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CHECK report for tRanslatome on machv2

This page was generated on 2021-05-14 12:42:12 -0400 (Fri, 14 May 2021).

To the developers/maintainers of the tRanslatome package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1947/2039HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tRanslatome 1.29.2  (landing page)
Toma Tebaldi , Erik Dassi
Snapshot Date: 2021-05-13 14:50:11 -0400 (Thu, 13 May 2021)
URL: https://git.bioconductor.org/packages/tRanslatome
Branch: master
Last Commit: 4ee27ef
Last Changed Date: 2020-11-25 10:50:17 -0400 (Wed, 25 Nov 2020)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: tRanslatome
Version: 1.29.2
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_1.29.2.tar.gz
StartedAt: 2021-05-14 08:31:58 -0400 (Fri, 14 May 2021)
EndedAt: 2021-05-14 08:38:18 -0400 (Fri, 14 May 2021)
EllapsedTime: 380.8 seconds
RetCode: 0
Status:   OK  
CheckDir: tRanslatome.Rcheck
Warnings: 0

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_1.29.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/tRanslatome.Rcheck’
* using R version 4.1.0 RC (2021-05-10 r80283)
* 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 ‘1.29.2’
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
GOComparison 17.841  1.287  19.137
GOEnrichment 16.538  0.143  16.688
* 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: 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
CVplot0.1430.0110.153
DEGs0.0010.0010.002
DEGs.table0.1640.2220.386
EnrichedSets0.0010.0010.002
FC.threshold0.0600.0060.065
GOComparison17.841 1.28719.137
GOEnrichment16.538 0.14316.688
GOsets0.0010.0010.001
GOsims0.0000.0010.001
Heatmap0.1490.0090.158
Histogram0.0740.0060.080
IdentityPlot0.0500.0060.056
MAplot0.0790.0100.089
Radar0.1180.0080.125
RegulatoryEnrichment2.5450.0302.577
SDplot0.0840.0080.092
Scatterplot0.1170.0060.124
SimilarityPlot0.0660.0050.072
TranslatomeDataset0.0010.0010.002
average.similarity.scores0.1100.0060.117
computeDEGs0.5340.0100.545
enriched.table0.0540.0060.060
getConditionA0.0570.0050.062
getConditionB0.0620.0060.068
getConditionC0.0710.0070.077
getConditionD0.0700.0060.076
getConditionLabels0.0620.0050.066
getDEGs0.0690.0040.072
getDEGsMethod0.0620.0060.067
getDataType0.0510.0030.055
getExprMatrix0.1140.1170.232
getLevelLabels0.0640.0060.069
identity.matrix0.0640.0050.067
label.condition0.0640.0040.069
label.level.DEGs0.0660.0030.070
label.level.enriched0.0630.0060.069
newTranslatomeDataset0.0720.0070.078
significance.threshold0.0640.0040.068
similarity.matrix0.0540.0040.057
tRanslatomeSampleData0.0620.0030.065