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BioC 3.0: CHECK report for tRanslatome on oaxaca

This page was generated on 2015-04-10 10:07:23 -0700 (Fri, 10 Apr 2015).

Package 896/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tRanslatome 1.4.0
Toma Tebaldi , Erik Dassi
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/tRanslatome
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: tRanslatome
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch tRanslatome_1.4.0.tar.gz
StartedAt: 2015-04-10 03:55:48 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 04:00:24 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 276.2 seconds
RetCode: 0
Status:  OK 
CheckDir: tRanslatome.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch tRanslatome_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/tRanslatome.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.4.0’
* 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’
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 ... [24s/24s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘DESeq’ ‘GOSemSim’ ‘Heatplus’ ‘RankProd’ ‘anota’ ‘edgeR’ ‘gplots’
  ‘limma’ ‘methods’ ‘org.Hs.eg.db’ ‘plotrix’ ‘samr’ ‘sigPathway’
  ‘topGO’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
comparisonBetweenTwoLists: no visible global function definition for
  ‘goSim’
createspecifictable: no visible global function definition for
  ‘annFUN.org’
createspecifictable: no visible global function definition for
  ‘inverseList’
createspecifictable: no visible binding for global variable
  ‘annFUN.gene2GO’
createspecifictable: no visible global function definition for
  ‘runTest’
createspecifictable: no visible global function definition for ‘score’
createspecifictable: no visible global function definition for
  ‘GenTable’
methodANOTA: no visible global function definition for ‘anotaPerformQc’
methodANOTA: no visible global function definition for
  ‘anotaGetSigGenes’
methodDESeq: no visible global function definition for
  ‘newCountDataSet’
methodDESeq: no visible global function definition for
  ‘estimateSizeFactors’
methodDESeq: no visible global function definition for
  ‘estimateDispersions’
methodDESeq: no visible global function definition for ‘nbinomTest’
methodEdgeR: no visible global function definition for ‘DGEList’
methodEdgeR: no visible global function definition for
  ‘calcNormFactors’
methodEdgeR: no visible global function definition for
  ‘estimateCommonDisp’
methodEdgeR: no visible global function definition for
  ‘estimateTagwiseDisp’
methodEdgeR: no visible global function definition for ‘exactTest’
methodLimma: no visible global function definition for ‘lmFit’
methodLimma: no visible global function definition for ‘makeContrasts’
methodLimma: no visible global function definition for ‘contrasts.fit’
methodLimma: no visible global function definition for ‘eBayes’
methodSAM: no visible global function definition for ‘samr’
methodSAM: no visible global function definition for
  ‘samr.pvalues.from.perms’
methodTTest: no visible global function definition for ‘calcTStatFast’
newTranslatomeDataset: no visible global function definition for
  ‘exprs’
GOEnrichment,DEGs: no visible global function definition for ‘toTable’
GOEnrichment,DEGs: no visible binding for global variable
  ‘org.Hs.egSYMBOL’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [43s/43s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
GOEnrichment 23.244  0.179  23.545
* 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/tRanslatome.Rcheck/00check.log’
for details.

tRanslatome.Rcheck/00install.out:

* 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.
* DONE (tRanslatome)

tRanslatome.Rcheck/tRanslatome-Ex.timings:

nameusersystemelapsed
CVplot0.0930.0090.104
DEGs0.0030.0000.003
DEGs.table0.1600.0910.251
EnrichedSets0.0020.0000.002
FC.threshold0.0580.0050.063
GOComparison1.1170.0201.180
GOEnrichment23.244 0.17923.545
GOsets0.0010.0000.001
GOsims0.0010.0010.001
Heatmap0.0990.0060.106
Histogram0.0640.0050.068
IdentityPlot0.0580.0050.063
MAplot0.0700.0060.076
Radar0.0750.0050.082
RegulatoryEnrichment3.5100.0263.550
SDplot0.0700.0040.075
Scatterplot0.0860.0040.091
SimilarityPlot0.0600.0040.065
TranslatomeDataset0.0020.0000.002
average.similarity.scores0.0580.0040.063
computeDEGs0.5920.0060.599
enriched.table0.0640.0040.068
getConditionA0.0720.0050.075
getConditionB0.0570.0040.061
getConditionC0.0590.0050.063
getConditionD0.0580.0040.062
getConditionLabels0.0580.0040.064
getDEGs0.0580.0040.065
getDEGsMethod0.0560.0040.062
getDataType0.0590.0050.065
getExprMatrix0.1030.0450.148
getLevelLabels0.0600.0040.064
identity.matrix0.0580.0050.063
label.condition0.0570.0040.062
label.level.DEGs0.0580.0040.062
label.level.enriched0.0590.0050.063
newTranslatomeDataset0.0630.0040.067
significance.threshold0.0590.0040.065
similarity.matrix0.0590.0050.063
tRanslatomeSampleData0.0580.0040.062