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BioC 3.5: CHECK report for tRanslatome on tokay2

This page was generated on 2017-08-16 13:22:23 -0400 (Wed, 16 Aug 2017).

Package 1329/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tRanslatome 1.14.0
Toma Tebaldi , Erik Dassi
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/tRanslatome
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: tRanslatome
Version: 1.14.0
Command: rm -rf tRanslatome.buildbin-libdir tRanslatome.Rcheck && mkdir tRanslatome.buildbin-libdir tRanslatome.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=tRanslatome.buildbin-libdir tRanslatome_1.14.0.tar.gz >tRanslatome.Rcheck\00install.out 2>&1 && cp tRanslatome.Rcheck\00install.out tRanslatome-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=tRanslatome.buildbin-libdir --install="check:tRanslatome-install.out" --force-multiarch --no-vignettes --timings tRanslatome_1.14.0.tar.gz
StartedAt: 2017-08-16 03:20:51 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 03:27:07 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 376.9 seconds
RetCode: 0
Status:  OK  
CheckDir: tRanslatome.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf tRanslatome.buildbin-libdir tRanslatome.Rcheck && mkdir tRanslatome.buildbin-libdir tRanslatome.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=tRanslatome.buildbin-libdir tRanslatome_1.14.0.tar.gz >tRanslatome.Rcheck\00install.out 2>&1 && cp tRanslatome.Rcheck\00install.out tRanslatome-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=tRanslatome.buildbin-libdir --install="check:tRanslatome-install.out" --force-multiarch --no-vignettes --timings tRanslatome_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/tRanslatome.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'tRanslatome/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'tRanslatome' version '1.14.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'limma' 'sigPathway' 'samr' 'anota' 'DESeq' '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 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
* loading checks for arch 'i386'
** 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 loading without being on the library search path ... OK
* loading checks for arch 'x64'
** 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 loading without being on the library search path ... 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'
methodSAM: 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 'plot'
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 'plot'
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 'plot'
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 'plot'
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 plot 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", "plot", "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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
GOEnrichment 23.83   0.10   25.28
GOComparison 10.52   0.54   11.07
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
GOEnrichment 24.53   0.11   24.64
GOComparison 15.81   0.67   16.48
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/tRanslatome.Rcheck/00check.log'
for details.

tRanslatome.Rcheck/00install.out:


install for i386

* installing *source* package 'tRanslatome' ...
** R
** data
** inst
** preparing 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

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

install for x64

* installing *source* package 'tRanslatome' ...
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* MD5 sums
packaged installation of 'tRanslatome' as tRanslatome_1.14.0.zip
* DONE (tRanslatome)

tRanslatome.Rcheck/examples_i386/tRanslatome-Ex.timings:

nameusersystemelapsed
CVplot0.110.020.12
DEGs000
DEGs.table0.150.030.18
EnrichedSets000
FC.threshold0.080.000.08
GOComparison10.52 0.5411.07
GOEnrichment23.83 0.1025.28
GOsets000
GOsims000
Heatmap0.340.010.36
Histogram0.080.020.09
IdentityPlot0.090.000.09
MAplot0.080.000.08
Radar0.160.000.16
RegulatoryEnrichment2.290.112.40
SDplot0.110.010.13
Scatterplot0.100.020.11
SimilarityPlot0.070.000.08
TranslatomeDataset0.020.000.01
average.similarity.scores0.090.010.11
computeDEGs1.100.041.13
enriched.table0.070.000.07
getConditionA0.090.000.09
getConditionB0.100.030.13
getConditionC0.090.010.11
getConditionD0.100.020.11
getConditionLabels0.090.010.11
getDEGs0.090.020.11
getDEGsMethod0.100.020.11
getDataType0.070.000.07
getExprMatrix0.150.040.19
getLevelLabels0.110.000.11
identity.matrix0.090.020.11
label.condition0.100.010.11
label.level.DEGs0.080.020.09
label.level.enriched0.070.030.11
newTranslatomeDataset0.080.000.08
significance.threshold0.060.000.06
similarity.matrix0.080.000.08
tRanslatomeSampleData0.050.030.08

tRanslatome.Rcheck/examples_x64/tRanslatome-Ex.timings:

nameusersystemelapsed
CVplot0.140.010.16
DEGs000
DEGs.table0.180.010.19
EnrichedSets0.000.020.01
FC.threshold0.060.000.07
GOComparison15.81 0.6716.48
GOEnrichment24.53 0.1124.64
GOsets000
GOsims000
Heatmap0.360.000.36
Histogram0.060.020.08
IdentityPlot0.050.000.05
MAplot0.060.000.06
Radar0.110.020.13
RegulatoryEnrichment1.770.001.77
SDplot0.060.010.07
Scatterplot0.060.020.08
SimilarityPlot0.050.010.06
TranslatomeDataset000
average.similarity.scores0.060.020.08
computeDEGs1.160.001.16
enriched.table0.060.020.08
getConditionA0.060.010.07
getConditionB0.050.020.07
getConditionC0.060.010.08
getConditionD0.070.000.06
getConditionLabels0.060.000.06
getDEGs0.060.000.06
getDEGsMethod0.060.000.07
getDataType0.070.030.09
getExprMatrix0.140.000.14
getLevelLabels0.080.000.07
identity.matrix0.090.000.10
label.condition0.080.020.10
label.level.DEGs0.090.010.11
label.level.enriched0.110.000.11
newTranslatomeDataset0.100.020.10
significance.threshold0.070.020.10
similarity.matrix0.080.010.09
tRanslatomeSampleData0.080.020.10