BioC 2.14: CHECK report for tRanslatome on petty

Package: tRanslatome

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch tRanslatome_1.2.0.tar.gz

StartedAt: 2014-10-08 00:28:23 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:36:40 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 496.2 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 --no-vignettes --timings --no-multiarch tRanslatome_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/tRanslatome.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.2.0’
* 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 ... [41s/43s] 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:
  ‘anota’ ‘DESeq’ ‘edgeR’ ‘GOSemSim’ ‘gplots’ ‘Heatplus’ ‘limma’
  ‘methods’ ‘org.Hs.eg.db’ ‘plotrix’ ‘RankProd’ ‘samr’ ‘sigPathway’
  ‘topGO’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... [88s/88s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
GOEnrichment         53.193   2.67  55.576
RegulatoryEnrichment  5.884   0.20   6.062
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/tRanslatome.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
CVplot	0.131	0.016	0.148
DEGs	0.003	0.001	0.004
DEGs.table	0.281	0.165	0.447
EnrichedSets	0.003	0.000	0.003
FC.threshold	0.076	0.010	0.086
GOComparison	2.346	0.107	2.511
GOEnrichment	53.193	2.670	55.576
GOsets	0.002	0.000	0.003
GOsims	0.002	0.000	0.003
Heatmap	0.162	0.014	0.175
Histogram	0.088	0.009	0.097
IdentityPlot	0.082	0.007	0.088
MAplot	0.101	0.009	0.111
Radar	0.128	0.010	0.141
RegulatoryEnrichment	5.884	0.200	6.062
SDplot	0.101	0.009	0.111
Scatterplot	0.112	0.011	0.123
SimilarityPlot	0.082	0.008	0.090
TranslatomeDataset	0.003	0.000	0.004
average.similarity.scores	0.085	0.007	0.092
computeDEGs	0.998	0.062	1.050
enriched.table	0.093	0.010	0.103
getConditionA	0.076	0.007	0.083
getConditionB	0.085	0.008	0.092
getConditionC	0.080	0.009	0.088
getConditionD	0.083	0.008	0.091
getConditionLabels	0.080	0.008	0.088
getDEGs	0.082	0.008	0.091
getDEGsMethod	0.084	0.009	0.092
getDataType	0.082	0.009	0.091
getExprMatrix	0.168	0.078	0.245
getLevelLabels	0.086	0.009	0.096
identity.matrix	0.080	0.009	0.089
label.condition	0.080	0.008	0.088
label.level.DEGs	0.081	0.009	0.092
label.level.enriched	0.083	0.009	0.091
newTranslatomeDataset	0.087	0.008	0.095
significance.threshold	0.082	0.008	0.090
similarity.matrix	0.079	0.008	0.088
tRanslatomeSampleData	0.081	0.008	0.088