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This page was generated on 2021-09-20 15:06:01 -0400 (Mon, 20 Sep 2021).

CHECK results for tRanslatome on machv2

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- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tRanslatome.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1949/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tRanslatome 1.30.0  (landing page)
Toma Tebaldi , Erik Dassi
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/tRanslatome
git_branch: RELEASE_3_13
git_last_commit: 256a394
git_last_commit_date: 2021-05-19 11:59:02 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: tRanslatome
Version: 1.30.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:tRanslatome.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings tRanslatome_1.30.0.tar.gz
StartedAt: 2021-09-20 00:49:54 -0400 (Mon, 20 Sep 2021)
EndedAt: 2021-09-20 00:56:23 -0400 (Mon, 20 Sep 2021)
EllapsedTime: 389.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: tRanslatome.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:tRanslatome.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings tRanslatome_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/tRanslatome.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tRanslatome/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tRanslatome’ version ‘1.30.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'limma', 'sigPathway', 'anota', 'DESeq2', 'edgeR', 'RankProd',
  'topGO', 'org.Hs.eg.db', 'GOSemSim', 'Heatplus', 'gplots', 'plotrix',
  'Biobase'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘tRanslatome’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
computeGeneListEnrichment: no visible global function definition for
  ‘data’
computeGeneListEnrichment: no visible binding for global variable
  ‘tRanslatomeSampleData’
computeGeneListEnrichment: no visible global function definition for
  ‘fisher.test’
computeGeneListEnrichment: no visible global function definition for
  ‘p.adjust’
createspecifictable: no visible global function definition for ‘str’
createspecifictable: no visible global function definition for
  ‘p.adjust’
methodANOTA: no visible global function definition for ‘p.adjust’
methodEdgeR: no visible global function definition for ‘p.adjust’
methodLimma: no visible global function definition for ‘model.matrix’
methodLimma: no visible global function definition for ‘lmFit’
methodLimma: no visible global function definition for ‘p.adjust’
methodTTest: no visible global function definition for ‘p.adjust’
CVplot,DEGs: no visible global function definition for ‘pdf’
CVplot,DEGs: no visible global function definition for ‘postscript’
CVplot,DEGs: no visible global function definition for ‘jpeg’
CVplot,DEGs: no visible global function definition for ‘par’
CVplot,DEGs: no visible global function definition for ‘layout’
CVplot,DEGs: no visible global function definition for ‘points’
CVplot,DEGs: no visible global function definition for ‘abline’
CVplot,DEGs: no visible global function definition for ‘legend’
CVplot,DEGs: no visible global function definition for ‘text’
CVplot,DEGs: no visible global function definition for ‘dev.off’
GOEnrichment,DEGs: no visible global function definition for ‘toTable’
Heatmap,EnrichedSets: no visible global function definition for ‘pdf’
Heatmap,EnrichedSets: no visible global function definition for
  ‘postscript’
Heatmap,EnrichedSets: no visible global function definition for ‘jpeg’
Heatmap,EnrichedSets: no visible global function definition for ‘png’
Heatmap,EnrichedSets: no visible global function definition for
  ‘dev.off’
Heatmap,GOsets: no visible global function definition for ‘pdf’
Heatmap,GOsets: no visible global function definition for ‘postscript’
Heatmap,GOsets: no visible global function definition for ‘jpeg’
Heatmap,GOsets: no visible global function definition for ‘png’
Heatmap,GOsets: no visible global function definition for ‘dev.off’
Histogram,DEGs: no visible global function definition for ‘pdf’
Histogram,DEGs: no visible global function definition for ‘postscript’
Histogram,DEGs: no visible global function definition for ‘jpeg’
Histogram,DEGs: no visible global function definition for ‘par’
Histogram,DEGs: no visible global function definition for ‘barplot’
Histogram,DEGs: no visible global function definition for ‘legend’
Histogram,DEGs: no visible global function definition for ‘mtext’
Histogram,DEGs: no visible global function definition for ‘dev.off’
IdentityPlot,GOsims: no visible global function definition for ‘pdf’
IdentityPlot,GOsims: no visible global function definition for
  ‘postscript’
IdentityPlot,GOsims: no visible global function definition for ‘jpeg’
IdentityPlot,GOsims: no visible global function definition for
  ‘barplot’
IdentityPlot,GOsims: no visible global function definition for
  ‘dev.off’
MAplot,DEGs: no visible global function definition for ‘pdf’
MAplot,DEGs: no visible global function definition for ‘postscript’
MAplot,DEGs: no visible global function definition for ‘jpeg’
MAplot,DEGs: no visible global function definition for ‘par’
MAplot,DEGs: no visible global function definition for ‘layout’
MAplot,DEGs: no visible global function definition for ‘points’
MAplot,DEGs: no visible global function definition for ‘abline’
MAplot,DEGs: no visible global function definition for ‘legend’
MAplot,DEGs: no visible global function definition for ‘text’
MAplot,DEGs: no visible global function definition for ‘dev.off’
Radar,EnrichedSets: no visible global function definition for ‘pdf’
Radar,EnrichedSets: no visible global function definition for
  ‘postscript’
Radar,EnrichedSets: no visible global function definition for ‘jpeg’
Radar,EnrichedSets: no visible global function definition for ‘png’
Radar,EnrichedSets: no visible global function definition for ‘par’
Radar,EnrichedSets: no visible global function definition for ‘legend’
Radar,EnrichedSets: no visible global function definition for ‘dev.off’
Radar,GOsets: no visible global function definition for ‘pdf’
Radar,GOsets: no visible global function definition for ‘postscript’
Radar,GOsets: no visible global function definition for ‘jpeg’
Radar,GOsets: no visible global function definition for ‘png’
Radar,GOsets: no visible global function definition for ‘par’
Radar,GOsets: no visible global function definition for ‘legend’
Radar,GOsets: no visible global function definition for ‘dev.off’
SDplot,DEGs: no visible global function definition for ‘pdf’
SDplot,DEGs: no visible global function definition for ‘postscript’
SDplot,DEGs: no visible global function definition for ‘jpeg’
SDplot,DEGs: no visible global function definition for ‘par’
SDplot,DEGs: no visible global function definition for ‘layout’
SDplot,DEGs: no visible global function definition for ‘points’
SDplot,DEGs: no visible global function definition for ‘abline’
SDplot,DEGs: no visible global function definition for ‘legend’
SDplot,DEGs: no visible global function definition for ‘text’
SDplot,DEGs: no visible global function definition for ‘dev.off’
Scatterplot,DEGs: no visible global function definition for ‘pdf’
Scatterplot,DEGs: no visible global function definition for
  ‘postscript’
Scatterplot,DEGs: no visible global function definition for ‘jpeg’
Scatterplot,DEGs: no visible global function definition for ‘mtext’
Scatterplot,DEGs: no visible global function definition for ‘cor.test’
Scatterplot,DEGs: no visible global function definition for ‘points’
Scatterplot,DEGs: no visible global function definition for ‘abline’
Scatterplot,DEGs: no visible global function definition for ‘legend’
Scatterplot,DEGs: no visible global function definition for ‘text’
Scatterplot,DEGs: no visible global function definition for ‘dev.off’
SimilarityPlot,GOsims: no visible global function definition for ‘pdf’
SimilarityPlot,GOsims: no visible global function definition for
  ‘postscript’
SimilarityPlot,GOsims: no visible global function definition for ‘jpeg’
SimilarityPlot,GOsims: no visible global function definition for
  ‘barplot’
SimilarityPlot,GOsims: no visible global function definition for
  ‘legend’
SimilarityPlot,GOsims: no visible global function definition for
  ‘dev.off’
computeDEGs,TranslatomeDataset : <anonymous>: no visible global
  function definition for ‘sd’
show,DEGs: no visible global function definition for ‘head’
show,GOsims: no visible global function definition for ‘head’
show,TranslatomeDataset: no visible global function definition for
  ‘head’
Undefined global functions or variables:
  abline barplot cor.test data dev.off fisher.test head jpeg layout
  legend lmFit model.matrix mtext p.adjust par pdf png points
  postscript sd str tRanslatomeSampleData text toTable
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "pdf", "png", "postscript")
  importFrom("graphics", "abline", "barplot", "layout", "legend",
             "mtext", "par", "points", "text")
  importFrom("stats", "cor.test", "fisher.test", "model.matrix",
             "p.adjust", "sd")
  importFrom("utils", "data", "head", "str")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: 'RGBColVec' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
GOComparison 18.166  1.384  19.561
GOEnrichment 16.856  0.184  17.047
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/tRanslatome.Rcheck/00check.log’
for details.



Installation output

tRanslatome.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL tRanslatome
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘tRanslatome’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package can be loaded from final location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package keeps a record of temporary installation path
* DONE (tRanslatome)

Tests output


Example timings

tRanslatome.Rcheck/tRanslatome-Ex.timings

nameusersystemelapsed
CVplot0.0930.0070.100
DEGs0.0010.0010.001
DEGs.table0.1260.1720.298
EnrichedSets0.0020.0010.002
FC.threshold0.0510.0050.057
GOComparison18.166 1.38419.561
GOEnrichment16.856 0.18417.047
GOsets0.0000.0010.001
GOsims0.0010.0010.002
Heatmap0.1540.0100.164
Histogram0.0700.0050.076
IdentityPlot0.0610.0050.066
MAplot0.0840.0090.094
Radar0.1220.0060.130
RegulatoryEnrichment2.6610.0262.688
SDplot0.0820.0080.090
Scatterplot0.1380.0070.147
SimilarityPlot0.0650.0030.069
TranslatomeDataset0.0010.0010.002
average.similarity.scores0.0520.0050.057
computeDEGs0.4240.0070.431
enriched.table0.0510.0040.055
getConditionA0.0520.0030.056
getConditionB0.0510.0030.054
getConditionC0.0490.0030.052
getConditionD0.0550.0030.058
getConditionLabels0.0540.0040.057
getDEGs0.0520.0040.055
getDEGsMethod0.0640.0060.069
getDataType0.0700.0060.076
getExprMatrix0.1150.1230.238
getLevelLabels0.0580.0050.062
identity.matrix0.1290.0070.137
label.condition0.0620.0030.066
label.level.DEGs0.0580.0040.063
label.level.enriched0.0530.0060.058
newTranslatomeDataset0.0580.0030.062
significance.threshold0.0550.0050.060
similarity.matrix0.0610.0050.066
tRanslatomeSampleData0.0500.0030.053