Package: tRanslatome

Version: 1.18.5

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:tRanslatome.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings tRanslatome_1.18.5.tar.gz

StartedAt: 2018-10-16 04:15:47 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 04:18:34 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 167.1 seconds

RetCode: 0

Status:  OK

CheckDir: tRanslatome.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:tRanslatome.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings tRanslatome_1.18.5.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/tRanslatome.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 ‘1.18.5’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘limma’ ‘sigPathway’ ‘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 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 ‘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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
GOEnrichment 12.720  0.012  12.740
GOComparison  9.524  0.216   9.754
* 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/tRanslatome.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL tRanslatome
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘tRanslatome’ ...
** 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

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (tRanslatome)

name	user	system	elapsed
CVplot	0.080	0.004	0.083
DEGs	0.000	0.000	0.001
DEGs.table	0.076	0.060	0.134
EnrichedSets	0.000	0.000	0.001
FC.threshold	0.088	0.000	0.088
GOComparison	9.524	0.216	9.754
GOEnrichment	12.720	0.012	12.740
GOsets	0.004	0.000	0.001
GOsims	0	0	0
Heatmap	0.076	0.004	0.077
Histogram	0.056	0.000	0.054
IdentityPlot	0.052	0.000	0.053
MAplot	0.060	0.000	0.058
Radar	0.06	0.00	0.06
RegulatoryEnrichment	1.656	0.004	1.658
SDplot	0.056	0.000	0.056
Scatterplot	0.060	0.000	0.058
SimilarityPlot	0.052	0.000	0.051
TranslatomeDataset	0.004	0.000	0.001
average.similarity.scores	0.052	0.000	0.053
computeDEGs	0.608	0.008	0.616
enriched.table	0.072	0.004	0.073
getConditionA	0.068	0.004	0.072
getConditionB	0.072	0.000	0.069
getConditionC	0.068	0.004	0.071
getConditionD	0.072	0.000	0.070
getConditionLabels	0.068	0.000	0.068
getDEGs	0.060	0.004	0.067
getDEGsMethod	0.068	0.004	0.072
getDataType	0.072	0.000	0.071
getExprMatrix	0.112	0.020	0.130
getLevelLabels	0.072	0.000	0.071
identity.matrix	0.064	0.004	0.069
label.condition	0.068	0.000	0.067
label.level.DEGs	0.048	0.000	0.050
label.level.enriched	0.048	0.000	0.048
newTranslatomeDataset	0.052	0.000	0.049
significance.threshold	0.048	0.000	0.049
similarity.matrix	0.052	0.000	0.050
tRanslatomeSampleData	0.048	0.000	0.048