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This page was generated on 2022-06-24 12:08:16 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for tRanslatome on merida1


To the developers/maintainers of the tRanslatome package:
- 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? 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 2040/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tRanslatome 1.34.0  (landing page)
Toma Tebaldi , Erik Dassi
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/tRanslatome
git_branch: RELEASE_3_15
git_last_commit: 50053cc
git_last_commit_date: 2022-04-26 11:15:02 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    NA  

Summary

Package: tRanslatome
Version: 1.34.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:tRanslatome.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings tRanslatome_1.34.0.tar.gz
StartedAt: 2022-06-24 10:04:34 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 10:13:58 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 564.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: tRanslatome.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:tRanslatome.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings tRanslatome_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/tRanslatome.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘1.34.0’
* 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 ... OK
* 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
GOEnrichment 25.266  0.336  25.831
GOComparison 23.258  1.332  24.827
* 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/tRanslatome.Rcheck/00check.log’
for details.



Installation output

tRanslatome.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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
CVplot0.1540.0100.166
DEGs0.0020.0000.002
DEGs.table0.1780.1290.313
EnrichedSets0.0010.0000.001
FC.threshold0.0740.0050.083
GOComparison23.258 1.33224.827
GOEnrichment25.266 0.33625.831
GOsets0.0010.0000.001
GOsims0.0000.0000.001
Heatmap0.1750.0080.184
Histogram0.0800.0050.086
IdentityPlot0.0720.0050.078
MAplot0.1050.0080.114
Radar0.1430.0070.150
RegulatoryEnrichment3.1420.0403.208
SDplot0.1100.0090.120
Scatterplot0.1610.0090.174
SimilarityPlot0.0770.0060.085
TranslatomeDataset0.0000.0000.001
average.similarity.scores0.0730.0050.080
computeDEGs0.6400.0090.661
enriched.table0.0810.0060.088
getConditionA0.0740.0040.078
getConditionB0.0740.0050.081
getConditionC0.0690.0040.074
getConditionD0.0710.0050.077
getConditionLabels0.0740.0060.080
getDEGs0.0760.0060.081
getDEGsMethod0.0740.0050.079
getDataType0.0730.0050.078
getExprMatrix0.1210.0650.189
getLevelLabels0.0730.0060.080
identity.matrix0.0750.0040.080
label.condition0.0750.0060.082
label.level.DEGs0.0750.0060.082
label.level.enriched0.0750.0050.081
newTranslatomeDataset0.0780.0060.086
significance.threshold0.0750.0050.080
similarity.matrix0.0740.0050.080
tRanslatomeSampleData0.0730.0050.079