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 0x1f31, 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.2019-11-16.txt’
  ‘Example.t.overall.Dest.loci.2019-11-16.txt’
  ‘Example.t.overall.Dest.loci.ci2019-11-16.txt’
  ‘Example.t.overall.Dest.loci.p.2019-11-16.txt’
  ‘Example.t.overall.Dest.mean.2019-11-16.txt’
  ‘Example.t.overall.Dest.mean.ci2019-11-16.txt’
  ‘Example.t.overall.Dest.mean.p.2019-11-16.txt’
  ‘Example.t.sample.sizes.2019-11-16.txt’ ‘Example.u.H.values.txt’
  ‘Example.u.Hest_loci.values.txt’ ‘Example.u.Hest_mean.values.txt’
  ‘Example.u.allelefreq.2019-11-16.txt’
  ‘Example.u.pairwise.Gst.loci.2019-11-16.txt’
  ‘Example.u.pairwise.Gst.mean.2019-11-16.txt’
  ‘Example.u.sample.sizes.2019-11-16.txt’ ‘Output-Inputformat.txt’
Package required but not available: ‘oligo’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘test-all.R’ [31s/38s]
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.
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.
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.
Running examples in ‘DevTreatRules-Ex.R’ failed
The error most likely occurred in:

> ### Name: CompareRulesOnValidation
> ### Title: Build treatment rules on a development dataset and evaluate
> ###   performance on an independent validation dataset
> ### Aliases: CompareRulesOnValidation
> 
> ### ** Examples
> 
> set.seed(123)
> example.split <- SplitData(data=obsStudyGeneExpressions,
+                                     n.sets=3, split.proportions=c(0.5, 0.25, 0.25))
> development.data <- example.split[example.split$partition == "development", ]
> validation.data <- example.split[example.split$partition == "validation", ]
> model.selection <- CompareRulesOnValidation(development.data=development.data,
+                validation.data=validation.data,
+                study.design.development="observational",
+                vec.approaches=c("split.regression", "OWL.framework", "direct.interactions"),
+                vec.rule.methods=c("glm.regression", "lasso"),
+                vec.propensity.methods="logistic.regression",
+                name.outcome.development="no_relapse",
+                type.outcome.development="binary",
+                name.treatment.development="intervention",
+                names.influencing.treatment.development=c("prognosis", "clinic", "age"),
+                names.influencing.rule.development=c("age", paste0("gene_", 1:10)),
+                desirable.outcome.development=TRUE)
Error in predict.cv.glmnet(one.cv.glmnet, newx = features, s = optimal.lambda,  : 
  could not find function "predict.cv.glmnet"
Calls: CompareRulesOnValidation -> BuildRule -> DoPrediction
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘my-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

Quitting from lines 84-97 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
could not find function "predict.cv.glmnet"
--- failed re-building ‘my-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
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.
Package required but not available: ‘missMethyl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
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.
Error(s) in re-building vignettes:
--- re-building ‘vignette_disto.Rmd’ using rmarkdown
! Missing number, treated as zero.
<to be read again> 
                   \protect 
l.428 ...nter}\rule{0.5\linewidth}{\linethickness}
                                                  \end{center} 

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

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

Error: Vignette re-building failed.
Execution halted
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_2019-11-16.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
File ‘EL/libs/EL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘AER’ ‘pROC’ ‘pander’
  All declared Imports should be used.
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.
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
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘colorspace’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘EpiCurve.Rmd’ using rmarkdown
Loading required package: ggplot2
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

Loading required package: ISOweek
Loading required package: scales
! Missing number, treated as zero.
<to be read again> 
                   \protect 
l.136 ...nter}\rule{0.5\linewidth}{\linethickness}
                                                  \end{center} 

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

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

Error: Vignette re-building failed.
Execution halted
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
Error(s) in re-building vignettes:
--- re-building ‘EpiStats.Rmd’ using rmarkdown
Loading required package: epiR
Loading required package: survival
Package epiR 1.0-4 is loaded
Type help(epi.about) for summary information


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

! Missing number, treated as zero.
<to be read again> 
                   \protect 
l.136 ...nter}\rule{0.5\linewidth}{\linethickness}
                                                  \end{center} 

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

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

Error: Vignette re-building failed.
Execution halted
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_statistics2019-11-21_12.38.37.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.
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
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.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
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.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/flowDiv.Rcheck/00install.out’ for details.
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.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
File ‘fmrs/libs/fmrs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 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’ [171s/175s]
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
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
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.
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.
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
installed size is 45.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  43.0Mb
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’ [88s/97s]
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()).
! Missing number, treated as zero.
<to be read again> 
                   \protect 
l.248 ...nter}\rule{0.5\linewidth}{\linethickness}
                                                  \end{center} 

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

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

SUMMARY: processing the following file failed:
  ‘MPG_algorithm.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.2019-11-16.1.1’
  ‘cat.expressions.dir.2019-11-16.1.2’
  ‘cat.expressions.dir.2019-11-16.1.3’
  ‘cat.expressions.dir.2019-11-16.1.4’
  ‘cat.expressions.dir.2019-11-16.1.5’
  ‘cat.expressions.dir.2019-11-16.1.6’
  ‘cat.expressions.dir.2019-11-16.1.7’
  ‘cat.expressions.dir.2019-11-16.1.8’
  ‘cat.expressions.dir.2019-11-16.1.9’
  ‘cat.expressions.dir.2019-11-16.2’
  ‘cat.expressions.dir.2019-11-16.2.1’
  ‘cat.expressions.dir.2019-11-16.2.2’
  ‘cat.expressions.dir.2019-11-16.2.3’
  ‘cat.expressions.dir.2019-11-16.2.4’
  ‘cat.expressions.dir.2019-11-16.2.5’
  ‘cat.expressions.dir.2019-11-16.2.6’
  ‘cat.expressions.dir.2019-11-16.2.7’ ‘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.
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
Found the following significant warnings:
  ../inst/include/hesim/utils.h:78:23: warning: 'bind2nd<std::__1::plus<double>, double>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/hesim.Rcheck/00install.out’ for details.
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
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_20191116.xlsx’
  ‘1-Reasonableness_Var2_check_errors_20191116.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.
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.
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 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
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.
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.
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.
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
Namespace in Imports field not imported from: ‘ggpubr’
  All declared Imports should be used.
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.
Running ‘testthat.R’ [23s/61s]
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
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 ‘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  5.4Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.5Mb
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
Package required but not available: ‘topGO’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
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.
Error: package or namespace load failed for ‘mht’:
 .onAttach failed in attachNamespace() for 'mht', details:
  call: packageDescription("mht")
  error: could not find function "packageDescription"
Execution halted
File ‘mht/libs/mht.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.4Mb
  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.
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-2019-11-16-21-42-45.mm’ ‘md.R’ ‘md.mm’
  ‘mindr.md’ ‘mindr.mm’ ‘mm.md’ ‘outline-2019-11-16-21-42-46.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]
  :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.
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.
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.
! Missing number, treated as zero.
<to be read again> 
                   \protect 
l.1157 ...ter}\rule{0.5\linewidth}{\linethickness}
                                                  \end{center} 

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
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.
Error(s) in re-building vignettes:
--- re-building ‘How_to_use_mvMORPH.Rmd’ using rmarkdown
Loading required package: phytools
Loading required package: ape
Loading required package: maps
Loading required package: corpcor
Loading required package: subplex
##
## mvMORPH package (1.1.0)
## Multivariate evolutionary models
##
## See the tutorials: browseVignettes("mvMORPH")
##
## To cite package 'mvMORPH': citation("mvMORPH")
##
Done.
Efficient parameterization is not yet implemented for user-defined constraints
Please check the results carefully!!
Efficient parameterization is not yet implemented for user-defined constraints
Please check the results carefully!!
! Missing number, treated as zero.
<to be read again> 
                   \protect 
l.137 ...nter}\rule{0.5\linewidth}{\linethickness}
                                                  \end{center} 

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

--- re-building ‘tutorial_mvMORPH.Rmd’ using rmarkdown
Done.
! Missing number, treated as zero.
<to be read again> 
                   \protect 
l.133 ...nter}\rule{0.5\linewidth}{\linethickness}
                                                  \end{center} 

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

SUMMARY: processing the following files failed:
  ‘How_to_use_mvMORPH.Rmd’ ‘tutorial_mvMORPH.Rmd’

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    java  13.8Mb
installed size is  5.6Mb
  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
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.
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.
Found the following significant warnings:
  neighbour_search_wrapper.cpp:8:25: warning: 'bind2nd<std::__1::plus<int>, int>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/nonlinearTseries.Rcheck/00install.out’ for details.
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 University20191116.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.
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
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
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.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘SnowballC’ ‘cluster’ ‘graph’
  All declared Imports should be used.
File ‘pgee.mixed/libs/pgee.mixed.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ph2bye/libs/ph2bye.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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
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:
  ‘file9ba160e14fa2.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.
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:
  ‘Legend78f93f126f8.png’ ‘Legend78f97c72c299.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.
Running examples in ‘plsmselect-Ex.R’ failed
The error most likely occurred in:

> ### Name: cumbasehaz
> ### Title: Cumulative Baseline Hazard of a gamlasso object
> ### Aliases: cumbasehaz
> 
> ### ** Examples
> 
> library(plsmselect)
> library(tidyverse)
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──
✔ ggplot2 3.2.1     ✔ purrr   0.3.3
✔ tibble  2.1.3     ✔ dplyr   0.8.3
✔ tidyr   1.0.0     ✔ stringr 1.4.0
✔ readr   1.3.1     ✔ forcats 0.4.0
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
> 
> data(simData)
> 
> ## Fit Cox gamlasso model using the formula approach:
> ## (L1-penalty both on X terms and smooth terms (bs="ts"))
> simData$X = model.matrix(~x1+x2+x3+x4+x5+x6+x7+x8+x9+x10, data=simData)[,-1]
> 
> cfit = gamlasso(time ~ X +
+                   s(z1, bs="ts", k=5) +
+                   s(z2, bs="ts", k=5) +
+                   s(z3, bs="ts", k=5) +
+                   s(z4, bs="ts", k=5),
+                 data = simData,
+                 family = "cox",
+                 weights="status",
+                 seed=1)
Fitting a lasso and gam loop ... 

Error: 'predict.cv.glmnet' is not an exported object from 'namespace:glmnet'
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘plsmselect.Rmd’ using rmarkdown
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──
✔ ggplot2 3.2.1     ✔ purrr   0.3.3
✔ tibble  2.1.3     ✔ dplyr   0.8.3
✔ tidyr   1.0.0     ✔ stringr 1.4.0
✔ readr   1.3.1     ✔ forcats 0.4.0
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Fitting a lasso and gam loop ... 

Quitting from lines 168-180 (plsmselect.Rmd) 
Error: processing vignette 'plsmselect.Rmd' failed with diagnostics:
'predict.cv.glmnet' is not an exported object from 'namespace:glmnet'
--- failed re-building ‘plsmselect.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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’
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.
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.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
File ‘PRIMAL/libs/PRIMAL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
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.
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.
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
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.
Package suggested but not available for checking: ‘Heatplus’
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.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/randomcoloR.Rcheck/00install.out’ for details.
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.
Running examples in ‘rarhsmm-Ex.R’ failed
The error most likely occurred in:

> ### Name: hmm.predict
> ### Title: 1-step forward prediction for (autoregressive) Gaussian hidden
> ###   Markov model
> ### Aliases: hmm.predict
> 
> ### ** Examples
> 
> set.seed(15562)
> m <- 2
> mu <- list(c(3,4,5),c(-2,-3,-4))
> sigma <- list(diag(1.3,3), 
+             matrix(c(1,-0.3,0.2,-0.3,1.5,0.3,0.2,0.3,2),3,3,byrow=TRUE))
> delta <- c(0.5,0.5)
> gamma <- matrix(c(0.8,0.2,0.1,0.9),2,2,byrow=TRUE)
> auto <- list(matrix(c(0.3,0.2,0.1,0.4,0.3,0.2,
+                      -0.3,-0.2,-0.1,0.3,0.2,0.1,
+                       0,0,0,0,0,0),3,6,byrow=TRUE),
+             matrix(c(0.2,0,0,0.4,0,0,
+                       0,0.2,0,0,0.4,0,
+                      0,0,0.2,0,0,0.4),3,6,byrow=TRUE))
> mod <- list(m=m,mu=mu,sigma=sigma,delta=delta,gamma=gamma,auto=auto,arp=2)
> sim <- hmm.sim(2000,mod)
> y <- sim$series
> state <- sim$state
> fit <- em.hmm(y=y, mod=mod, arp=2, tol=1e-5)
Error: 'predict.mrelnet' is not an exported object from 'namespace:glmnet'
Execution halted
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
Error(s) in re-building vignettes:
--- re-building ‘RClone_qmsevpops.Rmd’ using rmarkdown
! Missing number, treated as zero.
<to be read again> 
                   \protect 
l.142 ...nter}\rule{0.5\linewidth}{\linethickness}
                                                  \end{center} 

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

--- re-building ‘RClone_quickmanual.rmd’ using rmarkdown
! Missing number, treated as zero.
<to be read again> 
                   \protect 
l.142 ...nter}\rule{0.5\linewidth}{\linethickness}
                                                  \end{center} 

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

SUMMARY: processing the following files failed:
  ‘RClone_qmsevpops.Rmd’ ‘RClone_quickmanual.rmd’

Error: Vignette re-building failed.
Execution halted
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.
Error(s) in re-building vignettes:
--- re-building ‘GuideToVignettes.Rmd’ using rmarkdown
tlmgr search --file --global '/tikzlibrarytopaths.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'
! Missing number, treated as zero.
<to be read again> 
                   \protect 
l.74 ...enter}\rule{0.5\linewidth}{\linethickness}
                                                  \end{center} 

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

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

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

--- re-building ‘MiniDIFDUP_1.Rnw’ using Sweave
--- finished re-building ‘MiniDIFDUP_1.Rnw’

--- re-building ‘MiniDIFDUP_2.Rnw’ using Sweave
--- finished re-building ‘MiniDIFDUP_2.Rnw’

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

Error: Vignette re-building failed.
Execution halted
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
Running ‘testthat.R’ [72s/179s]
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. 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  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 18.0Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  15.6Mb
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.
Running examples in ‘regsel-Ex.R’ failed
The error most likely occurred in:

> ### Name: glmsel
> ### Title: Generalised linear models with variable selection
> ### Aliases: glmsel
> 
> ### ** Examples
> 
> data(bank)
> glmsel(y~age+as.factor(job)+as.factor(marital)+as.factor(education)+as.factor(default)+balance
+ +as.factor(housing)+as.factor(loan)+as.factor(contact)+as.factor(day)+month+duration+campaign
+ +pdays+previous, data=bank, varsel="enet")
Error in predict.cv.glmnet(cv, type = "coefficients") : 
  could not find function "predict.cv.glmnet"
Calls: glmsel -> glmsel.default
Execution halted
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 53.3Mb
  sub-directories of 1Mb or more:
    libs  52.0Mb
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.
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
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 ‘rinatVignette.Rmd’ using rmarkdown
Quitting from lines 100-102 (rinatVignette.Rmd) 
Error: processing vignette 'rinatVignette.Rmd' failed with diagnostics:
cannot open the connection to 'http://www.inaturalist.org/observations/project/597.csv?page=1&per_page=100'
--- failed re-building ‘rinatVignette.Rmd’

SUMMARY: processing the following file failed:
  ‘rinatVignette.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
Package suggested but not available for checking: ‘topGO’
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.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
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.
Found the following files/directories:
  ‘Sambada-error-log-20191122-192340.txt’
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’
Found the following files/directories:
  ‘atesttif.tif’
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 42.2Mb
  sub-directories of 1Mb or more:
    include   2.6Mb
    libs     39.3Mb
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.
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.
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.
Package suggested but not available for checking: ‘oligoClasses’
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.
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 10000 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.
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_2019-11-16.txt’ ‘results_2019-11-16_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.
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:
  ‘test24426-270.rData’ ‘test24426-35.rData’ ‘test24426-48.rData’
  ‘test24426-92.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/13s]
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/Rtmpu80tHY/working_dir/RtmpckM5sh/file219b2228c7f
  ── 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
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  7.0Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    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.
Running examples in ‘superml-Ex.R’ failed
The error most likely occurred in:

> ### Name: LMTrainer
> ### Title: Linear Models Trainer
> ### Aliases: LMTrainer
> ### Keywords: datasets
> 
> ### ** Examples
> 
> LINK <- "http://archive.ics.uci.edu/ml/machine-learning-databases/housing/housing.data"
> housing <- read.table(LINK)
> names <- c("CRIM","ZN","INDUS","CHAS","NOX","RM","AGE","DIS",
+            "RAD","TAX","PTRATIO","B","LSTAT","MEDV")
> names(housing)  <-  names
> lf <- LMTrainer$new(family = 'gaussian', alpha=1)
> lf$fit(X = housing, y = 'MEDV')
> predictions <- lf$predict(df = housing)
> 
> 
> # cross validation model
> lf$cv_model(X = housing, y = 'MEDV', nfolds = 5, parallel = FALSE)
Computation done.
> predictions <- lf$cv_predict(df = housing)
Error: 'predict.cv.glmnet' is not an exported object from 'namespace:glmnet'
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 143-148 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
'predict.cv.glmnet' is not an exported object from 'namespace:glmnet'
--- 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:
  ‘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.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
Found the following files/directories:
  ‘moment_20191117_0244.lp’
Found the following files/directories:
  ‘cfFVA1_cnd_det.csv’ ‘cfFVA1_cnd_res.csv’
  ‘glpk_llFBA_20191117_0244.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’ [104s/72s]
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
Running examples in ‘TANDEM-Ex.R’ failed
The error most likely occurred in:

> ### Name: coef.tandem
> ### Title: Returns the regression coefficients from a TANDEM fit
> ### Aliases: coef.tandem
> 
> ### ** Examples
> 
> # unpack example data
> x = example_data$x
> y = example_data$y
> upstream = example_data$upstream
> 
> # fit a tandem model, determine the coefficients and create a prediction
> fit = tandem(x, y, upstream, alpha=0.5)
Error: 'predict.cv.glmnet' is not an exported object from 'namespace:glmnet'
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Loading required package: Matrix
Loaded glmnet 3.0-1

Quitting from lines 27-31 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
'predict.cv.glmnet' is not an exported object from 'namespace:glmnet'
--- failed re-building ‘my-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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/RtmpiXQcV6/working_dir/RtmpePuuEI/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 ...QcV6/working_dir/RtmpePuuEI/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
Running ‘mv_genz.R’
  Running ‘mv_tlr.R’
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 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.
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-2019-11-17_030921.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.
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
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
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 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.
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_17_035300.xlsx’
  ‘myXLfile_2019_11_17_035301.xlsx’ ‘myXLfile_2019_11_17_035303.xlsx’
  ‘myXLfile_2019_11_17_035305.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_2019-11-18.jpeg’ ‘discordanceDelta_2019-11-18.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 0xad44a50, 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:
  ‘outhaplo171119101412799YDGABKNRWJ.txt’
  ‘outhaplo171119101415739XNBMRYFAHT.txt’
  ‘outhaplo171119101420090LOATCFJWUY.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-20191117-180158.txt’
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/BootValidation.Rcheck/00install.out’ for details.
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.
Error(s) in re-building vignettes:
Warning: elapsed-time limit of 30 minutes reached for sub-process
--- re-building ‘chk-benchmarking.Rmd’ using rmarkdown

Execution halted
--- re-building ‘chk-families.Rmd’ using rmarkdown
--- finished re-building ‘chk-families.Rmd’

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

SUMMARY: processing the following file failed:
  ‘chk-benchmarking.Rmd’

Error: Vignette re-building failed.
Execution halted
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.
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
Running ‘test.R’ [190s/118s]
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
Running ‘testthat.R’ [44s/49s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ctmle)
  Loading required package: SuperLearner
  Loading required package: nnls
  Super Learner
  Version: 2.0-25
  Package created on 2019-08-05
  
  Loading required package: tmle
  Loading required package: glmnet
  Loading required package: Matrix
  Loaded glmnet 3.0-1
  
  Welcome to the tmle package, version 1.4.0.1
  
  Use tmleNews() to see details on changes and bug fixes
  > 
  > test_check("ctmle")
  ── 1. Error: (unknown) (@test-ctmleGeneral.R#73)  ──────────────────────────────
  could not find function "predict.cv.glmnet"
  
  ── 2. Error: (unknown) (@test-ctmleGlmnet.R#69)  ───────────────────────────────
  could not find function "predict.cv.glmnet"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 9 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: (unknown) (@test-ctmleGeneral.R#73) 
  2. Error: (unknown) (@test-ctmleGlmnet.R#69) 
  
  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.
Package required but not available: ‘flowDensity’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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 0x611, 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 ...
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.2019-11-17.txt’
  ‘Example.t.overall.Dest.loci.2019-11-17.txt’
  ‘Example.t.overall.Dest.loci.ci2019-11-17.txt’
  ‘Example.t.overall.Dest.loci.p.2019-11-17.txt’
  ‘Example.t.overall.Dest.mean.2019-11-17.txt’
  ‘Example.t.overall.Dest.mean.ci2019-11-17.txt’
  ‘Example.t.overall.Dest.mean.p.2019-11-17.txt’
  ‘Example.t.sample.sizes.2019-11-17.txt’ ‘Example.u.H.values.txt’
  ‘Example.u.Hest_loci.values.txt’ ‘Example.u.Hest_mean.values.txt’
  ‘Example.u.allelefreq.2019-11-17.txt’
  ‘Example.u.pairwise.Gst.loci.2019-11-17.txt’
  ‘Example.u.pairwise.Gst.mean.2019-11-17.txt’
  ‘Example.u.sample.sizes.2019-11-17.txt’ ‘Output-Inputformat.txt’
Running ‘test-all.R’ [32s/34s]
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:
  /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]
  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 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_2019-11-17.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_statistics2019-11-21_13.34.35.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.
Package required but not available: ‘flowWorkspace’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [184s/445s]
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’ [90s/98s]
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.2019-11-17.1.1’
  ‘cat.expressions.dir.2019-11-17.1.2’
  ‘cat.expressions.dir.2019-11-17.1.3’
  ‘cat.expressions.dir.2019-11-17.1.4’
  ‘cat.expressions.dir.2019-11-17.1.5’
  ‘cat.expressions.dir.2019-11-17.1.6’
  ‘cat.expressions.dir.2019-11-17.1.7’
  ‘cat.expressions.dir.2019-11-17.1.8’
  ‘cat.expressions.dir.2019-11-17.1.9’
  ‘cat.expressions.dir.2019-11-17.2’
  ‘cat.expressions.dir.2019-11-17.2.1’
  ‘cat.expressions.dir.2019-11-17.2.2’
  ‘cat.expressions.dir.2019-11-17.2.3’
  ‘cat.expressions.dir.2019-11-17.2.4’
  ‘cat.expressions.dir.2019-11-17.2.5’
  ‘cat.expressions.dir.2019-11-17.2.6’
  ‘cat.expressions.dir.2019-11-17.2.7’ ‘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’
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:
  ../inst/include/hesim/Rbase/integrate.h:1687:5: warning: array subscript -1 is outside array bounds of ‘double [52]’ [-Warray-bounds]
See ‘/data/gannet/ripley/R/packages/tests-devel/hesim.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_20191117.xlsx’
  ‘1-Reasonableness_Var2_check_errors_20191117.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.
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.
Running ‘testthat.R’ [23s/54s]
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 ‘/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-2019-11-17-23-46-50.mm’ ‘md.R’ ‘md.mm’
  ‘mindr.md’ ‘mindr.mm’ ‘mm.md’ ‘outline-2019-11-17-23-46-51.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.
Found the following files/directories:
  ‘001509Nova Southeastern University20191118.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_logistic_sparse.h:10:36: warning: statement has no effect [-Wunused-value]
  oem_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_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_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_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:
  ‘file433395cb489.md’
Found the following files/directories:
  ‘Legend7a8021b5409f.png’ ‘Legend7a80384aa4a3.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.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/randomcoloR.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.
Running ‘testthat.R’ [75s/94s]
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. 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
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 files/directories:
  ‘Sambada-error-log-20191122-212510.txt’
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.
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_2019-11-17.txt’ ‘results_2019-11-17_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:
  ‘test35652-270.rData’ ‘test35652-35.rData’ ‘test35652-48.rData’
  ‘test35652-92.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/16s]
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/Rtmp9azzC9/working_dir/Rtmp9dJiZg/file5b473e2c56fc
  ── 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.
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: 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: ‘frac_harvk’ 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: ‘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-devel/SWATmodel.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘moment_20191118_0551.lp’ ‘moment_20191118_0552.lp’
Found the following files/directories:
  ‘cfFVA1_cnd_det.csv’ ‘cfFVA1_cnd_res.csv’
  ‘glpk_llFBA_20191118_0551.lp’
Running ‘testthat.R’ [84s/87s]
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/Rtmp1NfTAw/working_dir/RtmpBDmyMc/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 ...fTAw/working_dir/RtmpBDmyMc/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-2019-11-18_061744.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_18_072017.xlsx’
  ‘myXLfile_2019_11_18_072019.xlsx’ ‘myXLfile_2019_11_18_072021.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  5.8Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
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
Running 'test-all.R' [3s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > library(bagRboostR)
  > 
  > test_package("bagRboostR")
  -- 1. Error: samme returns a character vector of predicted classes (@test_samme.
  Need at least two classes to do classification.
  Backtrace:
   1. bagRboostR::samme(activity ~ ., train, test, 3, ntree = 5, trace = F) tests/test_samme.R:6:2
   3. randomForest:::randomForest.formula(...)
   4. randomForest:::randomForest.default(m, y, ...)
  
  == testthat results  ===========================================================
  [ OK: 39 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: samme returns a character vector of predicted classes (@test_samme.R#6) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  Placing tests in `inst/tests` is deprecated. Please use `tests/testthat` instead 
  Execution halted
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
Running examples in 'BART-Ex.R' failed
The error most likely occurred in:

> ### Name: crisk2.bart
> ### Title: BART for competing risks
> ### Aliases: crisk2.bart mc.crisk2.bart
> ### Keywords: nonparametric survival model nonproportional hazards
> 
> ### ** Examples
> 
> 
> data(transplant)
> 
> pfit <- survfit(Surv(futime, event) ~ abo, transplant)
Error in if (flag["teleport"] > 0) { : 
  missing value where TRUE/FALSE needed
Calls: survfit -> survfit.formula -> survfitCI -> survcheck2
Execution halted
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'
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
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/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 150.9Mb
  sub-directories of 1Mb or more:
    include  149.9Mb
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/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
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/BootValidation.Rcheck/00install.out' for details.
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.
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.
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  5.1Mb
  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.
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.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/CrypticIBDcheck.Rcheck/00install.out' for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    shp   7.8Mb
Running 'testthat.R' [48s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ctmle)
  Loading required package: SuperLearner
  Loading required package: nnls
  Super Learner
  Version: 2.0-25
  Package created on 2019-08-05
  
  Loading required package: tmle
  Loading required package: glmnet
  Loading required package: Matrix
  Loaded glmnet 3.0-1
  
  Welcome to the tmle package, version 1.4.0.1
  
  Use tmleNews() to see details on changes and bug fixes
  > 
  > test_check("ctmle")
  -- 1. Error: (unknown) (@test-ctmleGeneral.R#73)  ------------------------------
  could not find function "predict.cv.glmnet"
  
  -- 2. Error: (unknown) (@test-ctmleGlmnet.R#69)  -------------------------------
  could not find function "predict.cv.glmnet"
  
  == testthat results  ===========================================================
  [ OK: 9 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: (unknown) (@test-ctmleGeneral.R#73) 
  2. Error: (unknown) (@test-ctmleGlmnet.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown
Quitting from lines 147-160 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
could not find function "predict.cv.glmnet"
--- failed re-building 'vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
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/DALEXtra.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:11095 (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.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.8Mb
    help   1.4Mb
    libs   1.8Mb
Running examples in 'DevTreatRules-Ex.R' failed
The error most likely occurred in:

> ### Name: CompareRulesOnValidation
> ### Title: Build treatment rules on a development dataset and evaluate
> ###   performance on an independent validation dataset
> ### Aliases: CompareRulesOnValidation
> 
> ### ** Examples
> 
> set.seed(123)
> example.split <- SplitData(data=obsStudyGeneExpressions,
+                                     n.sets=3, split.proportions=c(0.5, 0.25, 0.25))
> development.data <- example.split[example.split$partition == "development", ]
> validation.data <- example.split[example.split$partition == "validation", ]
> model.selection <- CompareRulesOnValidation(development.data=development.data,
+                validation.data=validation.data,
+                study.design.development="observational",
+                vec.approaches=c("split.regression", "OWL.framework", "direct.interactions"),
+                vec.rule.methods=c("glm.regression", "lasso"),
+                vec.propensity.methods="logistic.regression",
+                name.outcome.development="no_relapse",
+                type.outcome.development="binary",
+                name.treatment.development="intervention",
+                names.influencing.treatment.development=c("prognosis", "clinic", "age"),
+                names.influencing.rule.development=c("age", paste0("gene_", 1:10)),
+                desirable.outcome.development=TRUE)
Error in predict.cv.glmnet(one.cv.glmnet, newx = features, s = optimal.lambda,  : 
  could not find function "predict.cv.glmnet"
Calls: CompareRulesOnValidation -> BuildRule -> DoPrediction
Execution halted
Error(s) in re-building vignettes:
--- re-building 'my-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

Quitting from lines 84-97 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
could not find function "predict.cv.glmnet"
--- failed re-building 'my-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
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:11040 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11040 (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:11144 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11144 (sockconn)
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    5.1Mb
    libs   1.4Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    5.6Mb
    libs   1.4Mb
installed size is  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
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.
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' [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
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.
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
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
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
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'
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.
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').
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/GET.Rcheck/00install.out' for details.
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/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' [105s]
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:11641 (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:11282 (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'
Running 'testthat.R' [31s]
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: 2 | 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 '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.
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
Running examples in 'HCTR-Ex.R' failed
The error most likely occurred in:

> ### Name: highdim.p
> ### Title: p-values in high-dimensional linear model
> ### Aliases: highdim.p
> 
> ### ** Examples
> 
> set.seed(10)
> X <- matrix(rnorm(20000), nrow = 100)
> beta <- rep(0, 200)
> beta[1:100] <- 5
> Y <- MASS::mvrnorm(n = 1, mu = X%*%beta, Sigma = diag(100))
> result <- highdim.p(Y=Y, X=X, type = "Lasso", B = 2, fold.num = 10)
Error: 'coef.cv.glmnet' is not an exported object from 'namespace:glmnet'
Execution halted
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
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  6.9Mb
  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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Irescale.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:11411 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11411 (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:11383 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11383 (sockconn)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/ISM.Rcheck/00install.out' for details.
installed size is  6.3Mb
  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
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  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
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.
Running examples in 'mbclusterwise-Ex.R' failed
The error most likely occurred in:

> ### Name: cw.tenfold
> ### Title: F-Fold cross-validation for clusterwise multiblock analyses
> ### Aliases: cw.tenfold
> ### Keywords: multivariate cluster
> 
> ### ** Examples
> 
>   data(simdata.red) 
>   Data.X <- simdata.red[c(1:8, 21:28), 1:10]
>   Data.Y <- simdata.red[c(1:8, 21:28), 11:13]
>   res1   <- list()
>   res2   <- list()
> 
>   ## Note that the options (INIT=2) and (parallel.level = "low") are chosen to quickly
>   ## illustrate the function. 
>   ## For real data, instead choose (INIT=20) to avoid local optima and (parallel.level = "high")
>   ## to improve the computing speed.
> 
>   for (H in c(1:2)){
+     print(paste("H=", H, sep=""))
+     res1[[H]] <- cw.tenfold(Y = Data.Y, X = Data.X, blo = c(5, 5), option = "none", G = 1, H,  
+       FOLD = 2, INIT = 2, method = "mbpls", Gamma = NULL, parallel.level = "low")
+     res2[[H]] <- cw.tenfold(Y = Data.Y, X = Data.X, blo = c(5, 5), option = "none", G = 2, H,
+        FOLD = 2, INIT = 2, method = "mbpls", Gamma = NULL, parallel.level = "low")
+   }
[1] "H=1"
[1] "Fold 1"
Warning in res$lX[, h]/sqrt(t(res$lX[, h]) %*% res$lX[, h]) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

[1] "Fold 2"
Warning in res$lX[, h]/sqrt(t(res$lX[, h]) %*% res$lX[, h]) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

[1] "Fold 1"
Warning in e$fun(obj, substitute(ex), parent.frame(), e$data) :
  already exporting variable(s): mbreg
Error in { : task 1 failed - "0 x 0 matrix"
Calls: cw.tenfold -> cw.multiblock -> %dopar% -> <Anonymous>
Execution halted
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.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      1.5Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/melviewr.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/MergeGUI.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.1Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/metagear.Rcheck/00install.out' for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.1Mb
Packages suggested but not available for checking: 'doMC', 'doSMP'
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
Loading required package: glmnet
Loading required package: Matrix
Loaded glmnet 3.0-1

Error: package or namespace load failed for 'mht':
 .onAttach failed in attachNamespace() for 'mht', details:
  call: packageDescription("mht")
  error: could not find function "packageDescription"
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
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' [33s]
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' [40s]
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 17.4Mb
  sub-directories of 1Mb or more:
    R        2.5Mb
    libs     7.2Mb
    models   4.7Mb
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
Running examples in 'plsmselect-Ex.R' failed
The error most likely occurred in:

> ### Name: cumbasehaz
> ### Title: Cumulative Baseline Hazard of a gamlasso object
> ### Aliases: cumbasehaz
> 
> ### ** Examples
> 
> library(plsmselect)
> library(tidyverse)
-- Attaching packages --------------------------------------- tidyverse 1.2.1 --
v ggplot2 3.2.1     v purrr   0.3.3
v tibble  2.1.3     v dplyr   0.8.3
v tidyr   1.0.0     v stringr 1.4.0
v readr   1.3.1     v forcats 0.4.0
-- Conflicts ------------------------------------------ tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x dplyr::lag()    masks stats::lag()
> 
> data(simData)
> 
> ## Fit Cox gamlasso model using the formula approach:
> ## (L1-penalty both on X terms and smooth terms (bs="ts"))
> simData$X = model.matrix(~x1+x2+x3+x4+x5+x6+x7+x8+x9+x10, data=simData)[,-1]
> 
> cfit = gamlasso(time ~ X +
+                   s(z1, bs="ts", k=5) +
+                   s(z2, bs="ts", k=5) +
+                   s(z3, bs="ts", k=5) +
+                   s(z4, bs="ts", k=5),
+                 data = simData,
+                 family = "cox",
+                 weights="status",
+                 seed=1)
Fitting a lasso and gam loop ... 

Error: 'predict.cv.glmnet' is not an exported object from 'namespace:glmnet'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'plsmselect.Rmd' using rmarkdown
-- Attaching packages --------------------------------------- tidyverse 1.2.1 --
v ggplot2 3.2.1     v purrr   0.3.3
v tibble  2.1.3     v dplyr   0.8.3
v tidyr   1.0.0     v stringr 1.4.0
v readr   1.3.1     v forcats 0.4.0
-- Conflicts ------------------------------------------ tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x dplyr::lag()    masks stats::lag()
Fitting a lasso and gam loop ... 

Quitting from lines 168-180 (plsmselect.Rmd) 
Error: processing vignette 'plsmselect.Rmd' failed with diagnostics:
'predict.cv.glmnet' is not an exported object from 'namespace:glmnet'
--- failed re-building 'plsmselect.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   1.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
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.
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
Rd conversion errors:
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  for details.
*
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
Running examples in 'PxWebApiData-Ex.R' failed
The error most likely occurred in:

> ### Name: ApiData
> ### Title: PX-Web Data by API
> ### Aliases: ApiData pxwebData PxData
> 
> ### ** Examples
> 
> ##### Advanced use using list. See details above. Try returnApiQuery=TRUE on the same examples. 
> ApiData(4861, Region = list("03*"), ContentsCode = 1, Tid = 5i) # "all" can be dropped from the list
Warning in open.connection(con, "rb") :
  cannot open URL 'http://data.ssb.no/api/v0/no/table/04861': HTTP status was '503 Service Unavailable'
Error in open.connection(con, "rb") : cannot open the connection
Calls: ApiData ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
Execution halted
Error(s) in re-building vignettes:
--- re-building 'Introduction.Rmd' using rmarkdown
Quitting from lines 40-43 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'Introduction.Rmd'

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

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

> ### Name: hmm.predict
> ### Title: 1-step forward prediction for (autoregressive) Gaussian hidden
> ###   Markov model
> ### Aliases: hmm.predict
> 
> ### ** Examples
> 
> set.seed(15562)
> m <- 2
> mu <- list(c(3,4,5),c(-2,-3,-4))
> sigma <- list(diag(1.3,3), 
+             matrix(c(1,-0.3,0.2,-0.3,1.5,0.3,0.2,0.3,2),3,3,byrow=TRUE))
> delta <- c(0.5,0.5)
> gamma <- matrix(c(0.8,0.2,0.1,0.9),2,2,byrow=TRUE)
> auto <- list(matrix(c(0.3,0.2,0.1,0.4,0.3,0.2,
+                      -0.3,-0.2,-0.1,0.3,0.2,0.1,
+                       0,0,0,0,0,0),3,6,byrow=TRUE),
+             matrix(c(0.2,0,0,0.4,0,0,
+                       0,0.2,0,0,0.4,0,
+                      0,0,0.2,0,0,0.4),3,6,byrow=TRUE))
> mod <- list(m=m,mu=mu,sigma=sigma,delta=delta,gamma=gamma,auto=auto,arp=2)
> sim <- hmm.sim(2000,mod)
> y <- sim$series
> state <- sim$state
> fit <- em.hmm(y=y, mod=mod, arp=2, tol=1e-5)
Error: 'predict.mrelnet' is not an exported object from 'namespace:glmnet'
Execution halted
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.
Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'rqubic',
  'BicARE', 's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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
Running examples in 'regsel-Ex.R' failed
The error most likely occurred in:

> ### Name: glmsel
> ### Title: Generalised linear models with variable selection
> ### Aliases: glmsel
> 
> ### ** Examples
> 
> data(bank)
> glmsel(y~age+as.factor(job)+as.factor(marital)+as.factor(education)+as.factor(default)+balance
+ +as.factor(housing)+as.factor(loan)+as.factor(contact)+as.factor(day)+month+duration+campaign
+ +pdays+previous, data=bank, varsel="enet")
Error in predict.cv.glmnet(cv, type = "coefficients") : 
  could not find function "predict.cv.glmnet"
Calls: glmsel -> glmsel.default
Execution halted
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  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
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      5.5Mb
'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.
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 11.0Mb
  sub-directories of 1Mb or more:
    include   2.5Mb
    libs      8.1Mb
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/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 10.6Mb
  sub-directories of 1Mb or more:
    include   9.4Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    doc  10.3Mb
    nc    4.5Mb
installed size is  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  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    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.
Running examples in 'superml-Ex.R' failed
The error most likely occurred in:

> ### Name: LMTrainer
> ### Title: Linear Models Trainer
> ### Aliases: LMTrainer
> ### Keywords: datasets
> 
> ### ** Examples
> 
> LINK <- "http://archive.ics.uci.edu/ml/machine-learning-databases/housing/housing.data"
> housing <- read.table(LINK)
> names <- c("CRIM","ZN","INDUS","CHAS","NOX","RM","AGE","DIS",
+            "RAD","TAX","PTRATIO","B","LSTAT","MEDV")
> names(housing)  <-  names
> lf <- LMTrainer$new(family = 'gaussian', alpha=1)
> lf$fit(X = housing, y = 'MEDV')
> predictions <- lf$predict(df = housing)
> 
> 
> # cross validation model
> lf$cv_model(X = housing, y = 'MEDV', nfolds = 5, parallel = FALSE)
Computation done.
> predictions <- lf$cv_predict(df = housing)
Error: 'predict.cv.glmnet' is not an exported object from 'namespace:glmnet'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown
Quitting from lines 143-148 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
'predict.cv.glmnet' is not an exported object from 'namespace:glmnet'
--- failed re-building 'introduction.Rmd'

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

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

> ### Name: coef.tandem
> ### Title: Returns the regression coefficients from a TANDEM fit
> ### Aliases: coef.tandem
> 
> ### ** Examples
> 
> # unpack example data
> x = example_data$x
> y = example_data$y
> upstream = example_data$upstream
> 
> # fit a tandem model, determine the coefficients and create a prediction
> fit = tandem(x, y, upstream, alpha=0.5)
Error: 'predict.cv.glmnet' is not an exported object from 'namespace:glmnet'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'my-vignette.Rmd' using rmarkdown
Loading required package: Matrix
Loaded glmnet 3.0-1

Quitting from lines 27-31 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
'predict.cv.glmnet' is not an exported object from 'namespace:glmnet'
--- failed re-building 'my-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
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 '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  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
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/4.0v3/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/4.0v3/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/4.0v3/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/4.0v3/aslib.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/audio.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/AWR.Athena.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/AWR.Kinesis.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/AWR.KMS.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/AWR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/awsjavasdk.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/BALD.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/bartMachineJARs.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/BASiNET.Rcheck/00install.out' for details.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/bayesCL.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/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/4.0v3/BEACH.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/beadarrayMSV.Rcheck/00install.out' for details.
installed size is 150.3Mb
  sub-directories of 1Mb or more:
    include  149.4Mb
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/4.0v3/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0v3/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0v3/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0v3/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0v3/bigalgebra.Rcheck/00install.out' for details.
Found the following significant warnings:
  D:/RCompile/CRANpkg/lib/4.0v3/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0v3/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0v3/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0v3/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0v3/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0v3/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0v3/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0v3/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0v3/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0v3/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/Biocomb.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/boilerpipeR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/BonEV.Rcheck/00install.out' for details.
installed size is 62.2Mb
  sub-directories of 1Mb or more:
    include   8.6Mb
    lib      53.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/BootValidation.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/BPEC.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/C50.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/Cairo.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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
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/4.0v3/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/4.0v3/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/4.0v3/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/4.0v3/clv.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/CollapsABEL.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/collUtils.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'commonsMath.Rmd' using rmarkdown
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

Quitting from lines 32-37 (commonsMath.Rmd) 
Error: processing vignette 'commonsMath.Rmd' failed with diagnostics:
Error in scalaConfig(FALSE): 

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

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

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


--- failed re-building 'commonsMath.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/corehunter.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/CovSelHigh.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/cplexAPI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/Crossover.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/4.0v3/CrypticIBDcheck.Rcheck/00install.out' for details.
Running 'testthat.R' [40s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ctmle)
  Loading required package: SuperLearner
  Loading required package: nnls
  Super Learner
  Version: 2.0-25
  Package created on 2019-08-05
  
  Loading required package: tmle
  Loading required package: glmnet
  Loading required package: Matrix
  Loaded glmnet 3.0-1
  
  Welcome to the tmle package, version 1.4.0.1
  
  Use tmleNews() to see details on changes and bug fixes
  > 
  > test_check("ctmle")
  -- 1. Error: (unknown) (@test-ctmleGeneral.R#73)  ------------------------------
  could not find function "predict.cv.glmnet"
  
  -- 2. Error: (unknown) (@test-ctmleGlmnet.R#69)  -------------------------------
  could not find function "predict.cv.glmnet"
  
  == testthat results  ===========================================================
  [ OK: 9 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: (unknown) (@test-ctmleGeneral.R#73) 
  2. Error: (unknown) (@test-ctmleGlmnet.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
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/4.0v3/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/4.0v3/Cubist.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: No CA bundle found. SSL validation disabled.
See 'd:/Rcompile/CRANpkg/local/4.0v3/curl.Rcheck/00install.out' for details.
Running 'spelling.R' [0s]
  Running 'testthat.R' [62s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(curl)
  Warning message:
  No CA bundle found. SSL validation disabled. 
  > 
  > # Comply with CRAN policy: skip tests if no internet
  > if(curl::has_internet()){
  +   test_check("curl")
  + }
  This is libcurl version 7.64.1 with OpenSSL/1.1.1a (Schannel) 
  Using test server: http://hb.opencpu.org 
  -- 1. Failure: Invalid domain raises an error (@test-certificates.R#15)  -------
  `curl_fetch_memory(fake_url)` did not throw an error.
  
  == testthat results  ===========================================================
  [ OK: 216 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Invalid domain raises an error (@test-certificates.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'spelling.R' [0s]
  Running 'testthat.R' [70s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(curl)
  Warning message:
  No CA bundle found. SSL validation disabled. 
  > 
  > # Comply with CRAN policy: skip tests if no internet
  > if(curl::has_internet()){
  +   test_check("curl")
  + }
  This is libcurl version 7.64.1 with OpenSSL/1.1.1a (Schannel) 
  Using test server: http://hb.opencpu.org 
  -- 1. Failure: Invalid domain raises an error (@test-certificates.R#15)  -------
  `curl_fetch_memory(fake_url)` did not throw an error.
  
  == testthat results  ===========================================================
  [ OK: 217 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Invalid domain raises an error (@test-certificates.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    libs   2.4Mb
Package required but not available: 'flowDensity'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  Warning: No CA bundle found. SSL validation disabled.
See 'd:/Rcompile/CRANpkg/local/4.0v3/CytobankAPI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/CytobankAPIstats.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: No CA bundle found. SSL validation disabled.
See 'd:/Rcompile/CRANpkg/local/4.0v3/CytobankBridgeR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/DALEXtra.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/DatabaseConnectorJars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/DataClean.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/DataGraph.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/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:11776 (sockconn)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/DecorateR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/DeducerPlugInExample.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/DeducerPlugInScaling.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/Deducer.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/DeducerSpatial.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/DeducerSurvival.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/DeducerText.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/deisotoper.Rcheck/00install.out' for details.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
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  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.7Mb
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/4.0v3/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/4.0v3/dialrjars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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:11309 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11309 (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:11435 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11435 (sockconn)
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    5.1Mb
    libs   2.0Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    5.6Mb
    libs   2.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/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/4.0v3/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
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:
> ### Title: Trim and Format Address Information
> ### Aliases: trim_address
> 
> ### ** Examples
> 
> addr_string <- " 2 Dept of Urology, Feinberg School of Medicine," 
> addr_string <- paste(addr_string, "Chicago, US; Dept of Mol Bio as well...")
> print(addr_string)
[1] " 2 Dept of Urology, Feinberg School of Medicine, Chicago, US; Dept of Mol Bio as well..."
> print(trim_address(addr = addr_string))
[1] "Dept of Urology, Feinberg School of Medicine, Chicago, US"
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  1.62 0.66 484.8 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Running examples in 'ecoseries-Ex.R' failed
The error most likely occurred in:

> ### Name: series_bacen
> ### Title: A function to extract BACEN series using their API
> ### Aliases: series_bacen
> ### Keywords: bacen
> 
> ### ** Examples
> 
> bacen = series_bacen(x=c(2465, 1242))
Error in function (type, msg, asError = TRUE)  : 
  Recv failure: Connection was reset
Calls: series_bacen ... <Anonymous> -> <Anonymous> -> curlPerform -> <Anonymous> -> fun
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/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/4.0v3/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/4.0v3/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/4.0v3/EnsembleBase.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/EnsembleCV.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/EnsemblePCReg.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/epanet2toolkit.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/evoper.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/expands.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/extraTrees.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   2.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/FactoInvestigate.Rcheck/00install.out' for details.
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/4.0v3/FastRWeb.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   2.0Mb
installed size is  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
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/4.0v3/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/4.0v3/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
Package required but not available: 'flowWorkspace'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
Found the following significant warnings:
  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/4.0v3/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/4.0v3/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/4.0v3/fsdaR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/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/4.0v3/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      5.1Mb
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/4.0v3/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/4.0v3/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/4.0v3/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/4.0v3/glmulti.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/GMKMcharlie.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: No CA bundle found. SSL validation disabled.
See 'd:/Rcompile/CRANpkg/local/4.0v3/GoogleKnowledgeGraphR.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/4.0v3/GPB.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/gpuR.Rcheck/00install.out' for details.
Running 'testthat.R' [82s]
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/4.0v3/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/4.0v3/GreedyExperimentalDesignJARs.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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:11142 (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:11256 (sockconn)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/growthPheno.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/gWidgets2RGtk2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/gWidgetsRGtk2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/haven.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/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/4.0v3/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/4.0v3/highlight.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   3.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.6Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   1.4Mb
    libs   2.9Mb
installed size is  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/4.0v3/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/4.0v3/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/4.0v3/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/4.0v3/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/4.0v3/InSilicoVA.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/intamapInteractive.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/InterfaceqPCR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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:11929 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11929 (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:11380 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11380 (sockconn)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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  6.8Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs           4.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/jdx.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/joinXL.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/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/4.0v3/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/4.0v3/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' [62s]
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/4.0v3/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/4.0v3/llama.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/LLM.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/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/4.0v3/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/4.0v3/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/4.0v3/lolog.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Running 'testthat.R' [39s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(loose.rock)
  > 
  > test_check("loose.rock")
  -- 1. Error: coding genes retrieves some genes (@test-coding.genes.R#4)  -------
  cannot open the connection
  Backtrace:
   1. loose.rock::coding.genes(verbose = FALSE)
   4. utils::read.table(...)
   6. base::open.connection(file, "rt")
  
  == testthat results  ===========================================================
  [ OK: 146 | SKIPPED: 2 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: coding genes retrieves some genes (@test-coding.genes.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
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/4.0v3/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/4.0v3/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/4.0v3/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/4.0v3/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/4.0v3/maGUI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/mailR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/mallet.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 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/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/4.0v3/matchingMarkets.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/mdendro.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/4.0v3/melviewr.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/metagear.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/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
Running examples in 'micropan-Ex.R' failed
The error most likely occurred in:

> ### Name: entrezDownload
> ### Title: Downloading genome data
> ### Aliases: entrezDownload
> 
> ### ** Examples
> 
> # Accession numbers for the chromosome and plasmid of Buchnera aphidicola, strain APS
> acc <- "BA000003.2,AP001071.1"
> tf <- tempfile(pattern="Buchnera_aphidicola",fileext=".fasta")
> txt <- entrezDownload(acc,out.file=tf)
Downloading genome...Warning in url(adr, open = "rt") :
  cannot open URL 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=BA000003.2,AP001071.1&retmode=text&rettype=fasta': HTTP status was '503 Service Unavailable'
Error in url(adr, open = "rt") : cannot open the connection
Calls: entrezDownload -> url
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/MigClim.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/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/4.0v3/mlDNA.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/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/4.0v3/mongolite.Rcheck/00install.out' for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
installed size is  5.6Mb
  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/4.0v3/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/4.0v3/multinet.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/mutossGUI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/mwa.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/Myrrixjars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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
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/4.0v3/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 19.4Mb
  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' [26s]
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' [31s]
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/4.0v3/NLPutils.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   2.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
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/4.0v3/odbc.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/ODB.Rcheck/00install.out' for details.
installed size is  5.9Mb
  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/4.0v3/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 17.8Mb
  sub-directories of 1Mb or more:
    R        2.5Mb
    libs     7.6Mb
    models   4.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/openNLPdata.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/openNLP.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/OpenStreetMap.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/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/4.0v3/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/4.0v3/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/4.0v3/PairwiseD.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/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/4.0v3/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/4.0v3/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
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs  13.1Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    libs   13.8Mb
    share  11.9Mb
Running examples in 'penDvine-Ex.R' failed
The error most likely occurred in:

> ### Name: penDvine-package
> ### Title: The package 'penDvine' offers routines for estimating densities
> ###   and copula distribution of D-vines.
> ### Aliases: penDvine-package
> 
> ### ** Examples
> 
> #This examples describes the estimation of a D-vine to winddata,
> #available in this package. After the margins are prepared, we estimate a
> #D-vine using B-splines with 9 (K+1) marginal knots and penalizing second (m=2)
> #order differences (pen=1) of the basis coefficients.
> 
> data(Winddata)
> ex.data<-Winddata[c(1:100),c(1:4)] #examplary subdata for fast calculation
> wind.example<-Dvine(ex.data,K=7,pen=1,lambda=100,order.Dvine=FALSE,base="B-spline",m=2,cores=2)
>   
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11870 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11870 (sockconn)
Execution halted
Running 'testthat.R' [31s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(pense)
  Loading required package: Matrix
  > 
  > test_check("pense")
  -- 1. Failure: enpy (@test.enpy.rr.R#43)  --------------------------------------
  sum(abs(diffs)) is not strictly less than 1e-08. Difference: 199
  
  == testthat results  ===========================================================
  [ OK: 119 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 1 ]
  1. Failure: enpy (@test.enpy.rr.R#43) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs        2.0Mb
    xvg-files   3.2Mb
Found the following significant warnings:
  permTest.c:20:3: warning: statement with no effect [-Wunused-value]
  permTest.c:62:3: warning: statement with no effect [-Wunused-value]
  permTest.c:90:3: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0v3/permDep.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/petro.One.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   2.2Mb
Running 'testthat.R' [79s]
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 194191 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 194191 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 194191 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 261232 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  6.8Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
    libs      2.0Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Error(s) in re-building vignettes:
--- re-building 'phybreak_intro.Rmd' using rmarkdown
Quitting from lines 30-45 (phybreak_intro.Rmd) 
Error: processing vignette 'phybreak_intro.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'phybreak_intro.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   3.2Mb
Warning in inla.print.version() :
  INLA_18.07.12: 32bit binaries are no longer supported!

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/PKgraph.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/plfMA.Rcheck/00install.out' for details.
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.
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/4.0v3/poibin.Rcheck/00install.out' for details.
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/4.0v3/PortfolioEffectEstim.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/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.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    gui          1.1Mb
    staticdocs   3.3Mb
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/4.0v3/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/4.0v3/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/4.0v3/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/Rcmdr.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/Rcplex.Rcheck/00install.out' for details.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    include   5.9Mb
    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  9.1Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib       3.8Mb
    libs      3.4Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
    libs      2.2Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib      13.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    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/4.0v3/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/4.0v3/Rdroolsjars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/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/4.0v3/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/4.0v3/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/4.0v3/RGtk2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/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/4.0v3/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/4.0v3/RInside.Rcheck/00install.out' for details.
installed size is 14.8Mb
  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/4.0v3/RJDBC.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/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/4.0v3/RKEAjars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/RKEA.Rcheck/00install.out' for details.
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    exe  23.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/Rknots.Rcheck/00install.out' for details.
Running examples in 'Rlabkey-Ex.R' failed
The error most likely occurred in:

> ### Name: getFolderPath
> ### Title: Returns the folder path associated with a session
> ### Aliases: getFolderPath
> ### Keywords: file
> 
> ### ** Examples
> 
> 
> # library(Rlabkey)
> 
> lks<- getSession("http://www.labkey.org", "/home")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  SSL certificate problem: unable to get local issuer certificate
Calls: getSession ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
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/4.0v3/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  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
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
Running examples in 'RMixtComp-Ex.R' failed
The error most likely occurred in:

> ### Name: RMixtComp-package
> ### Title: RMixtComp
> ### Aliases: RMixtComp-package
> ### Keywords: package
> 
> ### ** Examples
> 
> data(simData)
>  
> # define the algorithm's parameters: you can use createAlgo function
> algo <- list(nbBurnInIter = 50,
+              nbIter = 50,
+              nbGibbsBurnInIter = 50,
+              nbGibbsIter = 50,
+              nInitPerClass = 20,
+              nSemTry = 20,
+              confidenceLevel = 0.95)
> 
> # run RMixtComp for learning using only 3 variables
> resLearn <- mixtCompLearn(simData$dataLearn$matrix, simData$model$unsupervised[1:3], algo,
+                           nClass = 2:3, nRun = 2, nCore = 1)
====== Run MixtComp in learn mode with 2 run(s) per number of classes and 1 core(s)
Data: 200 individuals and 3 variables.
-- K = 2
Start run 1
Run 1 DONE 
Start run 2
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/RMOAjars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/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/4.0v3/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      6.2Mb
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/4.0v3/ROpenCVLite.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/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/4.0v3/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/4.0v3/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/4.0v3/RSclient.Rcheck/00install.out' for details.
Found the following significant warnings:
  RSserver.c:64:44: warning: passing argument 4 of 'setsockopt' from incompatible pointer type [-Wincompatible-pointer-types]
   #warning Please include winsock2.h before windows.h
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/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/4.0v3/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/4.0v3/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/4.0v3/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/4.0v3/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/4.0v3/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/4.0v3/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/4.0v3/RWekajars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/RWeka.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/RxnSim.Rcheck/00install.out' for details.
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
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/4.0v3/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/4.0v3/SeqGrapheR.Rcheck/00install.out' for details.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   3.6Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
    libs   2.0Mb
installed size is 95.5Mb
  sub-directories of 1Mb or more:
    doc     12.0Mb
    gdal     3.9Mb
    libs    70.6Mb
    proj     5.0Mb
    sqlite   1.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   3.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   4.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/SimuChemPC.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   3.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/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/4.0v3/slfm.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/smartR.Rcheck/00install.out' for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   3.1Mb
Running 'testthat.R' [86s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(smooth)
  Loading required package: greybox
  Package "greybox", v0.5.6 loaded.
  This is package "smooth", v2.5.4
  > 
  > test_check("smooth")
  -- 1. Failure: Select exogenous variables for GUMX on N1457 (@test_ges.R#40)  --
  suppressWarnings(testModel$xreg) is not null.
  
  == testthat results  ===========================================================
  [ OK: 72 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Select exogenous variables for GUMX on N1457 (@test_ges.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  createPosDef.cpp:84:13: warning: statement has no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0v3/smoothSurv.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.6Mb
    libs   2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/sonicscrewdriver.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   2.8Mb
Found the following significant warnings:
  fft.c:138:9: warning: array subscript -1 is below array bounds of 'int[15]' [-Warray-bounds]
See 'd:/Rcompile/CRANpkg/local/4.0v3/SpatialExtremes.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   2.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/spatsurv.Rcheck/00install.out' for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
    libs   3.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/spcosa.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   2.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   2.1Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   3.1Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   2.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/SqlRender.Rcheck/00install.out' for details.
Found the following significant warnings:
  dbfopenSSN.c:1119:6: warning: 'strncpy' output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:1100:6: warning: 'strncpy' output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:663:2: warning: 'strncpy' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopenSSN.c:1511:2: warning: 'strncpy' output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0v3/SSN.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/stacomiR.Rcheck/00install.out' for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    include   8.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.5Mb
Found the following significant warnings:
  MaxChi.c:468:20: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  Phylpro.c:457:24: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
See 'd:/Rcompile/CRANpkg/local/4.0v3/stepwise.Rcheck/00install.out' for details.
Running examples in 'stepwise-Ex.R' failed
The error most likely occurred in:

> ### Name: phylpro
> ### Title: Stepwise detection of recombination breakpoints using Phylpro
> ### Aliases: phylpro
> ### Keywords: htest
> 
> ### ** Examples
>  demo(phylpro) 


	demo(phylpro)
	---- ~~~~~~~

> inputFile<-system.file("extdata", "simulinfile.txt", package = "stepwise")

> breaks<-c(548, 735, 832)

> WinHalfWidth<-30

> permReps<-10

> b<-phylpro(inputFile, breaks, WinHalfWidth, permReps)

> summary.phylpro(b)
Error in siteChisqs[1] <- object$corrs[1] : replacement has length zero
Calls: demo ... source -> withVisible -> eval -> eval -> summary.phylpro
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.5Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   2.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   2.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/streamMOA.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.2Mb
Found the following significant warnings:
  icu61/common/cstring.h:43:70: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0v3/stringi.Rcheck/00install.out' for details.
installed size is 35.6Mb
  sub-directories of 1Mb or more:
    libs  34.8Mb
Found the following significant warnings:
  computeQ.cpp:75:15: warning: catching polymorphic type 'class std::runtime_error' by value [-Wcatch-value=]
  computeQ.cpp:134:15: warning: catching polymorphic type 'class std::runtime_error' by value [-Wcatch-value=]
  computeQ.cpp:142:17: warning: catching polymorphic type 'class std::runtime_error' by value [-Wcatch-value=]
See 'd:/Rcompile/CRANpkg/local/4.0v3/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=]
See 'd:/Rcompile/CRANpkg/local/4.0v3/subprocess.Rcheck/00install.out' for details.
Running 'testthat.R' [132s]
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
Running 'testthat.R' [131s]
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/4.0v3/subspace.Rcheck/00install.out' for details.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    help   1.0Mb
    libs   2.2Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
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/4.0v3/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: 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/4.0v3/SWATmodel.Rcheck/00install.out' for details.
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/table1xls.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/tabulizerjars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/tabulizer.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.9Mb
    libs   2.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   3.2Mb
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs      13.9Mb
    tessdata  14.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   2.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.0Mb
Found the following significant warnings:
  D:/RCompile/CRANpkg/lib/4.0v3/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]
  D:/RCompile/CRANpkg/lib/4.0v3/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 'd:/Rcompile/CRANpkg/local/4.0v3/text2vec.Rcheck/00install.out' for details.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    3.6Mb
    libs   2.6Mb
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    2.03 
> 
> 
> 
> cleanEx()

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

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11425 (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    2.42 
> 
> 
> 
> cleanEx()

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

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11474 (sockconn)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/textmining.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.9Mb
    libs      2.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs         2.2Mb
    references   1.1Mb
Found the following significant warnings:
  lmdb/mdb.c:1734:2: warning: array subscript 8192 is above array bounds of 'char[5120]' [-Warray-bounds]
See 'd:/Rcompile/CRANpkg/local/4.0v3/thor.Rcheck/00install.out' for details.
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    examples  19.5Mb
    include    2.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/tm.plugin.webmining.Rcheck/00install.out' for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   2.0Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs  11.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/TSsdmx.Rcheck/00install.out' for details.
Found the following significant warnings:
  libqhull/rboxlib.c:351:5: warning: 'strncat' output may be truncated copying between 0 and 199 bytes from a string of length 199 [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0v3/TukeyRegion.Rcheck/00install.out' for details.
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    doc         6.9Mb
    dummydata   1.4Mb
    libs        4.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.6Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.6Mb
    libs   2.8Mb
Found the following significant warnings:
  libunrtf/my_iconv.c:56:18: warning: passing argument 2 of 'libiconv' from incompatible pointer type [-Wincompatible-pointer-types]
  libunrtf/my_iconv.c:149:27: warning: passing argument 2 of 'libiconv' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0v3/unrtf.Rcheck/00install.out' for details.
Found the following significant warnings:
  gen_uuid.c:309:11: warning: ordered comparison of pointer with integer zero [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0v3/uuid.Rcheck/00install.out' for details.
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
Found the following significant warnings:
  include/rapidjson/document.h:1952:24: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'rapidjson::GenericValue<rapidjson::UTF8<> >::Member' {aka 'struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::MemoryPoolAllocator<> >'} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'class rapidjson::GenericValue<rapidjson::UTF8<> >' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  include/rapidjson/document.h:1952:24: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>::Member' {aka 'struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::CrtAllocator>'} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'class rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See 'd:/Rcompile/CRANpkg/local/4.0v3/validatejsonr.Rcheck/00install.out' for details.
installed size is 79.7Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    gdal      3.8Mb
    libs     69.4Mb
    proj      5.0Mb
Found the following significant warnings:
  Warning: No CA bundle found. SSL validation disabled.
See 'd:/Rcompile/CRANpkg/local/4.0v3/VarfromPDB.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/venneuler.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/VIMGUI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/vmsbase.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/vortexR.Rcheck/00install.out' for details.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    doc   11.9Mb
    libs   2.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   2.2Mb
Found the following significant warnings:
  tabix/razf.c:188:2: warning: 'strncpy' output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0v3/WhopGenome.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/WMCapacity.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/wordnet.Rcheck/00install.out' for details.
Found the following significant warnings:
  assp/dsputils.c:414:13: warning: value computed is not used [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0v3/wrassp.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/x12GUI.Rcheck/00install.out' for details.
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/4.0v3/x13binary.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/XLConnectJars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/XLConnect.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/xlsxjars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/xlsx.Rcheck/00install.out' for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Found the following significant warnings:
  RSDTD.c:298:23: warning: passing argument 2 of 'xmlHashScan' from incompatible pointer type [-Wincompatible-pointer-types]
  RSDTD.c:372:23: warning: passing argument 2 of 'xmlHashScan' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0v3/XML.Rcheck/00install.out' for details.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    exampleData   1.3Mb
    examples      4.5Mb
    libs          4.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    include   3.4Mb
    libs      2.1Mb
Found the following significant warnings:
  emitter.c:28:6: warning: value computed is not used [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0v3/yaml.Rcheck/00install.out' for details.
Dependence on R version ‘3.4.2’ not with patchlevel 0
Found the following significant warnings:
  pa.c:247:2: warning: initialization of ‘struct audio_instance * (*)(struct SEXPREC *, float,  int)’ from incompatible pointer type ‘void * (*)(struct SEXPREC *, float,  int)’ [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Blasso.cpp:451:53: warning: ‘*<unknown>.Blasso::icept’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/bayesCL.Rcheck/00install.out’ for details.
Dependence on R version ‘3.4.1’ not with patchlevel 0
Found the following significant warnings:
  mcmc.c:337:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/BayHap.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/BootValidation.Rcheck/00install.out’ for details.
Found the following significant warnings:
  hash.c:144:5: warning: ‘strncpy’ specified bound 2048 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/C50.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [25s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(circumplex)
  > 
  > test_check("circumplex")
  ── 1. Failure: Quantile for circular radians works (@test-ssm_bootstrap.R#17)  ─
  `qb` not equivalent to as_radian(as_degree(c(180, 225, 270, 315, 0))).
  1/5 mismatches
  [5] 6.28 - 0 == 6.28
  
  ── 2. Failure: Quantile for circular radians works (@test-ssm_bootstrap.R#27)  ─
  `qb` not equivalent to as_radian(as_degree(c(270, 315, 0, 45, 90))).
  1/5 mismatches
  [3] 6.28 - 0 == 6.28
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 204 | SKIPPED: 6 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: Quantile for circular radians works (@test-ssm_bootstrap.R#17) 
  2. Failure: Quantile for circular radians works (@test-ssm_bootstrap.R#27) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘test.R’ [177s/109s]
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
Running ‘testthat.R’ [38s/41s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ctmle)
  Loading required package: SuperLearner
  Loading required package: nnls
  Super Learner
  Version: 2.0-25
  Package created on 2019-08-05
  
  Loading required package: tmle
  Loading required package: glmnet
  Loading required package: Matrix
  Loaded glmnet 3.0-1
  
  Welcome to the tmle package, version 1.4.0.1
  
  Use tmleNews() to see details on changes and bug fixes
  > 
  > test_check("ctmle")
  ── 1. Error: (unknown) (@test-ctmleGeneral.R#73)  ──────────────────────────────
  could not find function "predict.cv.glmnet"
  
  ── 2. Error: (unknown) (@test-ctmleGlmnet.R#69)  ───────────────────────────────
  could not find function "predict.cv.glmnet"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 9 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: (unknown) (@test-ctmleGeneral.R#73) 
  2. Error: (unknown) (@test-ctmleGlmnet.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  hash.c:144:5: warning: ‘strncpy’ specified bound 2048 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Cubist.Rcheck/00install.out’ for details.
Running ‘test-all.R’ [27s/30s]
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:
  clipper.cpp:721:34: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct ClipperLib::TEdge’; use assignment or value-initialization instead [-Wclass-memaccess]
  dbfopen.c:1346:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:1328:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:879:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopen.c:1693:9: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
  dbfopen.c:2065:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/dggridR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/dpglasso.Rcheck/00install.out’ for details.
Rd file 'mosaicPermDialog.Rd':
  \usage lines wider than 90 characters:
                                                             displayPermCommand=TRUE, extendedOptions=TRUE)
     setMosaicPalette(palettename,reverse=FALSE)                                                     

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  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 ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/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 ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Killed
Rd file 'POICalc.Rd':
  \examples lines wider than 100 characters:
        irisPOI@wordsInQuery <- c('high.Sepal.Length', 'high.Sepal.Width', 'high.Petal.Length', 'high.Petal.Width',
                                  'low.Sepal.Length', 'low.Sepal.Width', 'low.Petal.Length', 'low.Petal.Width')

Rd file 'POIcoords_-.Rd':
  \examples lines wider than 100 characters:
        irisPOI@wordsInQuery <- c('high.Sepal.Length', 'high.Sepal.Width', 'high.Petal.Length', 'high.Petal.Width',
                                  'low.Sepal.Length', 'low.Sepal.Width', 'low.Petal.Length', 'low.Petal.Width')

Rd file 'plotPOI.Rd':
  \examples lines wider than 100 characters:
          graphPOI@docs <- matrix(c(seq(1:nrow(graphPOI@objeto)), seq(1:nrow(graphPOI@objeto))), ncol = 2)
        graphPOI@objeto <- graphPOI@objeto <- rbind(c(0,.05), c(.05,0), c(0,-.05), c(-.05,0) ,round(circulo(0,0,.3,PLOT = FALSE),2))
         1 - (max(USArrests[,4]) - USArrests[,4]) / (max(max(USArrests[,4]) - USArrests[,4])),                                               ... [TRUNCATED]
        usaPOI@wordsInQuery <- c(paste('High', names(USArrests[,c(1,2,4)])), paste('Low', names(USArrests[,c(1,2,4)])))

These lines will be truncated in the PDF manual.
Running ‘testthat.R’ [140s/153s]
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:
  RngStream.c:275:7: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/freeknotsplines.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Gdmlib.cpp:2352:19: warning: ‘%lf’ directive writing between 3 and 317 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gdm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_41_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gglasso.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘gglogo-alphabet.Rmd’ using rmarkdown

Attaching package: 'gglogo'

The following object is masked from 'package:ggplot2':

    fortify

Killed
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()).
! Missing number, treated as zero.
<to be read again> 
                   \protect 
l.248 ...nter}\rule{0.5\linewidth}{\linethickness}
                                                  \end{center} 

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

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

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gwsem.Rcheck/00install.out’ for details.
Found the following significant warnings:
  gener.c:39:26: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/hier.part.Rcheck/00install.out’ for details.
Rd file 'N2.cohen.kappa.Rd':
  \examples lines wider than 100 characters:
       N2.cohen.kappa(c(0.2, 0.25, 0.55), k1=0.6, k0=0.4)                                                            

These lines will be truncated in the PDF manual.
Dependence on R version ‘3.4.4’ not with patchlevel 0
Running ‘testthat.R’ [11s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lingtypology)
  > 
  > test_check("lingtypology")
  ── 1. Failure: map.feature colors (@test-mapfeature.R#151)  ────────────────────
  map_colorless$x$calls[[4]]$args[6][[1]]$color not equal to c("#1F77B4", "#1F77B4").
  2/2 mismatches
  x[1]: "#1f77b4"
  y[1]: "#1F77B4"
  
  x[2]: "#1f77b4"
  y[2]: "#1F77B4"
  
  ── 2. Failure: map.feature colors (@test-mapfeature.R#155)  ────────────────────
  map_lang_colors$x$calls[[4]]$args[6][[1]]$color not equal to c("#000080", "#000080").
  2/2 mismatches
  x[1]: "navy"
  y[1]: "#000080"
  
  x[2]: "navy"
  y[2]: "#000080"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 106 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: map.feature colors (@test-mapfeature.R#151) 
  2. Failure: map.feature colors (@test-mapfeature.R#155) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp: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]
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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]
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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 ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lolog.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘MLTA_Gollini_2019.Rmd’ using rmarkdown
Loading required package: MASS
Loading required package: ergm
Loading required package: network
network: Classes for Relational Data
Version 1.15 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.


ergm: version 3.10.4, created on 2019-06-10
Copyright (c) 2019, Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Carter T. Butts, University of California -- Irvine
                    Steven M. Goodreau, University of Washington
                    Pavel N. Krivitsky, University of Wollongong
                    Martina Morris, University of Washington
                    with contributions from
                    Li Wang
                    Kirk Li, University of Washington
                    Skye Bender-deMoll, University of Washington
                    Chad Klumb
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("ergm").

NOTE: Versions before 3.6.1 had a bug in the implementation of the bd()
constriant which distorted the sampled distribution somewhat. In
addition, Sampson's Monks datasets had mislabeled vertices. See the
NEWS and the documentation for more details.

NOTE: Some common term arguments pertaining to vertex attribute and
level selection have changed in 3.10.0. See terms help for more
details. Use 'options(ergm.term=list(version="3.9.4"))' to use old
behavior.

Killed
Running ‘testthat.R’ [18s/20s]
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 ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ManifoldOptim.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [10m/11m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(matrixTests)
  > 
  > test_check("matrixTests")
  Killed
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 ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MigClim.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘milr-intro.Rmd’ using rmarkdown
Use the user-defined lambda vector.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 3.6867.
The penalty term is selected automatically with 50 candidates.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 4.9895.
The penalty term is selected automatically with 50 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 2.8390.
trying URL ‘http://www.cs.columbia.edu/~andrews/mil/data/MIL-Data-2002-Musk-Corel-Trec9.tgz’
Content type 'application/x-gzip' length 6249673 bytes (6.0 MB)
==================================================
downloaded 6.0 MB

Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Warning: 'switch' is deprecated.
Use 'strip.position' instead.
See help("Deprecated")
The penalty term is selected automatically with 100 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 3.2909.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Killed
Error(s) in re-building vignettes:
  ...
--- re-building ‘modistools-vignette.Rmd’ using rmarkdown
Quitting from lines 55-69 (modistools-vignette.Rmd) 
Error: processing vignette 'modistools-vignette.Rmd' failed with diagnostics:
arguments imply differing number of rows: 1, 0
--- failed re-building ‘modistools-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘How_to_use_mvMORPH.Rmd’ using rmarkdown
Loading required package: phytools
Loading required package: ape
Loading required package: maps
Loading required package: corpcor
Loading required package: subplex
##
## mvMORPH package (1.1.0)
## Multivariate evolutionary models
##
## See the tutorials: browseVignettes("mvMORPH")
##
## To cite package 'mvMORPH': citation("mvMORPH")
##
Done.
Efficient parameterization is not yet implemented for user-defined constraints
Please check the results carefully!!
Efficient parameterization is not yet implemented for user-defined constraints
Please check the results carefully!!
! Missing number, treated as zero.
<to be read again> 
                   \protect 
l.137 ...nter}\rule{0.5\linewidth}{\linethickness}
                                                  \end{center} 

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

--- re-building ‘tutorial_mvMORPH.Rmd’ using rmarkdown
Done.
! Missing number, treated as zero.
<to be read again> 
                   \protect 
l.133 ...nter}\rule{0.5\linewidth}{\linethickness}
                                                  \end{center} 

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

SUMMARY: processing the following files failed:
  ‘How_to_use_mvMORPH.Rmd’ ‘tutorial_mvMORPH.Rmd’

Error: Vignette re-building failed.
Execution halted
Dependence on R version ‘3.4.3’ not with patchlevel 0
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 ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/odbc.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 ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/opusminer.Rcheck/00install.out’ for details.
Rd file 'dmes.Rd':
  \examples lines wider than 100 characters:
     > #cf. Efron, B. & Tibshirani (1993). An Introduction to the Bootstrap. New York/London: Chapman&Hall.
     > #Ruscio, J. & Mullen, T. (2012). Confidence Intervals for the Probability of Superiority Effect Size Measure and the Area Under a Rec ... [TRUNCATED]

Rd file 'orddom_f.Rd':
  \examples lines wider than 100 characters:
     orddom_f(con_pre,ex_pre,alpha=0.025,decimalpt=",",description="EXP 01: Between groups at time 01")   
     orddom_f(con_post,ex_post,alpha=0.025,decimalpt=",",description="EXP 01: Between groups at time 02") 
     orddom_f(ex_pre,ex_post,alpha=0.025,paired=TRUE,decimalpt=",",description="EXP 01: Within exp 01 to 02") 
     orddom_f(con_pre,con_post,alpha=0.025,paired=TRUE,decimalpt=",",description="EXP 01: Within con 01 to 02") 

These lines will be truncated in the PDF manual.
Rd file 'CalGIF.Rd':
  \examples lines wider than 100 characters:
     ###calculate the global influence factor (GIF) by using the random walk with restart (RWR) algorithm###
     #Each element is the GIF score and whose name correspond to gene symbol in the gene expression data. 
     #Each element is the GIF score and whose name correspond to gene symbol in the gene expression data. 

Rd file 'PAGI.Main.Rd':
  \examples lines wider than 100 characters:
     #Its columns include "Gene number in the (sorted) pathway", "gene symbol from the gene express data",
     #"location of the gene in the sorted gene list", "the T-score of gene between two biological states",
     #Its columns include "Gene number in the (sorted) pathway", "gene symbol from the gene express data",
     #"location of the gene in the sorted gene list", "the T-score of gene between two biological states",

These lines will be truncated in the PDF manual.
Rd file 'envelopeArea_and_Perimeter.Rd':
  \examples lines wider than 100 characters:
     cat("envelope area = ", envelopeStats["area"], " perimeter = ", envelopeStats["perimeter"],"\n")        
     cat("circle area = ", pi * r^2, " = ", sum(pi * r^2), "\ncircle perimenter = ",  2 * pi * r, " = ",  2 * pi * sum(r), "\n")

Rd file 'generateEnvelope.Rd':
  \examples lines wider than 100 characters:
     cat("envelope area = ", envelopeStats["area"], " perimeter = ", envelopeStats["perimeter"],"\n")        
     cat("circle area = ", pi * r^2, " = ", sum(pi * r^2), "\ncircle perimenter = ",  2 * pi * r, " = ",  2 * pi * sum(r), "\n")
     grid.polygon(envelopeXY[,1], envelopeXY[,2], gp=gpar(fill="pink", col="transparent", lwd=5), default.units="npc")

Rd file 'tangentLine.Rd':
  \examples lines wider than 100 characters:
                     tangent <- tangentLine(centers[1,], centers[2,], r0, r[2], k=k)  # compute coefficients for the tangent line, if NA, th ... [TRUNCATED]
                             grid.abline(-tangent["c"] / tangent["b"], -tangent["a"] / tangent["b"], gp=gpar(col="blue", lwd=ii), units="npc ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Rd file 'ppoistweedie.Rd':
  \examples lines wider than 100 characters:
     layout.show(1)                                                                                                                          ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  R4dfp-object.c:253:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
  R4dfp-object.c:260:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/R4dfp.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/randomcoloR.Rcheck/00install.out’ for details.
Rd file 'predict.randomGLM.Rd':
  \examples lines wider than 100 characters:
     RGLM = randomGLM(xTrain, yTrain, nCandidateCovariates=ncol(xTrain), nBags=30, keepModels = TRUE, nThreads = 1)

Rd file 'randomGLM.Rd':
  \usage lines wider than 90 characters:
       # Multi-level classification options - only apply to classification with multi-level response
  \examples lines wider than 100 characters:
     RGLM = randomGLM(xTrain, yTrain, xTest, classify=FALSE, nCandidateCovariates=ncol(xTrain), nBags=10, 

Rd file 'thinRandomGLM.Rd':
  \examples lines wider than 100 characters:
     RGLM = randomGLM(xTrain, yTrain, nCandidateCovariates=ncol(xTrain), nBags=30, keepModels = TRUE, nThreads = 1)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  avc_binwr.c:166:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:173:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:180:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:187:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:1453:29: warning: ‘%4.4d’ directive writing between 4 and 10 bytes into a region of size 5 [-Wformat-overflow=]
  avc_binwr.c:1553:28: warning: ‘%s’ directive writing up to 39 bytes into a region of size between 38 and 77 [-Wformat-overflow=]
  avc_e00write.c:386:30: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  avc_e00write.c:387:30: warning: ‘-ID’ directive writing 3 bytes into a region of size between 1 and 40 [-Wformat-overflow=]
  avc_e00write.c:401:61: warning: ‘%s’ directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:397:61: warning: ‘%s’ directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:409:39: warning: ‘%s’ directive writing up to 39 bytes into a region of size 33 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RArcInfo.Rcheck/00install.out’ for details.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rblpapi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rreadsdpa.c:608:15: warning: ‘strncpy’ output may be truncated copying 3999 bytes from a string of length 3999 [-Wstringop-truncation]
  Rreadsdpa.c:1041:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  Rreadsdpa.c:1042:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:164:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:165:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rdsdp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  compile.cc:292:69: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class re2::Prog::Inst’; use assignment or value-initialization instead [-Wclass-memaccess]
  regexp.cc:343:33: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
  regexp.cc:344:32: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/re2r.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘GuideToVignettes.Rmd’ using rmarkdown
tlmgr search --file --global '/tikzlibrarytopaths.code.tex'
TLPDB: not a directory, not loading: /home/hornik/lib/texmf/
tlmgr: running in usermode, did you call `tlmgr init-usertree'?
Warning in system2("tlmgr", args, ...) :
  running command ‘'tlmgr' search --file --global '/tikzlibrarytopaths.code.tex'’ had status 2
Warning in parse_packages(logfile, quiet = c(TRUE, FALSE, FALSE)) :
  Failed to find a package that contains tikzlibrarytopaths.code.tex
! Missing number, treated as zero.
<to be read again> 
                   \protect 
l.74 ...enter}\rule{0.5\linewidth}{\linethickness}
                                                  \end{center} 

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

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

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

--- re-building ‘MiniDIFDUP_1.Rnw’ using Sweave
--- finished re-building ‘MiniDIFDUP_1.Rnw’

--- re-building ‘MiniDIFDUP_2.Rnw’ using Sweave
--- finished re-building ‘MiniDIFDUP_2.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [54s/57s]
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. 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
Error(s) in re-building vignettes:
  ...
--- re-building ‘UsingrerddapXtracto.Rmd’ using rmarkdown
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
Quitting from lines 523-533 (UsingrerddapXtracto.Rmd) 
Error: processing vignette 'UsingrerddapXtracto.Rmd' failed with diagnostics:
'Error {
    code=404;
    message="Not Found: Currently unknown datasetID=CORIOLIS_GLOBAL_NRTOA_OBS_TIME_SERIE_PSAL";
}
' does not exist in current working directory ('/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rerddapXtracto.Rcheck/vign_test/rerddapXtracto/vignettes').
--- failed re-building ‘UsingrerddapXtracto.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  DbResult.cpp:81:41: warning: catching polymorphic type ‘class MariaResultPrep::UnsupportedPS’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RMariaDB.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 ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rncl.Rcheck/00install.out’ for details.
Found the following significant warnings:
  bgc_hmm.c:241:31: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
  rph_tfbs.c:371:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:351:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:819:5: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rphast.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  RngStreams.c:332:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rstream.Rcheck/00install.out’ for details.
Found the following significant warnings:
  bgc_hmm.c:241:31: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
  rph_tfbs.c:371:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:351:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:819:5: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rtfbs.Rcheck/00install.out’ for details.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RVowpalWabbit.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘rxnat.Rmd’ using rmarkdown
Quitting from lines 98-100 (rxnat.Rmd) 
Error: processing vignette 'rxnat.Rmd' failed with diagnostics:
error during HTTP request
--- failed re-building ‘rxnat.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/scio.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_1_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/sdwd.Rcheck/00install.out’ for details.
Running examples in ‘sharpshootR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: LL2PLSS
> ### Title: PLSS2LL
> ### Aliases: LL2PLSS plssMeridians d4
> ### Keywords: manip
> 
> ### ** Examples
> 
> library(sp)
> 
> # create coordinates
> x <- -115.3823 
> y <- 48.88228
> 
> # fetch PLSS geometry for these coordinates
> p.plss <- LL2PLSS(x, y)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘coordinates’ for signature ‘"NULL"’
Calls: LL2PLSS ... Polygons -> stopifnot -> Polygon -> coordinates -> <Anonymous>
Execution halted
Rd file 'SJ.Rd':
  \examples lines wider than 100 characters:
     #with standard deviations of 1, 0.5 and 0.5, (i.e. giving more weight to linear association than quadratic or cubic)
     #Fit conditional independence graph at one lambda , using the default basis functions (cubic polynomials).
     plot(g, layout=mylayout, edge.color = "gray50", vertex.color = "red", vertex.size = 3, vertex.label = NA, edge.arrow.size = 0.4, main=" ... [TRUNCATED]

Rd file 'generate.dag.data.Rd':
  \usage lines wider than 90 characters:
     generate.dag.data(g, n, basesd = 1, basemean = 0, bfuns = function(x){cbind(x, x^2, x^3)}, 
  \examples lines wider than 100 characters:
     #with standard deviations of 1, 0.5 and 0.5, (i.e. giving more weight to linear association than quadratic or cubic)

Rd file 'spacejam-package.Rd':
  \examples lines wider than 100 characters:
     #with standard deviations of 1, 0.5 and 0.5, (i.e. giving more weight to linear association than quadratic or cubic)
     plot(g, layout=mylayout, edge.color = "gray50", vertex.color = "red", vertex.size = 3, vertex.label = NA, edge.arrow.size = 0.4, main=" ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Running ‘testthat.R’ [13s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("SqlRender")
  Loading required package: SqlRender
  Reading SQL from package folder: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/SqlRender/sql/sql_server/test.sql
  Writing R function to: /tmp/Rtmph6Njn5/file394c7e2416d8
  ── 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:
  dbfopenSSN.c:1119:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:1100:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:663:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopenSSN.c:1511:2: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/SSN.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 ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/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=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/subprocess.Rcheck/00install.out’ for details.
Rd file 'SyNet-package.rd':
  \examples lines wider than 100 characters:
       # Run NAM method on the previously inferred sympatry network                                           

Rd file 'acshgral.rd':
  \examples lines wider than 100 characters:
       #Display relationships into a parenthetical notation. You can track the indices of the species in the

Rd file 'gridinfer.rd':
  \examples lines wider than 100 characters:
       #are nested inside it. In a network analysis this kind of element will behave as intermediary node.  

Rd file 'reweight.rd':
  \examples lines wider than 100 characters:
       plot(unlist(ej),unlist(reweight(ej)), xlab = "Input matrix", ylab = "Reweighted matrix", main = "First reweighting")

These lines will be truncated in the PDF manual.
Running ‘testthat.R’ [81s/61s]
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
Running examples in ‘TANDEM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coef.tandem
> ### Title: Returns the regression coefficients from a TANDEM fit
> ### Aliases: coef.tandem
> 
> ### ** Examples
> 
> # unpack example data
> x = example_data$x
> y = example_data$y
> upstream = example_data$upstream
> 
> # fit a tandem model, determine the coefficients and create a prediction
> fit = tandem(x, y, upstream, alpha=0.5)
Error: 'predict.cv.glmnet' is not an exported object from 'namespace:glmnet'
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Loading required package: Matrix
Loaded glmnet 3.0-1

Quitting from lines 27-31 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
'predict.cv.glmnet' is not an exported object from 'namespace:glmnet'
--- failed re-building ‘my-vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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/RtmpW9p8E8/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 \input{ /tmp/RtmpW9p8E8/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:
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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]
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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 ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/text2vec.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘tiler.Rmd’ using rmarkdown
Loading required package: sp
pandoc: /tmp/Rtmpg8FTAP/leaflet-providers_1.9.0.js: openBinaryFile: does not exist (No such file or directory)
Error: processing vignette 'tiler.Rmd' failed with diagnostics:
pandoc document conversion failed with error 1
--- failed re-building ‘tiler.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  libqhull/rboxlib.c:351:5: warning: ‘strncat’ output may be truncated copying between 0 and 199 bytes from a string of length 199 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TukeyRegion.Rcheck/00install.out’ for details.
Found the following significant warnings:
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<> >::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::MemoryPoolAllocator<> >’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<> >’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::CrtAllocator>’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/validatejsonr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  tabix/razf.c:188:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/WhopGenome.Rcheck/00install.out’ for details.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/x13binary.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘aaSEA_Documentation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in RColorBrewer::brewer.pal(N, "Set2") :
  n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors

Warning in RColorBrewer::brewer.pal(N, "Set2") :
  n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors

Quitting from lines 90-91 (aaSEA_Documentation.Rmd) 
Error: processing vignette 'aaSEA_Documentation.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘aaSEA_Documentation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    data       2.8Mb
    pictures   2.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R       1.4Mb
    data    1.3Mb
    files   1.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    doc   3.0Mb
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    data  20.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    4.8Mb
    help   1.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   2.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       2.9Mb
    extdata   1.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ahn.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 66-67 (ahn.Rmd) 
Error: processing vignette 'ahn.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘ahn.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘rsvg’
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    extdata  12.1Mb
Running examples in ‘amber-Ex.R’ failed
The error most likely occurred in:

> ### Name: scores.fluxnet.nc
> ### Title: Scores for FLUXNET reference data in NetCDF format
> ### Aliases: scores.fluxnet.nc
> 
> ### ** Examples
> 
> 
> library(amber)
> library(doParallel)
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> library(foreach)
> library(ncdf4)
> library(parallel)
> library(raster)
Loading required package: sp
> long.name <- 'Gross primary productivity'
> nc.mod <- system.file('extdata/modelRegular', 'gpp_monthly.nc', package = 'amber')
> nc.ref <- system.file('extdata/referenceRegular', 'gpp_FLUXNET.nc', package = 'amber')
> mod.id <- 'CLASSIC' # define a model experiment ID
> ref.id <- 'FLUXNET' # give reference dataset a name
> unit.conv.mod <- 86400*1000 # optional unit conversion for model data
> unit.conv.ref <- 86400*1000 # optional unit conversion for reference data
> variable.unit <- 'gC m$^{-2}$ day$^{-1}$' # unit after conversion (LaTeX notation)
> score.weights <- c(1,2,1,1,1) # score weights of S_bias, S_rmse, S_phase, S_iav, S_dist
> # global plot
> scores.fluxnet.nc(long.name, nc.mod, nc.ref, mod.id, ref.id, unit.conv.mod,
+  unit.conv.ref, variable.unit, score.weights)
Error in R_nc4_open: NetCDF: HDF error
Error in ncdf4::nc_open(nc.ref) : 
  Error in nc_open trying to open file /home/ripley/R/Lib32/amber/extdata/referenceRegular/gpp_FLUXNET.nc
Calls: scores.fluxnet.nc -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown_notangle
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 49-64 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   3.4Mb
Package suggested but not available for checking: ‘ssh’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   2.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    testdata   5.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘antares.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘antares.Rmd’

--- re-building ‘antaresH5.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 38-72 (antaresH5.Rmd) 
Error: processing vignette 'antaresH5.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘antaresH5.Rmd’

SUMMARY: processing the following file failed:
  ‘antaresH5.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [105s/119s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(antaresViz)
  Loading required package: antaresRead
  Loading required package: antaresProcessing
  
  Attaching package: 'antaresProcessing'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  Loading required package: spMaps
  Loading required package: sp
  Loading required package: raster
  
  Attaching package: 'raster'
  
  The following object is masked from 'package:antaresProcessing':
  
      getValues
  
  Loading required package: rgeos
  rgeos version: 0.5-2, (SVN revision 621)
   GEOS runtime version: 3.6.3-CAPI-1.10.3 
   Linking to sp version: 1.3-2 
   Polygon checking: TRUE 
  
  > 
  > test_check("antaresViz")
  ── 1. Error: (unknown) (@test-h5Request.R#3)  ──────────────────────────────────
  HDF5. File accessibilty. Unable to open file.
  Backtrace:
   1. testthat::describe(...)
   2. [ base::eval(...) ] with 1 more call
   6. antaresRead::writeAntaresH5(pathtemp, overwrite = TRUE)
   7. antaresRead::.writeAntaresH5Fun(...)
   8. rhdf5::h5createFile(path)
   9. rhdf5::H5Fcreate(file)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 264 | SKIPPED: 4 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: (unknown) (@test-h5Request.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘sdols’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘kebabs’
Error(s) in re-building vignettes:
  ...
--- re-building ‘apcluster.Rnw’ using knitr

Attaching package: 'apcluster'

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

    heatmap

Quitting from lines 387-408 (apcluster.Rnw) 
Error: processing vignette 'apcluster.Rnw' failed with diagnostics:
object 'apres2c' not found
--- failed re-building ‘apcluster.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘labs.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 32-34 (labs.Rmd) 
Error: processing vignette 'labs.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘labs.Rmd’

--- re-building ‘lines.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 39-40 (lines.Rmd) 
Error: processing vignette 'lines.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘lines.Rmd’

--- re-building ‘starting-with-apexcharts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 36-40 (starting-with-apexcharts.Rmd) 
Error: processing vignette 'starting-with-apexcharts.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘starting-with-apexcharts.Rmd’

SUMMARY: processing the following files failed:
  ‘labs.Rmd’ ‘lines.Rmd’ ‘starting-with-apexcharts.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.3Mb
Package suggested but not available for checking: ‘qCBA’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    fontawesome-5.3.1   2.8Mb
    help                1.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    help   1.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata   3.8Mb
Running ‘testthat.R’ [14s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("arulesCBA")
  Loading required package: Matrix
  Loading required package: arules
  
  Attaching package: 'arules'
  
  The following objects are masked from 'package:base':
  
      abbreviate, write
  
  Loading required package: discretization
  Loading required package: glmnet
  Loaded glmnet 3.0-1
  
  > 
  > test_check("arulesCBA")
  Apriori
  
  Parameter specification:
   confidence minval smax arem  aval originalSupport maxtime support minlen
          0.8    0.1    1 none FALSE            TRUE       5    0.01      1
   maxlen target   ext
       10  rules FALSE
  
  Algorithmic control:
   filter tree heap memopt load sort verbose
      0.1 TRUE TRUE  FALSE TRUE    2    TRUE
  
  Absolute minimum support count: 1 
  
  set item appearances ...[14 item(s)] done [0.00s].
  set transactions ...[14 item(s), 120 transaction(s)] done [0.00s].
  sorting and recoding items ... [14 item(s)] done [0.00s].
  creating transaction tree ... done [0.00s].
  checking subsets of size 1 2 3 4 5 done [0.00s].
  writing ... [76 rule(s)] done [0.00s].
  creating S4 object  ... done [0.00s].
  ── 1. Failure: (unknown) (@test-RCAR.R#7)  ─────────────────────────────────────
  length(rules(rcar_classifier)) not equal to 20L.
  1/1 mismatches
  [1] 21 - 20 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 11 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: (unknown) (@test-RCAR.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘REBayes’
Error(s) in re-building vignettes:
  ...
--- re-building ‘asmapvignette.Rnw’ using knitr
Warning in summary.cross(cross) :
  Some markers at the same position on chr 1B1,1D,2B,2D1,3A,3B,3D,4A,5A,5B,5D,6D,7A,7B,7D; use jittermap().
Warning in summary.cross(cross) :
  Some chromosomes > 1000 cM in length; there may be a problem with the genetic map.
  (Perhaps it is in basepairs?)
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7,L.8,L.9; use jittermap().
Warning in heatMap(mapBC6, chr = c("L.3", "L.5", "L.8", "L.9"), lmax = 70) :
  Running est.rf.
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7; use jittermap().
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc        2.4Mb
    full_doc   2.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Data_Analysis_with_augmentedRCBD.Rmd’ using rmarkdown_notangle
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 57-76 (Data_Analysis_with_augmentedRCBD.Rmd) 
Error: processing vignette 'Data_Analysis_with_augmentedRCBD.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
--- failed re-building ‘Data_Analysis_with_augmentedRCBD.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 73.8Mb
  sub-directories of 1Mb or more:
    java  73.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   3.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    data   1.1Mb
    doc    2.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.1Mb
Running ‘testthat.R’ [34s/41s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BAS)
  > 
  > test_check("BAS")
  ── 1. Failure: herdity and BAS (@test-bas-glm.R#420)  ──────────────────────────
  pima_BAS$probne0 not equal to pima_BAS_no$probne0.
  6/7 mismatches (average diff: 0.0696)
  [2] 0.11013 - 0.1136 == -3.47e-03
  [3] 1.00000 - 1.0000 == -2.54e-06
  [4] 0.63062 - 0.8284 == -1.98e-01
  [5] 0.02193 - 0.0220 == -1.03e-04
  [6] 0.00771 - 0.0101 == -2.42e-03
  [7] 0.31878 - 0.1051 ==  2.14e-01
  
  
   Marginal Posterior Summaries of Coefficients: 
  
   Using  BMA 
  
   Based on the top  16 models 
             post mean  post SD   post p(B != 0)
  Intercept  95.42308    0.67885   1.00000      
  X1          1.40116    0.35351   0.97454      
  X2          0.42326    0.38407   0.76017      
  X3         -0.03997    0.33398   0.30660      
  X4         -0.22077    0.36931   0.44354      
  
  Call:
  bas.lm(formula = Y ~ ., data = Hald, prior = "BIC", modelprior = uniform())
  
  
   Marginal Posterior Inclusion Probabilities: 
  Intercept         X1         X2         X3         X4  
     1.0000     0.9856     0.7921     0.4705     0.5220  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 150 | SKIPPED: 0 | WARNINGS: 105 | FAILED: 1 ]
  1. Failure: herdity and BAS (@test-bas-glm.R#420) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘article2-vignette.Rnw’ using knitr
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-8'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.0Mb
    libs   1.8Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   4.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   1.5Mb
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    libs  20.3Mb
Running ‘testthat.R’ [24s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bcgam)
  Loading required package: nimble
  nimble version 0.8.0 is loaded.
  For more information on NIMBLE and a User Manual,
  please visit http://R-nimble.org.
  
  Attaching package: 'nimble'
  
  The following object is masked from 'package:stats':
  
      simulate
  
  > 
  > test_check("bcgam")
  thin = 1: tau, betalpha, sigma, eta
  ── 1. Error: (unknown) (@testthat.R#3)  ────────────────────────────────────────
  Failed to create the shared library.
  Backtrace:
   1. bcgam::bcgam(...)
   2. bcgam:::bcgam.fit(...)
   3. nimble::compileNimble(gaus)
   4. project$compileModel(units[[i]], control = control, showCompilerOutput = showCompilerOutput)
   5. cppProj$compileFile(compileList, showCompilerOutput)
   6. nimble:::compileDynamicRegistrations(showCompilerOutput = showCompilerOutput)
   7. nimble:::compileStaticCode(dllName, cppName, showCompilerOutput)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: (unknown) (@testthat.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Bclim.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.7Mb
Package suggested but not available for checking: ‘BRugs’
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Package suggested but not available for checking: ‘lumi’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘abcd-laagdrempelige_nederlandse_uitleg.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 53-74 (abcd-laagdrempelige_nederlandse_uitleg.Rmd) 
Error: processing vignette 'abcd-laagdrempelige_nederlandse_uitleg.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘abcd-laagdrempelige_nederlandse_uitleg.Rmd’

--- re-building ‘abcd.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘abcd.Rmd’

--- re-building ‘matrix-van-aspecten-van-de-psychologie.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘matrix-van-aspecten-van-de-psychologie.Rmd’

SUMMARY: processing the following file failed:
  ‘abcd-laagdrempelige_nederlandse_uitleg.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/BFpack.Rcheck/00install.out’ for details.
installed size is 145.8Mb
  sub-directories of 1Mb or more:
    include  145.7Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    1.9Mb
Running examples in ‘bigdist-Ex.R’ failed
The error most likely occurred in:

> ### Name: bigdist
> ### Title: Read or Create a distance matrix on disk
> ### Aliases: bigdist
> 
> ### ** Examples
> 
> # basics of 'bigdist'
> # create a random matrix
> set.seed(1)
> amat <- matrix(rnorm(1e3), ncol = 10)
> td   <- tempdir()
> 
> # create a bigdist object with FBM (file-backed matrix) on disk
> temp <- bigdist(mat = amat, file = file.path(td, "temp_ex1"))
----
Location: /tmp/RtmpYDaOb6/working_dir/RtmpWZaa9d/temp_ex1_100_float.bk
Size on disk: 0 GB
Computing distances ... 
Completed!
----
> temp
$fbm
A Filebacked Big Matrix of type 'float' with 100 rows and 100 columns.

attr(,"class")
[1] "bigdist"
> temp$fbm$backingfile
[1] "/tmp/RtmpYDaOb6/working_dir/RtmpWZaa9d/temp_ex1_100_float.bk"
> temp$fbm[1, 2]
[1] 4.631341
> 
> # connect to FBM on disk as a bigdist object
> temp2 <- bigdist(file = file.path(td, "temp_ex1_100_float"))
> temp2
$fbm
A Filebacked Big Matrix of type 'float' with 100 rows and 100 columns.

attr(,"class")
[1] "bigdist"
> temp2$fbm[1,2]

 *** caught segfault ***
address fcbb0190, cause 'invalid permissions'

Traceback:
 1: extractMat(x$address, i, j)
 2: extract_matrix(x, transform_ind(i, n), transform_ind(j, m))
 3: temp2$fbm[1, 2]
 4: temp2$fbm[1, 2]
An irrecoverable exception occurred. R is aborting now ...
Error(s) in re-building vignettes:
  ...
--- re-building ‘analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Removed 199 rows containing non-finite values (stat_contour).
Warning in normalizePath(f2) :
  path[1]="webshot333b24a92a1f.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot333b24a92a1f.png': No such file or directory
Quitting from lines 245-248 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘analysis.Rmd’

--- re-building ‘methodology.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘methodology.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       3.1Mb
    extdata   2.5Mb
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘billboarder-intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 41-48 (billboarder-intro.Rmd) 
Error: processing vignette 'billboarder-intro.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘billboarder-intro.Rmd’

--- re-building ‘billboarder-mapping.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 44-46 (billboarder-mapping.Rmd) 
Error: processing vignette 'billboarder-mapping.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘billboarder-mapping.Rmd’

--- re-building ‘billboarder-options.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 26-29 (billboarder-options.Rmd) 
Error: processing vignette 'billboarder-options.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘billboarder-options.Rmd’

--- re-building ‘billboarder.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 37-56 (billboarder.Rmd) 
Error: processing vignette 'billboarder.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘billboarder.Rmd’

SUMMARY: processing the following files failed:
  ‘billboarder-intro.Rmd’ ‘billboarder-mapping.Rmd’
  ‘billboarder-options.Rmd’ ‘billboarder.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘csaw’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘BioCircos.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 64-67 (BioCircos.Rmd) 
Error: processing vignette 'BioCircos.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘BioCircos.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    extdata   7.8Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.7Mb
Running examples in ‘bioRad-Ex.R’ failed
The error most likely occurred in:

> ### Name: example_scan
> ### Title: Example object of class 'scan'
> ### Aliases: example_scan
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # get summary of example scan:
> summary(example_scan)
                  Polar scan (class scan)

     parameters:  VRADH DBZH ZDR RHOHV PHIDP 
elevation angle:  0.5 deg
           dims:  480 bins x 360 rays
> 
> # example_scan was created with:
> pvolfile <- system.file("extdata", "volume.h5", package = "bioRad")
> pvol <- read_pvolfile(pvolfile)
Error in H5Fopen(file, "H5F_ACC_RDONLY", native = native) : 
  HDF5. File accessibilty. Unable to open file.
Calls: read_pvolfile ... is.odimfile -> h5ls -> h5checktypeOrOpenLoc -> H5Fopen
Execution halted
Running ‘testthat.R’ [14s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bioRad)
  Welcome to bioRad version 0.4.0
  Warning: no running Docker daemon found Warning: bioRad functionality
  requiring Docker has been disabled
  
  To enable Docker functionality, start Docker and run 'check_docker()'
  in R
  > 
  > test_check("bioRad")
  ── 1. Error: Read a vertical profile (@test-read_vpfiles.R#5)  ─────────────────
  HDF5. File accessibilty. Unable to open file.
  Backtrace:
    1. testthat::expect_s3_class(readvp(vpfile), "vp")
    4. bioRad::readvp(vpfile)
    5. bioRad::read_vpfiles(...)
    6. bioRad:::read_vp(files)
    7. bioRad::is.vpfile(file)
    8. bioRad::get_odim_object_type(file)
    9. bioRad:::is.odimfile(file)
   10. rhdf5::h5ls(file, recursive = FALSE)
   11. rhdf5:::h5checktypeOrOpenLoc(file, readonly = TRUE, native = native)
   12. rhdf5::H5Fopen(file, "H5F_ACC_RDONLY", native = native)
  
  ── 2. Error: Read multiple vertical profiles (@test-read_vpfiles.R#13)  ────────
  HDF5. File accessibilty. Unable to open file.
  Backtrace:
    1. testthat::expect_is(readvp.list(c(vpfile, vpfile)), "list")
    4. bioRad::readvp.list(c(vpfile, vpfile))
    5. bioRad::read_vpfiles(...)
    6. base::lapply(files, read_vp)
    7. bioRad:::FUN(X[[i]], ...)
    8. bioRad::is.vpfile(file)
    9. bioRad::get_odim_object_type(file)
   10. bioRad:::is.odimfile(file)
   11. rhdf5::h5ls(file, recursive = FALSE)
   12. rhdf5:::h5checktypeOrOpenLoc(file, readonly = TRUE, native = native)
   13. rhdf5::H5Fopen(file, "H5F_ACC_RDONLY", native = native)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 19 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 2 ]
  1. Error: Read a vertical profile (@test-read_vpfiles.R#5) 
  2. Error: Read multiple vertical profiles (@test-read_vpfiles.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    help   2.2Mb
Package suggested but not available for checking: ‘Seurat’
Package suggested but not available for checking: ‘IHW’
Running ‘spelling.R’
  Running ‘testthat.R’ [12s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(blastula)
  > 
  > test_check("blastula")
  ── 1. Error: knitr_sidecar_prefix preconditions hold (@test-utils.R#10)  ───────
  pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Backtrace:
   1. rmarkdown::render(rmd_path, quiet = TRUE)
   2. rmarkdown::pandoc_available(required_pandoc, error = TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 188 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: knitr_sidecar_prefix preconditions hold (@test-utils.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Invalid maximum heap size: -Xmx4G
The specified size exceeds the maximum representable size.
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘gtools’ ‘knitr’ ‘nnet’ ‘parallel’ ‘rJava’ ‘reshape’
  ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
Missing or unexported object: ‘xgboost::predict’
Running examples in ‘blockcluster-Ex.R’ failed
The error most likely occurred in:

> ### Name: blockcluster
> ### Title: Co-Clustering Package
> ### Aliases: blockcluster
> 
> ### ** Examples
> 
> 
> ## Simple example with simulated binary data
> ## load data
> data(binarydata)
> ## usage of coclusterBinary function in its most simplest form
> out<-coclusterBinary(binarydata,nbcocluster=c(2,3))

 *** caught segfault ***
address c, cause 'memory not mapped'
Error(s) in re-building vignettes:
  ...
--- re-building ‘blockcluster_tutorial.Rnw’ using Sweave
Loading required package: rtkore
Loading required package: Rcpp

Attaching package: ‘rtkore’

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

    LdFlags

blockcluster version 4.4.3 loaded

----------------
Copyright (C)  <MODAL team @INRIA,Lille & U.M.R. C.N.R.S. 6599 Heudiasyc, UTC>
Please post questions and bugs at: <https://gforge.inria.fr/forum/forum.php?forum_id=11190&group_id=3679>
Running examples in ‘blockmodeling-Ex.R’ failed
The error most likely occurred in:

> ### Name: REGE
> ### Title: REGE - Algorithms for compiting (dis)similarities in terms of
> ###   regular equivalnece
> ### Aliases: REGE REGE.for REGE.nm.for REGE.ow REGE.ow.for REGE.ownm.for
> ###   REGD.for REGD.ow.for REGE.FC REGE.FC.ow REGD.ne.for REGD.ow.ne.for
> ###   REGE.ne.for REGE.nm.diag.for REGE.nm.ne.for REGE.ow.ne.for
> ###   REGE.ownm.diag.for REGE.ownm.ne.for
> ### Keywords: cluster graphs
> 
> ### ** Examples
> 
> n <- 20
> net <- matrix(NA, ncol = n, nrow = n)
> clu <- rep(1:2, times = c(5, 15))
> tclu <- table(clu)
> net[clu == 1, clu == 1] <- 0
> net[clu == 1, clu == 2] <- rnorm(n = tclu[1] * tclu[2], mean = 4, sd = 1) * sample(c(0, 1),
+    size = tclu[1] * tclu[2], replace = TRUE, prob = c(3/5, 2/5))
> net[clu == 2, clu == 1] <- 0
> net[clu == 2, clu == 2] <- 0
> 
> D <- REGE.for(M = net)$E # Any other REGE function can be used
> plot.mat(net, clu = cutree(hclust(d = as.dist(1 - D), method = "ward"),
+    k = 2))
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
> # REGE returns similarities, which have to be converted to
> # disimilarities
> 
> res <- optRandomParC(M = net, k = 2, rep = 10, approaches = "hom", homFun = "ss", blocks = "reg")


Starting optimization of the partiton 1 of 10 partitions.
Starting partition: 1 2 1 1 1 1 1 1 1 2 2 1 2 2 2 2 2 1 1 1 

 *** caught segfault ***
address f7d2544, cause 'memory not mapped'

Traceback:
 1: optParC(M = M, clu = temppar, approaches = approaches, blocks = blocks,     useMulti = useMulti, save.initial.param = save.initial.param.opt,     ...)
 2: optRandomParC(M = net, k = 2, rep = 10, approaches = "hom", homFun = "ss",     blocks = "reg")
An irrecoverable exception occurred. R is aborting now ...
Error(s) in re-building vignettes:
  ...
--- re-building ‘BoolNet_package_vignette.Snw.Rnw’ using Sweave

Error: processing vignette 'BoolNet_package_vignette.Snw.Rnw' failed with diagnostics:
 chunk 13 
Error in net$interactions[[idx]][[functionIndices[idx]]] : 
  subscript out of bounds

--- failed re-building ‘BoolNet_package_vignette.Snw.Rnw’

SUMMARY: processing the following file failed:
  ‘BoolNet_package_vignette.Snw.Rnw’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/BootValidation.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘break_caret.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: lattice
Loading required package: ggplot2
--- finished re-building ‘break_caret.Rmd’

--- re-building ‘break_glm.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘break_glm.Rmd’

--- re-building ‘break_lm.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘break_lm.Rmd’

--- re-building ‘break_randomForest.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘break_randomForest.Rmd’

Cpu Limit Exceeded - core dumped
--- re-building ‘break_ranger.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- re-building ‘break_svm.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘break_svm.Rmd’

--- re-building ‘break_xgboost.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘break_xgboost.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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    R     3.3Mb
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installed size is  5.1Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘simple_plotting.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: Removed 4550 rows containing missing values (geom_path).
Quitting from lines 173-174 (simple_plotting.Rmd) 
Error: processing vignette 'simple_plotting.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘simple_plotting.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'c3'

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

    %>%

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

    grid, legend

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot229413ae210e.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot229413ae210e.png': No such file or directory
Quitting from lines 56-65 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package which this enhances but not available for checking: ‘FastRWeb’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Task-queue-with-callr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 17-23 (Task-queue-with-callr.Rmd) 
Error: processing vignette 'Task-queue-with-callr.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘Task-queue-with-callr.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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Error(s) in re-building vignettes:
  ...
--- re-building ‘cartograflow.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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    intersect, setdiff, setequal, union

Quitting from lines 451-480 (cartograflow.Rmd) 
Error: processing vignette 'cartograflow.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘cartograflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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installed size is  5.3Mb
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Package suggested but not available for checking: ‘iptools’
installed size is  5.0Mb
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Running examples in ‘ChocoLattes-Ex.R’ failed
The error most likely occurred in:

> ### Name: make_productions_page
> ### Title: Generate HTML page with productions list and summary chart
> ### Aliases: make_productions_page
> 
> ### ** Examples
> 
> 
> # Load example data and convert it to a lattes list
> CV.dir <- system.file("extdata", package="ChocoLattes")
> 
> # Define the aliases of authors "Felipe Campelo" and "Lucas S. Batista":
> # (all aliases will be converted to the first name provided for each author)
> my.aliases <- list(c("Felipe Campelo",
+                      "Felipe Campelo Franca Pinto",
+                      "Felipe Campelo F. Pinto",
+                      "F.C.F. Pinto"),
+                    c("Lucas S. Batista",
+                      "Lucas Batista",
+                      "Lucas de Souza Batista",
+                      "Lucas Souza Batista"))
> 
> lattes.list <- lattes_to_list(CV.dir         = CV.dir,
+                               author.aliases = my.aliases)
> 
> 
> # Build productions page:
> make_productions_page(lattes.list,
+                       chart.type     = "ggplot2",
+                       h1.title       = "ORCS Lab",
+                       h2.title       = "UFMG, Brazil",
+                       language       = "EN")
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
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    doc    1.7Mb
    help   2.3Mb
Running ‘testthat.R’ [52s/64s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(circumplex)
  > 
  > test_check("circumplex")
  ── 1. Failure: Quantile for circular radians works (@test-ssm_bootstrap.R#17)  ─
  `qb` not equivalent to as_radian(as_degree(c(180, 225, 270, 315, 0))).
  1/5 mismatches
  [5] 6.28 - 0 == 6.28
  
  ── 2. Failure: Quantile for circular radians works (@test-ssm_bootstrap.R#27)  ─
  `qb` not equivalent to as_radian(as_degree(c(270, 315, 0, 45, 90))).
  1/5 mismatches
  [3] 6.28 - 0 == 6.28
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 204 | SKIPPED: 6 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: Quantile for circular radians works (@test-ssm_bootstrap.R#17) 
  2. Failure: Quantile for circular radians works (@test-ssm_bootstrap.R#27) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘rggobi’
Running ‘testthat.R’ [33s/43s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(classiFunc)
  > 
  > test_check("classiFunc")
  ── 1. Failure: computeDistMat works rucrdtw metrics (@test_computeDistMat.R#100)
  all(as.vector(dist1) <= as.vector(dist3)) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 54 | SKIPPED: 0 | WARNINGS: 780 | FAILED: 1 ]
  1. Failure: computeDistMat works rucrdtw metrics (@test_computeDistMat.R#100) 
  
  Error: testthat unit tests failed
  Execution halted
Package which this enhances but not available for checking: ‘RWeka’
Error(s) in re-building vignettes:
  ...
--- re-building ‘the_clusterR_package.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 404-417 (the_clusterR_package.Rmd) 
Error: processing vignette 'the_clusterR_package.Rmd' failed with diagnostics:
std::bad_alloc
--- failed re-building ‘the_clusterR_package.Rmd’

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

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

> ### Name: cmpproc
> ### Title: COM Poisson Process Parameter Estimation.
> ### Aliases: cmpproc
> 
> ### ** Examples
> 
> ## Standard usage
> data(floodcount)
> cmpproc(floodcount$Counts)
Error in solve.default(H) : 
  system is computationally singular: reciprocal condition number = 0
Calls: cmpproc -> single.cmp -> diag -> solve -> solve.default
Execution halted
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Error(s) in re-building vignettes:
  ...
--- re-building ‘Running-CoDiNA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 100-105 (Running-CoDiNA.Rmd) 
Error: processing vignette 'Running-CoDiNA.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
--- failed re-building ‘Running-CoDiNA.Rmd’

SUMMARY: processing the following file failed:
  ‘Running-CoDiNA.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [128s/166s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(shinytest)
  shinytest requires a headless web browser (PhantomJS) to record and run tests.
  To install it, run shinytest::installDependencies()
  If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
  > library(colocr)
  > 
  > test_check("colocr")
  ── 1. Failure: the app results are reproduced faithfuly (@test-reproduce_app.R#3
  all.equal(...) isn't true.
  
  ── 2. Failure: the app results are reproduced faithfuly (@test-reproduce_app.R#3
  all.equal(...) isn't true.
  
  ── 3. Failure: the app results are reproduced using imager only (@test-reproduce
  all.equal(round(stats$pcc, 3), round(unlist(corr), 3)) isn't true.
  
  ── 4. Failure: the app results are reproduced using imager only (@test-reproduce
  all.equal(round(stats$moc, 3), round(unlist(corr), 3)) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 38 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: the app results are reproduced faithfuly (@test-reproduce_app.R#32) 
  2. Failure: the app results are reproduced faithfuly (@test-reproduce_app.R#35) 
  3. Failure: the app results are reproduced using imager only (@test-reproduce_app.R#126) 
  4. Failure: the app results are reproduced using imager only (@test-reproduce_app.R#145) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.4Mb
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    doc       3.0Mb
    extdata   2.3Mb
installed size is  5.4Mb
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    java   5.2Mb
Package suggested but not available for checking: ‘rscala’
Error(s) in re-building vignettes:
  ...
--- re-building ‘commonsMath.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 32-37 (commonsMath.Rmd) 
Error: processing vignette 'commonsMath.Rmd' failed with diagnostics:
there is no package called 'rscala'
--- failed re-building ‘commonsMath.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
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installed size is  9.6Mb
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    data      6.5Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘chamber.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 32-33 (chamber.Rmd) 
Error: processing vignette 'chamber.Rmd' failed with diagnostics:
HTTP error 500
--- failed re-building ‘chamber.Rmd’

--- re-building ‘senate.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

--- finished re-building ‘senate.Rmd’

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

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

> ### Name: coocnet
> ### Title: coocnet
> ### Aliases: coocnet
> 
> ### ** Examples
> 
> cooccurNetwork  = coocnet(dataFile=getexample(dataType="protein"), dataType="protein")
reading file......
completed. (10,329)
preprocess file......Error in if (pred >= memsize * alpha || ncol > 150 || (nrow > 30000 &  : 
  missing value where TRUE/FALSE needed
Calls: coocnet ... cooccur.dataprepreprocess.preprocess -> inmemoryflag
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Extending-cooccurNet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 176-178 (Extending-cooccurNet.Rmd) 
Error: processing vignette 'Extending-cooccurNet.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘Extending-cooccurNet.Rmd’

SUMMARY: processing the following file failed:
  ‘Extending-cooccurNet.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R     2.4Mb
    doc   6.4Mb
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    help   1.8Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction_to_coveffectsplot.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 253-341 (introduction_to_coveffectsplot.Rmd) 
Error: processing vignette 'introduction_to_coveffectsplot.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction_to_coveffectsplot.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘SNPRelate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 399-421 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.4Mb
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    doc   8.0Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/csp.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [59s/87s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ctmle)
  Loading required package: SuperLearner
  Loading required package: nnls
  Super Learner
  Version: 2.0-25
  Package created on 2019-08-05
  
  Loading required package: tmle
  Loading required package: glmnet
  Loading required package: Matrix
  Loaded glmnet 3.0-1
  
  Welcome to the tmle package, version 1.4.0.1
  
  Use tmleNews() to see details on changes and bug fixes
  > 
  > test_check("ctmle")
  ── 1. Error: (unknown) (@test-ctmleGeneral.R#73)  ──────────────────────────────
  could not find function "predict.cv.glmnet"
  
  ── 2. Error: (unknown) (@test-ctmleGlmnet.R#69)  ───────────────────────────────
  could not find function "predict.cv.glmnet"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 9 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: (unknown) (@test-ctmleGeneral.R#73) 
  2. Error: (unknown) (@test-ctmleGlmnet.R#69) 
  
  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) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 147-160 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
could not find function "predict.cv.glmnet"
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/ctsem.Rcheck/00install.out’ for details.
Package required but not available: ‘scs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘cycling_data_analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 177-179 (cycling_data_analysis.Rmd) 
Error: processing vignette 'cycling_data_analysis.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘cycling_data_analysis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  5.2Mb
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    doc   4.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 27-38 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
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installed size is  6.7Mb
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installed size is  5.2Mb
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    Pied_Flycatchers_2   1.3Mb
    doc                  1.2Mb
installed size is  7.8Mb
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    java   7.8Mb
installed size is  5.2Mb
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    help   2.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘extending_dataMaid.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
Data report generation is finished. Please wait while your output file is being rendered.
Quitting from lines 729-768 (extending_dataMaid.Rmd) 
Error: processing vignette 'extending_dataMaid.Rmd' failed with diagnostics:
pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
--- failed re-building ‘extending_dataMaid.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘get_started.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 26-34 (get_started.Rmd) 
Error: processing vignette 'get_started.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘get_started.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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    doc       2.5Mb
    extdata   5.7Mb
installed size is  5.2Mb
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    doc    1.3Mb
    libs   2.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘applications.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘applications.Rmd’

--- re-building ‘data.tree.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 513-516 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘data.tree.Rmd’

SUMMARY: processing the following file failed:
  ‘data.tree.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/dbarts.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘RPostgres’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    sample_data   3.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘MultiObjectiveDecisionAnalysisinR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

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

    combine

Quitting from lines 84-97 (MultiObjectiveDecisionAnalysisinR.Rmd) 
Error: processing vignette 'MultiObjectiveDecisionAnalysisinR.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘MultiObjectiveDecisionAnalysisinR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘RC_units.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘RC_units.Rmd’

--- re-building ‘decoder.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘decoder.Rmd’

--- re-building ‘sjukhus.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Joining, by = "key"
Joining, by = "key"
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 102-122 (sjukhus.Rmd) 
Error: processing vignette 'sjukhus.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘sjukhus.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Running ‘test-all.R’ [45s/53s]
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:
    doc       5.0Mb
    extdata   2.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    2.0Mb
    help   1.4Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'Rmosek', 'Rsymphony'
Error(s) in re-building vignettes:
  ...
--- re-building ‘custom.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘custom.Rmd’

--- re-building ‘documentation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘documentation.Rmd’

--- re-building ‘objects.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 53-58 (objects.Rmd) 
Error: processing vignette 'objects.Rmd' failed with diagnostics:
Timeout was reached: [imgur.com] Resolving timed out after 1000 milliseconds
--- failed re-building ‘objects.Rmd’

--- re-building ‘sessioninfo.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘sessioninfo.Rmd’

--- re-building ‘tests_and_coverage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘tests_and_coverage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

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 84-97 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
could not find function "predict.cv.glmnet"
--- failed re-building ‘my-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘multistage_fundamentals.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.
Computing non-mst profile_tables over an mst design, did you mean to use profile_tables_mst?
Warning: Column `item_id` joining character vector and factor, coercing into character vector
Warning: Removed 33 rows containing missing values (geom_point).
Quitting from lines 369-405 (multistage_fundamentals.Rmd) 
Error: processing vignette 'multistage_fundamentals.Rmd' failed with diagnostics:
problem cannot be computed
--- failed re-building ‘multistage_fundamentals.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    1.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘DGVM3D.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: rgl
Loading required namespace: rmarkdown
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 230-234 (DGVM3D.Rmd) 
Error: processing vignette 'DGVM3D.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘DGVM3D.Rmd’

SUMMARY: processing the following file failed:
  ‘DGVM3D.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.3Mb
Package unavailable to check Rd xrefs: ‘Seurat’
Running examples in ‘diem-Ex.R’ failed
The error most likely occurred in:

> ### Name: convert_to_seurat
> ### Title: Convert an SCE object to Seurat
> ### Aliases: convert_to_seurat
> 
> ### ** Examples
> 
> mm_seur <- convert_to_seurat(x = mb_small, 
+                              targets = FALSE, 
+                              min.features = 500, 
+                              min.cells = 3, 
+                              project = mb_small@name)
Error: Package "Seurat" needed for convert_to_seurat. Please install.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘diem.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 305-311 (diem.Rmd) 
Error: processing vignette 'diem.Rmd' failed with diagnostics:
Package "Seurat" needed for convert_to_seurat. Please install.
--- failed re-building ‘diem.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc   9.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
Package suggested but not available for checking: ‘RcppRedis’
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 15.3Mb
  sub-directories of 1Mb or more:
    include  15.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   2.1Mb
Running ‘runit.R’ [18s/28s]
  Running ‘testthat.R’ [18s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > running_on_my_machines <- function() {
  +     sys_info <- Sys.info()
  +     r <- sys_info[["nodename"]] %in% c("h7") &&
  +         sys_info[["effective_user"]] == "qwer" &&
  +         .Platform[["OS.type"]] == "unix"
  +     return(r)
  + }
  > 
  > set_NOT_CRAN  <- function() {
  +     is_unset <- is.na(Sys.getenv("NOT_CRAN", unset = NA))
  +     if (running_on_my_machines() && is_unset)
  +         Sys.setenv("NOT_CRAN" = TRUE)
  + }
  > 
  > set_NOT_CRAN()
  > library("testthat")
  > library("document")
  > test_check("document")
  ── R CMD build ─────────────────────────────────────────────────────────────────
  * checking for file ‘.../DESCRIPTION’ ... OK
  * preparing ‘mini.mal’:
  * checking DESCRIPTION meta-information ... OK
  * checking for LF line-endings in source and make files and shell scripts
  * checking for empty or unneeded directories
  * building ‘mini.mal_2.0.0.tar.gz’
  
  ── 1. Error: (unknown) (@test_basic.R#13)  ─────────────────────────────────────
  Still alive
  Backtrace:
   1. document::document(file_name, check_package = TRUE, runit = TRUE)
   2. document:::check_package(...)
   3. rcmdcheck::rcmdcheck(...)
   4. rcmdcheck:::build_package(...)
   7. proc$get_built_file()
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: (unknown) (@test_basic.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Packages which this enhances but not available for checking:
  'gurobi', 'Rmosek'
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    DRomics-shiny   1.8Mb
    extdata         3.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_drtmle.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
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

Loading required package: nloptr
Loading required package: nloptr
Loading required package: quadprog
Loading required namespace: earth
Loading required package: quadprog
Loading required namespace: earth
Loading required package: future
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
Error(s) in re-building vignettes:
  ...
--- re-building ‘userGuide.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Using constraints: b = 1
Using constraints: b = 1
Running default monotherapy fitting. Note that if constraints are needed, run mono fitting manually first
Using constraints: b = 1
Using constraints: b = 1
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot556b63736407.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot556b63736407.png': No such file or directory
Quitting from lines 357-358 (userGuide.Rmd) 
Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘userGuide.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    appinformation   4.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘dsa-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 37-38 (dsa-vignette.Rmd) 
Error: processing vignette 'dsa-vignette.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
--- failed re-building ‘dsa-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Designing-33PC.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 163-164 (Designing-33PC.Rmd) 
Error: processing vignette 'Designing-33PC.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Designing-33PC.Rmd’

SUMMARY: processing the following file failed:
  ‘Designing-33PC.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    doc    1.8Mb
    libs   2.3Mb
Package suggested but not available for checking: ‘uwot’
Package unavailable to check Rd xrefs: ‘uwot’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
Running examples in ‘EasyMx-Ex.R’ failed
The error most likely occurred in:

> ### Name: EasyMx-package
> ### Title: EasyMx: Easy modeling in OpenMx
> ### Aliases: EasyMx-package EasyMx
> 
> ### ** Examples
> 
> 
> # Make and run a one factor model
> require(EasyMx)
> 
> data(demoOneFactor)
> fmod <- list(G=names(demoOneFactor))
> fit1 <- emxFactorModel(fmod, demoOneFactor, run=TRUE)
Running Model with 15 parameters
Error: C stack usage  203986068 is too close to the limit
Error: The job for model 'Model' exited abnormally with the error message: User interrupt
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    hac    4.3Mb
Running examples in ‘eDMA-Ex.R’ failed
The error most likely occurred in:

> ### Name: BacktestDMA
> ### Title: Backtest measures for Dynamic Model Averaging and comparison
> ###   with Dynamic Model Selection
> ### Aliases: BacktestDMA
> 
> ### ** Examples
> 
> 
> library(eDMA)
> 
> ## load data
> data("USData")
> 
> ## do DMA, keep the first three predictors fixed and the intercept
> Fit <- DMA(GDPDEF ~ Lag(GDPDEF, 1) + Lag(GDPDEF, 2) + Lag(GDPDEF, 3) +
+             Lag(ROUTP, 1) + Lag(UNEMP, 1), data = USData, vDelta = c(0.9, 0.95, 0.99),
+             vKeep = c(1, 2, 3))

error: sort(): detected NaN
Error in funcEstimate_Eff_par(vY, mF, vDelta, dAlpha, vKeep, dBeta, bZellnerPrior,  : 
  sort(): detected NaN
Calls: DMA -> funcEstimate_Eff_par
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc       5.3Mb
    extdata   5.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘EHRtemporalVariability.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Joining, by = "diagcode1"
Warning: Column `diagcode1` joining factor and character vector, coercing into character vector
# Missing values: 0 cases ( 0%)
# External causes codes: 0 cases ( 0%)
# V codes not mapped: 74330 cases ( 22.82%)
# Total ICD9-CM codes mapped: 146262 cases ( 44.9%)
# Unique ICD9-CM codes mapped: 3020
# Total PheWAS codes: 757
# ICD9 codes not mapped: 105180 cases ( 32.29%)
Quitting from lines 317-322 (EHRtemporalVariability.Rmd) 
Error: processing vignette 'EHRtemporalVariability.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘EHRtemporalVariability.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    examples   4.2Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/elrm.Rcheck/00install.out’ for details.
Package required but not available: ‘uwot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘spelling.R’
  Running ‘testthat.R’ [29s/43s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(EML)
  > 
  > test_check("EML")
  sh: +RTS:  not found
  ── 1. Error: set_method with additional input files (@test-additional-tests.R#43
  pandoc document conversion failed with error 127
  Backtrace:
   1. EML::set_methods(...)
   2. EML::set_TextType(sampling_file)
   3. EML:::to_docbook(file)
   4. rmarkdown::pandoc_convert(...)
  
  ══  1 queries  ═══════════════
  ✔  Found:  Macrocystis pyrifera
  ══  Results  ═════════════════
  
  ● Total: 1 
  ● Found: 1 
  ● Not Found: 0
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 83 | SKIPPED: 6 | WARNINGS: 2 | FAILED: 1 ]
  1. Error: set_method with additional input files (@test-additional-tests.R#43) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.6Mb
Running examples in ‘eNetXplorer-Ex.R’ failed
The error most likely occurred in:

> ### Name: plotContingency
> ### Title: generates plot of response vs out-of-bag predictions across
> ###   classes
> ### Aliases: plotContingency
> 
> ### ** Examples
> 
> ## Don't show: 
> set.seed(123)
> fit = eNetXplorer(x=matrix(rnorm(120),ncol=4),y=c(rep(0,15),rep(1,15)),
+ family="binomial",n_run=5, n_perm_null=4,alpha=c(0.5,1))
Error during execution of alpha =  0.5 
> plot(x=fit,plot.type="contingency")
Error in if (x$family %in% c("binomial", "multinomial")) { : 
  argument is of length zero
Calls: plot -> plot.eNetXplorer
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    doc    3.4Mb
    help   3.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘epicontacts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘epicontacts.Rmd’

--- re-building ‘epicontacts_class.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘epicontacts_class.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘epiflows-class.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘epiflows-class.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 117-120 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

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

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

> ### Name: runEpiSDReport
> ### Title: Run the EpiSignalDetection report (HTML markdown)
> ### Aliases: runEpiSDReport
> 
> ### ** Examples
> 
> #---> OR
> 
> #-- First setting the parameters to run the report for
> input <- list(
+ disease = "Salmonellosis",
+ country = "Portugal",
+ indicator = "Reported cases",
+ stratification = "Confirmed cases",
+ unit = "Month",
+ daterange = c("2011-01-01", "2016-12-31"),
+ algo = "FarringtonFlexible",
+ testingperiod = 6
+ )
> 
> #-- Second running the report based on the EpiSignalDetection::SignalData dataset
> #-- and store it in a temporary folder
> runEpiSDReport(input = input)
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Running 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
Running ‘sleep.R’
  Comparing ‘sleep.Rout’ to ‘sleep.Rout.save’ ... OK
  Running ‘testthat.R’ [80s/96s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(estimatr)
  > 
  > test_check("estimatr")
  ── 1. Failure: Handle perfect fits appropriately (@test-lm-robust-fes.R#682)  ──
  tidy(rfo)[rfo$term == "X", ] not equivalent to tidy(ro)[ro$term == "X", ].
  Component "std.error": 'is.NA' value mismatch: 1 in current 0 in target
  Component "statistic": 'is.NA' value mismatch: 1 in current 0 in target
  Component "p.value": 'is.NA' value mismatch: 1 in current 0 in target
  Component "conf.low": 'is.NA' value mismatch: 1 in current 0 in target
  Component "conf.high": 'is.NA' value mismatch: 1 in current 0 in target
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1326 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Handle perfect fits appropriately (@test-lm-robust-fes.R#682) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.1Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    exiftool  14.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_genExPrior.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 58-59 (using_genExPrior.Rmd) 
Error: processing vignette 'using_genExPrior.Rmd' failed with diagnostics:
Failed to create the shared library.
--- failed re-building ‘using_genExPrior.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Package suggested but not available for checking: ‘RWeka’
Package unavailable to check Rd xrefs: ‘RWeka’
Running ‘run-all.R’
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("farff")
  Loading required package: farff
  ── 1. Error: quick test with small arffs (@test_quick.R#6)  ────────────────────
  there is no package called 'RWeka'
  Backtrace:
   1. farff:::compareRWeka(INST_ARFF_DIR, "iris.arff", data.reader = dreader)
   2. RWeka::read.arff /home/ripley/R/packages/tests32/farff.Rcheck/tests/helper.R:17:2
   3. base::getExportedValue(pkg, name)
   4. base::asNamespace(ns)
   5. base::getNamespace(ns)
   6. base::loadNamespace(name)
   7. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   8. base:::withOneRestart(expr, restarts[[1L]])
   9. base:::doWithOneRestart(return(expr), restart)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: quick test with small arffs (@test_quick.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
Package suggested but not available for checking: ‘Rserve’
Installation failed.
See ‘/home/ripley/R/packages/tests32/FastRWeb.Rcheck/00install.out’ for details.
Running ‘tinytest.R’
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  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘FeatureHashing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 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
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘SentimentAnalysis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(felp)
  
  Attaching package: 'felp'
  
  The following object is masked from 'package:utils':
  
      ?
  
  > 
  > test_check("felp")
  Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
Package required but not available: ‘CVXR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘quick_charts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 125-134 (quick_charts.Rmd) 
Error: processing vignette 'quick_charts.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘quick_charts.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘lifeExpectancy.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 70-72 (lifeExpectancy.Rmd) 
Error: processing vignette 'lifeExpectancy.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘lifeExpectancy.Rmd’

--- re-building ‘selectIndicatorsRedRed.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘selectIndicatorsRedRed.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    help   3.2Mb
Package suggested but not available for checking: ‘multipanelfigure’
Running examples in ‘float-Ex.R’ failed
The error most likely occurred in:

> ### Name: eigen
> ### Title: eigen
> ### Aliases: eigen eigen,float32-method
> 
> ### ** Examples
> 
> library(float)
> 
> s = flrunif(10, 3)
> cp = crossprod(s)
> 
> eigen(cp)
Found the following significant warnings:
  Warning: namespace ‘rrcov’ is not available and has been replaced
  Warning: namespace ‘robustbase’ is not available and has been replaced
See ‘/home/ripley/R/packages/tests32/flowDiv.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    fonts   6.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    fonts   7.6Mb
Running ‘testthat.R’ [209s/208s]
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
Error(s) in re-building vignettes:
  ...
--- re-building ‘pcl-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 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 ‘formattable-data-frame.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 168-169 (formattable-data-frame.Rmd) 
Error: processing vignette 'formattable-data-frame.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘formattable-data-frame.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘formattable-data-frame.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction-to-formulaic.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 127-132 (Introduction-to-formulaic.Rmd) 
Error: processing vignette 'Introduction-to-formulaic.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Introduction-to-formulaic.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2', 'Rsymphony'
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    help   1.6Mb
    libs   5.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R   5.8Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
    doc    2.1Mb
Package unavailable to check Rd xrefs: ‘RMark’
Packages suggested but not available for checking: 'RWeka', 'FSelector'
Package unavailable to check Rd xrefs: ‘FSelector’
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    data  16.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘futureheatwaves.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 604-605 (futureheatwaves.Rmd) 
Error: processing vignette 'futureheatwaves.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘futureheatwaves.Rmd’

--- re-building ‘starting_from_netcdf.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘starting_from_netcdf.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc   9.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘chart_themes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
g3viz: visualizing gene/genome/gentics data for fun.
Any questions, please send emails to <g3viz.group@gmail.com>
Please send questions to cbioportal@googlegroups.com
Quitting from lines 48-58 (chart_themes.Rmd) 
Error: processing vignette 'chart_themes.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘chart_themes.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
g3viz: visualizing gene/genome/gentics data for fun.
Any questions, please send emails to <g3viz.group@gmail.com>
Quitting from lines 103-114 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘chart_themes.Rmd’ ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   3.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      2.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘gcbd.Rnw’ using Sweave
Warning in packageDescription("gputools") :
  no package 'gputools' was found
Error: processing vignette 'gcbd.Rnw' failed with diagnostics:
at gcbd.Rnw:860, subscript out of bounds
--- failed re-building ‘gcbd.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    L8NY18   2.1Mb
    doc      1.0Mb
    libs     2.3Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R  10.3Mb
Package suggested but not available for checking: ‘reactome.db’
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    data  27.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘geosample-vignette.Rnw’ using knitr
Loading required package: sf
Linking to GEOS 3.6.3, GDAL 2.2.4, PROJ 5.2.0
Loading required package: sp
Loading required package: geoR
--------------------------------------------------------------
 Analysis of Geostatistical Data
 For an Introduction to geoR go to http://www.leg.ufpr.br/geoR
 geoR version 1.7-5.2.1 (built on 2016-05-02) is now loaded
--------------------------------------------------------------

Loading required package: maxLik
Loading required package: miscTools

Please cite the 'maxLik' package as:
Henningsen, Arne and Toomet, Ott (2011). maxLik: A package for maximum likelihood estimation in R. Computational Statistics 26(3), 443-458. DOI 10.1007/s00180-010-0217-1.

If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/
Loading required package: raster

Attaching package: 'raster'

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

    maxValue

Loading required package: pdist
Loading required package: Matrix
Quitting from lines 476-516 (geosample-vignette.Rnw) 
Error: processing vignette 'geosample-vignette.Rnw' failed with diagnostics:
cannot allocate vector of size 3.0 Gb
--- failed re-building ‘geosample-vignette.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         2.4Mb
    extdata   2.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown_notangle
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 53-60 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    help   1.6Mb
Packages suggested but not available for checking: 'av', 'gifski'
Error(s) in re-building vignettes:
  ...
--- re-building ‘gganimate.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 253-258 (gganimate.Rmd) 
Error: processing vignette 'gganimate.Rmd' failed with diagnostics:
The av package is required to use av_renderer
--- failed re-building ‘gganimate.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggBubbles.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: knitr
Loading required package: ggplot2
Loading required package: ggBubbles
Quitting from lines 30-40 (ggBubbles.Rmd) 
Error: processing vignette 'ggBubbles.Rmd' failed with diagnostics:
could not find function "CRANpkg"
--- failed re-building ‘ggBubbles.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    help   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc         2.8Mb
    tutorials   1.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggimage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 101-103 (ggimage.Rmd) 
Error: processing vignette 'ggimage.Rmd' failed with diagnostics:
there is no package called 'rsvg'
--- failed re-building ‘ggimage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggPredict.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra

Attaching package: 'ggiraphExtra'

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

    addLabelDf, getMapping

Loading required package: plyr
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 45-49 (ggPredict.Rmd) 
Error: processing vignette 'ggPredict.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘ggPredict.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot1993505f2157.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot1993505f2157.png': No such file or directory
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘ggPredict.Rmd’ ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   4.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘extending-ggplot2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘extending-ggplot2.Rmd’

--- re-building ‘ggplot2-specs.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘ggplot2-specs.Rmd’

Profiling Timer Expired
--- re-building ‘profiling.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
SUMMARY: processing the following file failed:
  ‘profiling.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   9.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: Matrix
Quitting from lines 185-186 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggseas.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 125-126 (ggseas.Rmd) 
Error: processing vignette 'ggseas.Rmd' failed with diagnostics:
Process terminated
--- failed re-building ‘ggseas.Rmd’

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

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

> ### Name: plot.cv.glmnet
> ### Title: plot the cross-validation curve produced by cv.glmnet
> ### Aliases: plot.cv.glmnet plot.cv.relaxed
> ### Keywords: models regression
> 
> ### ** Examples
> 
> 
> set.seed(1010)
> n = 1000
> p = 100
> nzc = trunc(p/10)
> x = matrix(rnorm(n * p), n, p)
> beta = rnorm(nzc)
> fx = (x[, seq(nzc)] %*% beta)
> eps = rnorm(n) * 5
> y = drop(fx + eps)
> px = exp(fx)
> px = px/(1 + px)
> ly = rbinom(n = length(px), prob = px, size = 1)
> cvob1 = cv.glmnet(x, y)
Error in intI(j, n = x@Dim[2], dn[[2]], give.dn = FALSE) : 
  'NA' indices are not (yet?) supported for sparse Matrices
Calls: cv.glmnet ... NextMethod -> predict.glmnet -> [ -> [ -> subCsp_cols -> intI
Execution halted
Packages required but not available: 'SeqArray', 'SeqVarTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    4.3Mb
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    R  27.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘profiling.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Installation failed.
See ‘/home/ripley/R/packages/tests32/gwsem.Rcheck/00install.out’ for details.
installed size is 127.4Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    java  125.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 40-43 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    data   9.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Basic_use.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 122-128 (Basic_use.Rmd) 
Error: processing vignette 'Basic_use.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Basic_use.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  readstat/readstat_convert.c:18:42: warning: passing argument 2 of ‘libiconv’ from incompatible pointer type [-Wincompatible-pointer-types]
  src/spss/readstat_sav_parse.rl:89:17: warning: passing argument 2 of ‘libiconv’ from incompatible pointer type [-Wincompatible-pointer-types]
  src/spss/readstat_sav_parse.rl:197:17: warning: passing argument 2 of ‘libiconv’ from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/ripley/R/packages/tests32/haven.Rcheck/00install.out’ for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc           2.8Mb
    htmlwidgets   2.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hchinamap.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'https://czxb.github.io/br/chinadf.rda'
Content type 'application/octet-stream' length 3992 bytes
==================================================
downloaded 3992 bytes

Quitting from lines 50-58 (hchinamap.Rmd) 
Error: processing vignette 'hchinamap.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘hchinamap.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘hdf5r-Ex.R’ failed
The error most likely occurred in:

> ### Name: H5A-class
> ### Title: Class for representing HDF5 attributes
> ### Aliases: H5A-class H5A
> 
> ### ** Examples
> 
> fname <- tempfile(fileext = ".h5")
> file <- H5File$new(fname, mode = "a")
Error in H5File.open(filename, mode, file_create_pl, file_access_pl) : 
  HDF5-API Errors:
    error #000: H5F.c in H5Fcreate(): line 444: unable to create file
        class: HDF5
        major: File accessibilty
        minor: Unable to open file

    error #001: H5Fint.c in H5F__create(): line 1364: unable to open file
        class: HDF5
        major: File accessibilty
        minor: Unable to open file

    error #002: H5Fint.c in H5F_open(): line 1615: unable to lock the file
        class: HDF5
        major: File accessibilty
        minor: Unable to open file

    error #003: H5FD.c in H5FD_lock(): line 1640: driver lock request failed
        class: HDF5
        major: Virtual File Layer
        minor: Can't update object

    error #004: H5FDsec2.c in H5FD_sec2_lock(): line 941: unable to lock file, errno = 14, error message = 'Bad address'
        class: HDF5
        major: File accessibilty
        minor: Bad file ID accessed
Calls: <Anonymous> -> <Anonymous> -> H5File.open
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hdf5r.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Quitting from lines 73-77 (hdf5r.Rmd) 
Error: processing vignette 'hdf5r.Rmd' failed with diagnostics:
HDF5-API Errors:
    error #000: H5F.c in H5Fcreate(): line 444: unable to create file
        class: HDF5
        major: File accessibilty
        minor: Unable to open file

    error #001: H5Fint.c in H5F__create(): line 1364: unable to open file
        class: HDF5
        major: File accessibilty
        minor: Unable to open file

    error #002: H5Fint.c in H5F_open(): line 1615: unable to lock the file
        class: HDF5
        major: File accessibilty
        minor: Unable to open file

    error #003: H5FD.c in H5FD_lock(): line 1640: driver lock request failed
        class: HDF5
        major: Virtual File Layer
        minor: Can't update object

    error #004: H5FDsec2.c in H5FD_sec2_lock(): line 941: unable to lock file, errno = 14, error message = 'Bad address'
        class: HDF5
        major: File accessibilty
        minor: Bad file ID accessed

--- failed re-building ‘hdf5r.Rmd’

SUMMARY: processing the following file failed:
  ‘hdf5r.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hdnom.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

(process:8228): Pango-WARNING **: failed to create cairo scaled font, expect ugly output. the offending font is 'Helvetica Medium 10.5'

(process:8228): Pango-WARNING **: font_face status is: no error has occurred

(process:8228): Pango-WARNING **: scaled_font status is: invalid matrix (not invertible)

(process:8228): Pango-WARNING **: shaping failure, expect ugly output. shape-engine='BasicEngineFc', font='Helvetica Medium 10.5', text='M'
Quitting from lines 367-379 (hdnom.Rmd) 
Error: processing vignette 'hdnom.Rmd' failed with diagnostics:
NA/NaN/Inf in foreign function call (arg 16)
--- failed re-building ‘hdnom.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘heatmaply.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

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

    filter

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

    layout

Loading required package: viridis
Loading required package: viridisLite

======================
Welcome to heatmaply version 0.16.0

Type citation('heatmaply') for how to cite the package.
Type ?heatmaply for the main documentation.

The github page is: https://github.com/talgalili/heatmaply/
Please submit your suggestions and bug-reports at: https://github.com/talgalili/heatmaply/issues
Or contact: <tal.galili@gmail.com>
======================

Quitting from lines 88-90 (heatmaply.Rmd) 
Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘heatmaply.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘authentication.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘authentication.Rmd’

--- re-building ‘geocoder.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 51-58 (geocoder.Rmd) 
Error: processing vignette 'geocoder.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘geocoder.Rmd’

--- re-building ‘routing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 40-48 (routing.Rmd) 
Error: processing vignette 'routing.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘routing.Rmd’

--- re-building ‘traffic.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 44-52 (traffic.Rmd) 
Error: processing vignette 'traffic.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘traffic.Rmd’

--- re-building ‘weather.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 52-59 (weather.Rmd) 
Error: processing vignette 'weather.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘weather.Rmd’

SUMMARY: processing the following files failed:
  ‘geocoder.Rmd’ ‘routing.Rmd’ ‘traffic.Rmd’ ‘weather.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    4.9Mb
    libs   1.8Mb
Running ‘testthat.R’ [92s/115s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(hesim)
  > 
  > test_check("hesim")
  Error in flexsurvreg(formula = Surv(futime, fustat) ~ age, data = data_i,  : 
    Initial values for parameters 1,2 out of range
  Error in flexsurvreg(formula = Surv(futime, fustat) ~ age, data = data_i,  : 
    Initial values for parameters 1,2 out of range
  Error in flexsurvreg(formula = Surv(futime, fustat) ~ age, data = data_i,  : 
    Initial values for parameters 1,2 out of range
  ── 1. Failure: Simulate costs and QALYs (@test-ctstm.R#379)  ───────────────────
  all(costs[category == "drugs", costs] == 0) isn't true.
  
  ── 2. Failure: Simulate costs and QALYs (@test-ctstm.R#381)  ───────────────────
  all(costs$costs == 0) isn't true.
  
  sample = 1
  sample = 2
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 728 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: Simulate costs and QALYs (@test-ctstm.R#379) 
  2. Failure: Simulate costs and QALYs (@test-ctstm.R#381) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc           3.7Mb
    htmlwidgets   4.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
Found the following significant warnings:
  mapping.cpp:95:58: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
See ‘/home/ripley/R/packages/tests32/hilbertSimilarity.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘RProtoBuf’
Package unavailable to check Rd xrefs: ‘RProtoBuf’
Error(s) in re-building vignettes:
  ...
--- re-building ‘hpackedbubble.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 35-49 (hpackedbubble.Rmd) 
Error: processing vignette 'hpackedbubble.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘hpackedbubble.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   8.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.6Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   8.1Mb
    doc    2.7Mb
Running ‘testthat.R’ [6s/56s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("httr")
  Loading required package: httr
  ── 1. Failure: if request_perform() throws an error, RETRY passes it on (@test-r
  `RETRY(...)` threw an error with unexpected message.
  Expected match: "resolve host"
  Actual message: "Could not resolve: 98d90a2a254647889e2e4c236fb576cd.com (Domain name not found)"
  Backtrace:
   1. testthat::expect_error(...)
   6. httr::RETRY(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 158 | SKIPPED: 2 | WARNINGS: 4 | FAILED: 1 ]
  1. Failure: if request_perform() throws an error, RETRY passes it on (@test-retry.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'https://arxiv.org/e-print/1406.4806v1'
Content type 'application/x-eprint-tar' length 29273 bytes (28 KB)
==================================================
downloaded 28 KB

Quitting from lines 161-165 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hwordcloud.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 48-53 (hwordcloud.Rmd) 
Error: processing vignette 'hwordcloud.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘hwordcloud.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
Running examples in ‘IAPWS95-Ex.R’ failed
The error most likely occurred in:

> ### Name: TDh
> ### Title: Temperature, Function of Density and Enthalpy
> ### Aliases: TDh
> 
> ### ** Examples
> 
> D <- 838.025
> h <- 977.181624
> T_Dh <- TDh(D,h)
Error(s) in re-building vignettes:
  ...
--- re-building ‘ibmsunburst.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 25-37 (ibmsunburst.Rmd) 
Error: processing vignette 'ibmsunburst.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘ibmsunburst.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘BSgenome.Mmusculus.UCSC.mm10’
Package unavailable to check Rd xrefs: ‘BSgenome.Mmusculus.UCSC.mm10’
Error(s) in re-building vignettes:
  ...
--- re-building ‘example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 62-70 (example.Rmd) 
Quitting from lines 62-70 (example.Rmd) 
Error: processing vignette 'example.Rmd' failed with diagnostics:
invalid connection
--- failed re-building ‘example.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   1.5Mb
    doc    1.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘model_details.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 25-32 (model_details.Rmd) 
Error: processing vignette 'model_details.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘model_details.Rmd’

--- re-building ‘parameter_details.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 24-31 (parameter_details.Rmd) 
Error: processing vignette 'parameter_details.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘parameter_details.Rmd’

--- re-building ‘resources.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘resources.Rmd’

SUMMARY: processing the following files failed:
  ‘model_details.Rmd’ ‘parameter_details.Rmd’

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

> ### Name: ifa.bic
> ### Title: A function to compute the BIC
> ### Aliases: ifa.bic
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> data(memory)

 *** caught segfault ***
address 144959bc, cause 'memory not mapped'

Traceback:
 1: sub(".*\\.", "", x)
 2: fileExt(file)
 3: data(memory)
An irrecoverable exception occurred. R is aborting now ...
Running examples in ‘ifaTools-Ex.R’ failed
The error most likely occurred in:

> ### Name: univariatePrior
> ### Title: Univariate priors commonly used in IFA models
> ### Aliases: univariatePrior
> 
> ### ** Examples
> 
> model <- univariatePrior("logit-norm", "x1", -1)
> model$priorParam$values[1,1] <- -.6
> model <- mxRun(model)
Running univariatePrior with 1 parameter
Error: C stack usage  229807252 is too close to the limit
Error: The job for model 'univariatePrior' exited abnormally with the error message: User interrupt
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pritikin-schmidt.Rnw’ using knitr
Quitting from lines 1344-1399 (pritikin-schmidt.Rnw) 
Error: processing vignette 'pritikin-schmidt.Rnw' failed with diagnostics:
Fit not achieved
--- failed re-building ‘pritikin-schmidt.Rnw’

SUMMARY: processing the following file failed:
  ‘pritikin-schmidt.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.2Mb
    libs   6.5Mb
Package suggested but not available for checking: ‘tesseract’
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    doc       5.4Mb
    extdata   1.2Mb
    include   2.9Mb
    libs      4.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    help   1.4Mb
Package unavailable to check Rd xrefs: ‘minfi’
Running examples in ‘Inflation-Ex.R’ failed
The error most likely occurred in:

> ### Name: INFL.core_tf
> ### Title: Computes the triple filter core inflation
> ### Aliases: INFL.core_tf
> ### Keywords: core filter triple
> 
> ### ** Examples
> 
> ipca <- ipca_sub
> INFL.core_tf(subits.var=ipca$ipca_ts, weights = ipca$weights_ts)
Unsupported platform: SunOS 5.10
For this platform, the path to the binary executable of X-13
has to be manually specified. See ?seasonal for details.
No path to the binary executable of X-13 specified.

You can set 'X13_PATH' manually if you intend to use your own
binaries. See ?seasonal for details.

Error in checkX13(fail = TRUE, fullcheck = FALSE, htmlcheck = FALSE) : 
  Process terminated
Calls: INFL.core_tf -> <Anonymous> -> checkX13
Execution halted
Running ‘spelling.R’
  Running ‘testthat.R’ [11s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(inplace)
  > 
  > test_check("inplace")
  ── 1. Failure: in-place operators work in common cases (@test-operators.R#80)  ─
  `X` not identical to `X2`.
  Objects equal but not identical
  
  ── 2. Failure: in-place operators work in common cases (@test-sweep.R#49)  ─────
  `X` not identical to `X2`.
  Objects equal but not identical
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 806 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: in-place operators work in common cases (@test-operators.R#80) 
  2. Failure: in-place operators work in common cases (@test-sweep.R#49) 
  
  Error: testthat unit tests failed
  Execution halted