breaks <- (1:ntps) * (maxbreak/ntps)
> gtime <- findInterval(otime, breaks) + 1
> delta[gtime == r] <- FALSE
> dctime <- findInterval(ctime, breaks) + 1
> delta[gtime == dctime] <- FALSE
> delta <- as.numeric(delta)
> 
> # family-specific information
> m <- n/3
> fam_role <- rep(c("o","f","m"),m)
> fam_group <- as.character(rep(1:m,rep(3,m)))
> 
> # nuisance parameters
> alpha <- thetaEst(Z, gtime,delta)$alpha
> var <- 0.2
> 
> # compute efficient score statistics
> res   <- groupedSurvFam(x, fam_group, fam_role, alpha, var, gtime, delta) 
> res
            [,1]
[1,] -0.09108599
[2,] -0.03535880
[3,] -0.05805514
[4,] -0.07539618
[5,]  0.09537326
[6,]  0.50679716
[7,] -0.01163486
[8,] -0.02150784
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11364 (sockconn)
Execution halted
Running examples in 'groupedSurv-Ex.R' failed
The error most likely occurred in:

> ### Name: groupedSurvFam
> ### Title: Compute the Efficient Score Statistic for the Frailty Model
> ### Aliases: groupedSurvFam
> 
> ### ** Examples
> 
> # Generate dummy data
> set.seed(111)
> n <- 24
> 
> # effect size
> beta <- 0.3
> 
> # covariate parameters
> theta <- c(0.2, 0.2)
> 
> # variable of interest
> MAF <- 0.05
> x <- matrix(rbinom(n, 2, MAF), ncol = 1)
> 
> # covariate data (centered at 0)
> z1 <- rnorm(n)
> z2 <- rbinom(n, 1, 0.5) - 0.5
> Z  <- matrix(cbind(z1, z2), ncol = 2)
> 
> # continuous survival time
> lam0 <- 1
> cmax <- 3
> lami <- lam0 * exp(x*beta + Z[,1]*theta[1]+Z[,2]*theta[2])
> stime <- rexp(n, lami)
> ctime <- runif(n, 0, cmax)
> delta <- stime < ctime
> otime <- pmin(stime, ctime)
> 
> # number of observation times
> ntps <- 5
> 
> # number of intervals
> r <- ntps + 1
> 
> # last observation time
> maxbreakq <- 0.85
> maxbreak <- qexp(maxbreakq, lam0)
> 
> # grouped failure times
> breaks <- (1:ntps) * (maxbreak/ntps)
> gtime <- findInterval(otime, breaks) + 1
> delta[gtime == r] <- FALSE
> dctime <- findInterval(ctime, breaks) + 1
> delta[gtime == dctime] <- FALSE
> delta <- as.numeric(delta)
> 
> # family-specific information
> m <- n/3
> fam_role <- rep(c("o","f","m"),m)
> fam_group <- as.character(rep(1:m,rep(3,m)))
> 
> # nuisance parameters
> alpha <- thetaEst(Z, gtime,delta)$alpha
> var <- 0.2
> 
> # compute efficient score statistics
> res   <- groupedSurvFam(x, fam_group, fam_role, alpha, var, gtime, delta) 
> res
            [,1]
[1,] -0.09108599
[2,] -0.03535880
[3,] -0.05805514
[4,] -0.07539618
[5,]  0.09537326
[6,]  0.50679716
[7,] -0.01163486
[8,] -0.02150784
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11034 (sockconn)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/growthPheno.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/gWidgets2RGtk2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/gWidgetsRGtk2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/gwsem.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/h5.Rcheck/00install.out' for details.
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/helloJavaWorld.Rcheck/00install.out' for details.
Found the following significant warnings:
  ../inst/include/hesim/Rbase/integrate.h:1687:5: warning: array subscript -1 is below array bounds of 'double [52]' [-Warray-bounds]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/hesim.Rcheck/00install.out' for details.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs   4.4Mb
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.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
    libs   2.1Mb
Found the following significant warnings:
  codegenerator.cpp:464:4: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  codegenerator.cpp:1742:4: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  codegenerator.cpp:1743:4: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  languagedefinition.cpp:100:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/highlight.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/hive.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.5Mb
    libs   1.6Mb
installed size is  7.6Mb
  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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/hunspell.Rcheck/00install.out' for details.
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  6.4Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      2.3Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   7.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ie2misc.Rcheck/00install.out' for details.
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 17.0Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  14.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/imageData.Rcheck/00install.out' for details.
installed size is 24.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       5.3Mb
    include   2.8Mb
    libs     13.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ImportExport.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/InSilicoVA.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/intamapInteractive.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/InterfaceqPCR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/iplots.Rcheck/00install.out' for details.
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:11758 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11758 (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:11880 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11880 (sockconn)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ISM.Rcheck/00install.out' for details.
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/jdx.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/JGR.Rcheck/00install.out' for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   2.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/joinXL.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/jsr223.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   2.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/KoNLP.Rcheck/00install.out' for details.
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/lar.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.4Mb
    libs   2.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   2.8Mb
Running 'testthat.R' [76s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(lidR)
  Loading required package: raster
  Loading required package: sp
  > 
  > options(lidR.progress = FALSE)
  > 
  > test_check("lidR")
  -- 1. Failure: tree_detection LMF works with a RasterLayer (@test-tree_detection
  dim(ttops@data) not equal to c(158, 2).
  1/2 mismatches
  [1] 157 - 158 == -1
  
  -- 2. Failure: tree_detection LMF works with a RasterLayer (@test-tree_detection
  dim(ttops@data) not equal to c(185, 2).
  1/2 mismatches
  [1] 183 - 185 == -2
  
  == testthat results  ===========================================================
  [ OK: 599 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: tree_detection LMF works with a RasterLayer (@test-tree_detection.R#35) 
  2. Failure: tree_detection LMF works with a RasterLayer (@test-tree_detection.R#43) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.2Mb
  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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/lilikoi.Rcheck/00install.out' for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/llama.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/LLM.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/LLSR.Rcheck/00install.out' for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    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:183:19: 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:897:16: 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:197:19: 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
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      2.1Mb
Found the following significant warnings:
  ../../inst/include/lpkit.h:32:99: warning: right-hand operand of comma expression has no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/lpSolveAPI.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/4.0gcc8/lpSolve.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   3.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    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:4485:36: warning: too many arguments for format [-Wformat-extra-args]
  liblwgeom/lwgeom_topo.c:4536:38: 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 10.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
    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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/maGUI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/mailR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/mallet.Rcheck/00install.out' for details.
Running 'testthat.R' [22s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(manhplot)
  > 
  > test_check("manhplot")
  -- 1. Error: Run the manhplusplot function with default params (@testmanhplusplo
  missing value where TRUE/FALSE needed
  Backtrace:
   1. manhplot::manhplusplot(...)
   2. ggplot2::scale_fill_gradientn(...)
   5. scales::gradient_n_pal(colours, values, space)
   6. scales::colour_ramp(colours)
  
  -- 2. Error: Run the manhplusplot function with output as tiff file (@testmanhpl
  missing value where TRUE/FALSE needed
  Backtrace:
   1. manhplot::manhplusplot(...)
   2. ggplot2::scale_fill_gradientn(...)
   5. scales::gradient_n_pal(colours, values, space)
   6. scales::colour_ramp(colours)
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: Run the manhplusplot function with default params (@testmanhplusplot.R#9) 
  2. Error: Run the manhplusplot function with output as tiff file (@testmanhplusplot.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
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          8.2Mb
Found the following significant warnings:
  cuts.c:24:2: warning: statement with no effect [-Wunused-value]
  cuts.c:24:5: warning: statement with no effect [-Wunused-value]
  cuts.c:24:9: warning: statement with no effect [-Wunused-value]
  cuts.c:32:2: warning: statement with no effect [-Wunused-value]
  cuts.c:32:6: warning: statement with no effect [-Wunused-value]
  cuts.c:32:10: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/mapproj.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   2.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/matchingMarkets.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/mbgraphic.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   3.0Mb
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  7.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/mdendro.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/mdsOpt.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      2.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/melviewr.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/MergeGUI.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.6Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Running examples in 'metacart-Ex.R' failed
The error most likely occurred in:

> ### Name: REmrt
> ### Title: Random effects meta-tree
> ### Aliases: REmrt
> 
> ### ** Examples
> 
> data(dat.BCT2009)
> REtree <- REmrt(g ~ T1 + T2+ T4 +T25, vi = vi, data = dat.BCT2009, c = 0)
Error in .compute_tau_(g.unsplit, vi.unsplit, cnode.unsplit, unique(cnode.unsplit),  : 
  function 'enterRNGScope' not provided by package 'Rcpp'
Calls: REmrt ... do.call -> <Anonymous> -> re.cutoff_cpp -> .compute_tau_
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/metagear.Rcheck/00install.out' for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/metapro.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    help   2.0Mb
    libs   2.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/MetSizeR.Rcheck/00install.out' for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    1.1Mb
    libs   4.4Mb
    misc   1.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/MicroStrategyR.Rcheck/00install.out' for details.
Found the following significant warnings:
  migrate.c:179:30: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:186:26: warning: '.asc' directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:199:28: warning: '.asc' directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:286:27: warning: '%s' directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:312:29: warning: '%d' directive writing between 1 and 8 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:559:31: warning: '%s' directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:595:27: warning: '%s' directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:603:27: warning: '%s' directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/MigClim.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/MissingDataGUI.Rcheck/00install.out' for details.
Found the following significant warnings:
  GLMM_Deviance.cpp:153:9: warning: statement has no effect [-Wunused-value]
  GLMM_Deviance.cpp:708:11: warning: statement has no effect [-Wunused-value]
  GLMM_Deviance2.cpp:173:9: warning: statement has no effect [-Wunused-value]
  GLMM_Deviance2.cpp:780:11: warning: statement has no effect [-Wunused-value]
  GLMM_newData.cpp:183:9: warning: statement has no effect [-Wunused-value]
  GLMM_updateRanEf.cpp:161:9: warning: statement has no effect [-Wunused-value]
  GLMM_updateRanEf.cpp:626:11: warning: statement has no effect [-Wunused-value]
  GLMM_updateRanEf_QR.cpp:124:9: warning: statement has no effect [-Wunused-value]
  GLMM_updateRanEf_QR.cpp:328:11: warning: statement has no effect [-Wunused-value]
  MCMC_Moments_NormalApprox_QR.cpp:104:11: warning: statement has no effect [-Wunused-value]
  MCMC_Moments_NormalApprox_QR.cpp:209:11: warning: statement has no effect [-Wunused-value]
  NMix_updateMeansVars.cpp:516:16: warning: statement has no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/mixAK.Rcheck/00install.out' for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/mlDNA.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/mleap.Rcheck/00install.out' for details.
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/MODIStsp.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    1.8Mb
    libs   2.4Mb
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
Package vignette with placeholder title 'Vignette Title':
  'motmot.vignette.Rmd'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   1.6Mb
    libs   1.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   3.2Mb
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.0Mb
    libs  21.1Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/MSIseq.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Found the following significant warnings:
  eclat/tract/src/tract.c:1397:41: warning: too many arguments for format [-Wformat-extra-args]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/multinet.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/mutossGUI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/mwa.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Myrrixjars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Myrrix.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.4Mb
    libs   2.0Mb
Running 'testthat.R' [6s]
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
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 19.3Mb
  sub-directories of 1Mb or more:
    CppCode   2.6Mb
    R         5.8Mb
    include   5.6Mb
    libs      2.4Mb
    tests     1.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Running 'testthat.R' [42s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(NLMR)
  > 
  > test_check("NLMR")
  Failed with error:  'there is no package called 'igraph''
  -- 1. Error: (unknown) (@test_randomcluster.R#4)  ------------------------------
  you need to install the igraph package to be able to use this function
  Backtrace:
   1. base::suppressWarnings(...)
   3. NLMR::nlm_randomcluster(...)
   5. raster::clump(ranclumap, direction = neighbourhood, gaps = FALSE)
   6. raster:::.local(x, ...)
  
  == testthat results  ===========================================================
  [ OK: 63 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 1 ]
  1. Error: (unknown) (@test_randomcluster.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/NLPutils.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   2.2Mb
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    2.6Mb
    help   2.5Mb
    libs   2.5Mb
Found the following significant warnings:
  connection.cpp:67:36: warning: catching polymorphic type 'class nanodbc::database_error' by value [-Wcatch-value=]
  odbc_connection.cpp:37:36: warning: catching polymorphic type 'class nanodbc::database_error' by value [-Wcatch-value=]
  odbc_connection.cpp:75:36: warning: catching polymorphic type 'class nanodbc::database_error' by value [-Wcatch-value=]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/odbc.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ODB.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.4Mb
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  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.9Mb
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/4.0gcc8/openNLPdata.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/openNLP.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/OpenStreetMap.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/openVA.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      2.3Mb
Found the following significant warnings:
  opus_miner.cpp:90:15: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/opusminer.Rcheck/00install.out' for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/OSMscale.Rcheck/00install.out' for details.
Found the following significant warnings:
  likelihoods.cpp:479:38: warning: value computed is not used [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/outbreaker2.Rcheck/00install.out' for details.
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/PairwiseD.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'patternplot-intro.Rmd' using docco_linear
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/pbdBASE.Rcheck/00install.out' for details.
Packages required but not available: 'pbdBASE', 'pbdDMAT'

Package which this enhances but not available for checking: 'pmclust'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'pbdBASE'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Found the following significant warnings:
  igamx2d_.c:273:29: warning: passing argument 1 of 'MPI_Op_create' from incompatible pointer type [-Wincompatible-pointer-types]
  igamx2d_.c:277:29: warning: passing argument 1 of 'MPI_Op_create' from incompatible pointer type [-Wincompatible-pointer-types]
  dgamx2d_.c:274:29: warning: passing argument 1 of 'MPI_Op_create' from incompatible pointer type [-Wincompatible-pointer-types]
  dgamx2d_.c:278:29: warning: passing argument 1 of 'MPI_Op_create' from incompatible pointer type [-Wincompatible-pointer-types]
  igamn2d_.c:273:29: warning: passing argument 1 of 'MPI_Op_create' from incompatible pointer type [-Wincompatible-pointer-types]
  igamn2d_.c:277:29: warning: passing argument 1 of 'MPI_Op_create' from incompatible pointer type [-Wincompatible-pointer-types]
  dgamn2d_.c:274:29: warning: passing argument 1 of 'MPI_Op_create' from incompatible pointer type [-Wincompatible-pointer-types]
  dgamn2d_.c:278:29: warning: passing argument 1 of 'MPI_Op_create' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/pbdSLAP.Rcheck/00install.out' for details.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    lib    5.5Mb
    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  7.6Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   2.7Mb
    libs      2.3Mb
Found the following significant warnings:
  l1pcahp.c:82:3: warning: statement with no effect [-Wunused-value]
  l1pcahp.c:92:3: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/pcaL1.Rcheck/00install.out' for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.9Mb
Running 'test_LINGAM.R' [4s]
  Running 'test_addBgKnowledge.R' [3s]
  Running 'test_adjustment.R' [5s]
  Running 'test_ages.R' [3s]
  Running 'test_amat2dag.R' [2s]
  Running 'test_arges.R' [2s]
  Running 'test_backdoor.R' [9s]
  Comparing 'test_backdoor.Rout' to 'test_backdoor.Rout.save' ...
Rd conversion errors:
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Error in writeLines(x, con, useBytes = TRUE, ...) : 
  Error writing to connection:  No space left on device
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs  13.1Mb
Running examples in 'pcFactorStan-Ex.R' failed
The error occurred in:
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(pcFactorStan)
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Error(s) in re-building vignettes:
--- re-building 'pct-international.Rmd' using rmarkdown
--- finished re-building 'pct-international.Rmd'

--- re-building 'pct.Rmd' using rmarkdown
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in png(..., res = dpi, units = "in") :
  unable to open file 'pct_files/figure-html/pct-lines-min-1.png' for writing
Warning in png(..., res = dpi, units = "in") : opening device failed
Quitting from lines 162-164 (pct.Rmd) 
--- failed re-building 'pct.Rmd'

--- re-building 'pct_training.Rmd' using rmarkdown
Warning in close.connection(con) :
  Problem closing connection:  No space left on device

Attaching package: 'dplyr'

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

    filter, lag

The following objects are masked f* checking PDF version of manual ... ERROR
Rd conversion errors:
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in file(out, "wt") :
  cannot open file 'D:\temp\RtmpyA7zEt\ltx9a4812af6417/get_desire_lines.tex': No space left on device
Error in file(out, "wt") : cannot open the connection
Running examples in 'pder-Ex.R' failed
The error most likely occurred in:

> ### Name: TurkishBanks
> ### Title: Turkish Banks
> ### Aliases: TurkishBanks
> ### Keywords: datasets
> 
> ### ** Examples
> 
> #### Example 2-5
> 
> ## ------------------------------------------------------------------------
> data("TurkishBanks", package = "pder")
> library("plm")
> TurkishBanks <- na.omit(TurkishBanks)
> TB <- pdata.frame(TurkishBanks)
> summary(log(TB$output))
total sum of squares: 2691.819 
        id       time 
0.84730373 0.01255259 
> ercomp(log(cost) ~ log(output), TB)
                 var std.dev share
idiosyncratic 0.3291  0.5737 0.604
individual    0.2156  0.4643 0.396
theta:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.6191  0.6509  0.6509  0.6473  0.6509  0.6509 
> models <- c("within", "random", "pooling", "between")
> sapply(models, function(x)
+        coef(plm(log(cost) ~ log(output), TB, model = x))["log(output)"])
 within.log(output)  random.log(output) pooling.log(output) between.log(output) 
          0.5063813           0.6470614           0.8006578           0.8531416 
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:plm'

> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  54.16 2.17 57.75 NA NA 
> grDevices::dev.off()
Error in grDevices::dev.off() : write failed
Execution halted
Rd conversion errors:
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Error in writeLines(x, con, useBytes = TRUE, ...) : 
  Error writing to connection:  No space left on device
Rd conversion errors:
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in .pkg2tex(files, outfile, encoding = encoding, append = append,  :
  file 'D:\temp\RtmpuSVGYS\ltx2ae187b883449/summary-methods.tex' lacks a header: skipping
Warning in .pkg2tex(files, outfile, encoding = encoding, append = append,  :
  file 'D:\temp\RtmpuSVGYS\ltx2ae187b883449/wine.tex' lacks a header: skipping
Error in writeLines(readLines(f), outcon) : Error writing to connection
Running massageExamples to create 'pdfetch-Ex.R' failed
Error in file(out, "wt") : cannot open the connection
Calls: <Anonymous> -> Rd2ex -> file
In addition: Warning message:
In file(out, "wt") :
  cannot open file 'D:\temp\RtmpEZfFsL\file31bd454821b39/pdfetch_BUNDESBANK.R': No space left on device
Execution halted
 NONE
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    libs   13.8Mb
    share  11.9Mb
pdist-package.Rd: Sections \title, and \name must exist and be unique in Rd files
pdist.Rd: Sections \title, and \name must exist and be unique in Rd files
problems found in 'pdist-package.Rd', 'pdist.Rd'
TimedVector.Rd: Sections \title, and \name must exist and be unique in Rd files
averageBySession.Rd: Sections \title, and \name must exist and be unique in Rd files
calculateResponse.Rd: Sections \title, and \name must exist and be unique in Rd files
computeModel.Rd: Sections \title, and \name must exist and be unique in Rd files
fitModel.Rd: Sections \title, and \name must exist and be unique in Rd files
isTimedVector.Rd: Sections \title, and \name must exist and be unique in Rd files
modelObjectiveFunction.Rd: Sections \title, and \name must exist and be unique in Rd files
pdmod-package.Rd: Sections \title, and \name must exist and be unique in Rd files
plot.pdmod.Rd: Sections \title, and \name must exist and be unique in Rd files
problems found in 'TimedVector.Rd', 'averageBySession.Rd', 'calculateResponse.Rd', 'computeModel.Rd', 'fitModel.Rd', 'isTimedVector.Rd', 'modelObjectiveFunction.Rd', 'pdmod-package.Rd', 'plot.pdmod.Rd'
Rd conversion errors:
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in file(out, "wt") :
  cannot open file 'D:\temp\RtmpGMQeNc\ltxc50c38eb4a91/averageBySession.tex': No space left on device
Error in file(out, "wt") : cannot open the connection
Rd conversion errors:
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in file(out, "wt") :
  cannot open file 'D:\temp\RtmpOE30HK\ltx1b33835032a2e/model.tex': No space left on device
Error in file(out, "wt") : cannot open the connection
H.coeff.Rd: Sections \title, and \name must exist and be unique in Rd files
Error writing to connection:  No space left on device
InvWavTransf2D.Rd: Sections \title, and \name must exist and be unique in Rd files
Logm.Rd: Sections \title, and \name must exist and be unique in Rd files
Mid.Rd: Sections \title, and \name must exist and be unique in Rd files
Error writing to connection:  No space left on device
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
Warning in for (i in seq_len(n)) { : closing unused connection 4 ()
Warning in for (i in seq_len(n)) { : closing unused connection 3 ()
problems found in 'H.coeff.Rd', 'InvWavTransf1D.Rd', 'InvWavTransf2D.Rd', 'Logm.Rd', 'Mid.Rd', 'WavTransf1D.Rd', 'WavTransf2D.Rd', 'pdCART.Rd', 'pdDepth.Rd', 'pdDist.Rd', 'pdMean.Rd', 'pdMedian.Rd'
detect.spikes.Rd: Sections \title, and \name must exist and be unique in Rd files
helperpeak.Rd: Sections \title, and \name must exist and be unique in Rd files
keepmax.Rd: Sections \title, and \name must exist and be unique in Rd files
peakpick.Rd: Sections \title, and \name must exist and be unique in Rd files
problems found in 'detect.spikes.Rd', 'helperpeak.Rd', 'keepmax.Rd', 'peakpick.Rd'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs        2.0Mb
    xvg-files   3.2Mb
Error(s) in re-building vignettes:
Error in .get_package_metadata(pkgdir) : 
  Files 'DESCRIPTION' and 'DESCRIPTION.in' are missing.
Calls: <Anonymous> ... pkgVignettes -> loadVignetteBuilder -> .get_package_metadata
Execution halted
Rd conversion errors:
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in file(out, "wt") :
  cannot open file 'D:\temp\RtmpMz8HU3\ltx13f5c1f5178c9/testAssoDist.tex': No space left on device
Error in file(out, "wt") : cannot open the connection
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.0Mb
    libs      2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/phylotaR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/pid.Rcheck/00install.out'* DONE
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/PKgraph.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/pkr.Rcheck/00install.out'* DONE
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/pks.Rcheck/00install.out'* DONE
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.6Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   2.1Mb
Packages required but not available: 'pbdBASE', 'pbdDMAT'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/png.Rcheck/00install.out'* DONE
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/pnn.Rcheck/00install.out'* DONE
Installation failed.

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 ?) ========
See 
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 ?) ========
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/polyPK.Rcheck/00install.out' for details.
Found the following significant warnings:
  lpkit.c:632:9: warning: 'strcpy' accessing 1 byte at offsets [0, 2147483647] and [0, 2147483647] may overlap 1 byte at offset 0 [-Wrestrict]
  lpkit.c:790:9: warning: 'strcpy' accessing 1 byte at offsets [0, 2147483647] and [0, 2147483647] may overlap 1 byte at offset 0 [-Wrestrict]
  lpkit.c:632:9: warning: 'strcpy' accessing 1 byte at offsets [0, 9223372036854775807] and [0, 9223372036854775807] may overlap 1 byte at offset 0 [-Wrestrict]
  lpkit.c:790:9: warning: 'strcpy' accessing 1 byte at offsets [0, -25] and [0, -25] may overlap 1 byte at offset -9223372036854775808 [-Wrestrict]
See 'd:/Rcompile/CRANpkg/local/4.0v3/pomdp.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    1.1Mb
    libs   2.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/PortfolioEffectEstim.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/PortfolioEffectHFT.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/4.0gcc8/PPRL.Rcheck/00install.out' for details.
Running examples in 'prefmod-Ex.R' failed
The error most likely occurred in:

> ### Name: pattRrep.fit
> ### Title: Function to fit a pattern model for repeated rankings)
> ### Aliases: pattRrep.fit
> ### Keywords: models multivariate
> 
> ### ** Examples
> 
> # simulated data: 3 items, 2 timepoints
> dat1 <- simR(3, 100, c(.2, .7, .1))
> dat2 <- simR(3, 100, c(.5, .4, .1))
> dat  <- data.frame(dat1, dat2)
> res  <- pattLrep.fit(dat, nitems = 3, tpoints = 2, iaT = TRUE)
> res

Results of pattern model for repeated ratings 

Call:
pattLrep.fit(obj = dat, nitems = 3, tpoints = 2, iaT = TRUE) 

Deviance:  136.257 
log likelihood:  -241.0372 

no of iterations:  41  (Code: 1 )
Error in solve.default(obj$hessian) : 
  Lapack routine dgesv: system is exactly singular: U[6,6] = 0
Calls: <Anonymous> -> print.pattMod -> diag -> solve -> solve.default
Execution halted
installed size is  6.3Mb
  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  5.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/psData.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/qCBA.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/qdap.Rcheck/00install.out' for details.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data  11.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.0Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.6Mb
    doc       2.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   1.3Mb
    libs   3.6Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   2.6Mb
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 14.8Mb
  sub-directories of 1Mb or more:
    Output   2.2Mb
    bin     12.3Mb
Package suggested but not available for checking: 'scran'
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    5.9Mb
    libs   2.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.2Mb
    libs   3.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/rapidraker.Rcheck/00install.out' for details.
installed size is  8.4Mb
  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  8.0Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   4.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rbgs.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'rbiouml.Rnw' using Sweave
Loading required package: RCurl
Loading required package: bitops
Loading required package: RJSONIO

Error: processing vignette 'rbiouml.Rnw' failed with diagnostics:
 chunk 1 
Error in file(con, "r") : cannot open the connection

--- failed re-building 'rbiouml.Rnw'

SUMMARY: processing the following file failed:
  'rbiouml.Rnw'

Error: Vignette re-building failed.
Execution halted
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/4.0v3/rCBA.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/rcdklibs.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/rcdk.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/rChoiceDialogs.Rcheck/00install.out' for details.
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  9.5Mb
  sub-directories of 1Mb or more:
    include   6.1Mb
    libs      2.3Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 10.8Mb
  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  9.0Mb
  sub-directories of 1Mb or more:
    include   1.6Mb
    lib       3.8Mb
    libs      3.4Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      2.2Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    include   1.8Mb
    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   3.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rdroolsjars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rdrools.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 '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/4.0v3/re2r.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.1Mb
Running 'testthat.R' [52s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(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(package = "recipes")
  1 package is needed for this model and is not installed. (NMF). Start a clean R session then run: install.packages("NMF")-- 1. Error: quasiquotation (@test_slice.R#40)  --------------------------------
  `call` must be a call
  
  == testthat results  ===========================================================
  [ OK: 1394 | SKIPPED: 7 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: quasiquotation (@test_slice.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.8Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc    8.6Mb
    libs   2.3Mb
Running examples in 'rentrez-Ex.R' failed
The error most likely occurred in:

> ### Name: entrez_db_summary
> ### Title: Retrieve summary information about an NCBI database
> ### Aliases: entrez_db_summary
> 
> ### ** Examples
> 
> entrez_db_summary("pubmed")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [eutils.ncbi.nlm.nih.gov] Resolving timed out after 10000 milliseconds
Calls: entrez_db_summary ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/REPPlab.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.1Mb
Error(s) in re-building vignettes:
--- re-building 'rERR.Rmd' using rmarkdown
pandoc.exe: Could not fetch https://image.ibb.co/nqqQXd/Rplot.png
HttpExceptionRequest Request {
  host                 = "image.ibb.co"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/nqqQXd/Rplot.png"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (InternalException (HostCannotConnect "image.ibb.co" [connect: failed (Connection timed out (WSAETIMEDOUT))]))
Error: processing vignette 'rERR.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
--- failed re-building 'rERR.Rmd'

SUMMARY: processing the following file failed:
  'rERR.Rmd'

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/reshapeGUI.Rcheck/00install.out' for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RFreak.Rcheck/00install.out' for details.
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/4.0v3/rgeolocate.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      2.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/rggobi.Rcheck/00install.out' for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc     3.6Mb
    fonts   1.5Mb
    libs    1.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/rGroovy.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RGtk2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RH2.Rcheck/00install.out' for details.
Found the following significant warnings:
  blasctl.h:9:3: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RhpcBLASctl.Rcheck/00install.out' for details.
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/4.0v3/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/4.0v3/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/4.0v3/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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RJDBC.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RJDemetra.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/rjdqa.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/rJPSGCS.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RJSDMX.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/rJython.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/rkafkajars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/rkafka.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RKEAjars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RKEA.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rknots.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/rlang.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Found the following significant warnings:
  DbResult.cpp:19:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  DbResult.cpp:81:41: warning: catching polymorphic type 'class MariaResultPrep::UnsupportedPS' by value [-Wcatch-value=]
  connection.cpp:23:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RMariaDB.Rcheck/00install.out' for details.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    rmd   8.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/rmcfs.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   2.8Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   4.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RMOAjars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RMOA.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/rMouse.Rcheck/00install.out' for details.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RNCBIEUtilsLibs.Rcheck/00install.out' for details.
Found the following significant warnings:
  nxsreader.cpp:659:22: warning: catching polymorphic type 'class NxsException' by value [-Wcatch-value=]
  nxsreader.cpp:709:25: warning: catching polymorphic type 'class NxsException' by value [-Wcatch-value=]
See 'd:/Rcompile/CRANpkg/local/4.0v3/rncl.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RNetLogo.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doxygen   1.4Mb
    libs      2.7Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      6.3Mb
Error(s) in re-building vignettes:
--- re-building 'using_robotstxt.Rmd' using rmarkdown

 google.com                      Quitting from lines 48-51 (using_robotstxt.Rmd) 
Error: processing vignette 'using_robotstxt.Rmd' failed with diagnostics:
SSL certificate problem: unable to get local issuer certificate
--- failed re-building 'using_robotstxt.Rmd'

SUMMARY: processing the following file failed:
  'using_robotstxt.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  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/ROpenCVLite.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ROracle.Rcheck/00install.out' for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.3Mb
    libs   2.7Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    libs    2.2Mb
    tests   1.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/rpcdsearch.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=]
  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/4.0v3/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  7.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   5.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RQDA.Rcheck/00install.out' for details.
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/rrepast.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RSCAT.Rcheck/00install.out' for details.
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RSDA.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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/rsgcc.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
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.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.2Mb
    libs  17.5Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/rstap.Rcheck/00install.out' for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.6Mb
Found the following significant warnings:
  RngStreams.c:332:4: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
See 'd:/Rcompile/CRANpkg/local/4.0v3/rstream.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/rsubgroup.Rcheck/00install.out' for details.
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) (2019-11-14 r77415)
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/rSymPy.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rtextrankr.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=]
  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/4.0v3/rtfbs.Rcheck/00install.out' for details.
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RtutoR.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   2.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RunuranGUI.Rcheck/00install.out' for details.
Found the following significant warnings:
  vcglib/wrap/ply/plylib.cpp:3666:14: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rvcg.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/rviewgraph.Rcheck/00install.out' for details.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    include   2.5Mb
    libs      8.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RWekajars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RWeka.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RxnSim.Rcheck/00install.out' for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Error(s) in re-building vignettes:
--- re-building 'RxODE-intro.Rmd' using rmarkdown
Quitting from lines 36-47 (RxODE-intro.Rmd) 
Error: processing vignette 'RxODE-intro.Rmd' failed with diagnostics:
Error building model
--- failed re-building 'RxODE-intro.Rmd'

--- re-building 'RxODE-syntax.Rmd' using rmarkdown
--- finished re-building 'RxODE-syntax.Rmd'

SUMMARY: processing the following file failed:
  'RxODE-intro.Rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown
--- finished re-building 'introduction.Rmd'

--- re-building 'sentiment.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

Quitting from lines 44-46 (sentiment.Rmd) 
Error: processing vignette 'sentiment.Rmd' failed with diagnostics:
SSL certificate problem: unable to get local issuer certificate
--- failed re-building 'sentiment.Rmd'

SUMMARY: processing the following file failed:
  'sentiment.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.3Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.3Mb
    libs   2.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/SanzCircos.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         1.5Mb
    extdata   1.3Mb
    libs      2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/SBRect.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/scagnostics.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   2.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   4.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   3.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/SeqGrapheR.Rcheck/00install.out' for details.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   3.6Mb