Package: tRanslatome

Version: 1.22.0

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_1.22.0.tar.gz

StartedAt: 2019-10-16 07:28:47 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 07:34:29 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 342.0 seconds

RetCode: 0

Status:  OK

CheckDir: tRanslatome.Rcheck

Warnings: 0

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### Running command:
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###   /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_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/tRanslatome.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.22.0’
* 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 : : 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
GOEnrichment 24.470  0.568  25.046
GOComparison 13.972  1.621  15.629
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/tRanslatome.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL tRanslatome
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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)

name	user	system	elapsed
CVplot	0.119	0.017	0.136
DEGs	0.002	0.001	0.003
DEGs.table	0.291	0.266	0.559
EnrichedSets	0.002	0.001	0.003
FC.threshold	0.068	0.022	0.090
GOComparison	13.972	1.621	15.629
GOEnrichment	24.470	0.568	25.046
GOsets	0.001	0.000	0.001
GOsims	0.001	0.000	0.001
Heatmap	0.104	0.016	0.137
Histogram	0.077	0.020	0.097
IdentityPlot	0.070	0.018	0.087
MAplot	0.078	0.018	0.096
Radar	0.087	0.019	0.107
RegulatoryEnrichment	3.445	0.093	3.539
SDplot	0.082	0.016	0.098
Scatterplot	0.088	0.017	0.105
SimilarityPlot	0.061	0.013	0.073
TranslatomeDataset	0.002	0.001	0.003
average.similarity.scores	0.055	0.013	0.069
computeDEGs	0.702	0.020	0.723
enriched.table	0.065	0.015	0.080
getConditionA	0.054	0.014	0.068
getConditionB	0.049	0.011	0.060
getConditionC	0.051	0.009	0.061
getConditionD	0.050	0.009	0.060
getConditionLabels	0.048	0.011	0.060
getDEGs	0.050	0.012	0.063
getDEGsMethod	0.050	0.011	0.062
getDataType	0.050	0.011	0.061
getExprMatrix	0.120	0.086	0.207
getLevelLabels	0.050	0.012	0.061
identity.matrix	0.052	0.012	0.065
label.condition	0.049	0.012	0.062
label.level.DEGs	0.053	0.012	0.065
label.level.enriched	0.049	0.011	0.059
newTranslatomeDataset	0.075	0.015	0.090
significance.threshold	0.057	0.014	0.072
similarity.matrix	0.074	0.018	0.092
tRanslatomeSampleData	0.072	0.017	0.088