BioC 3.3: CHECK report for tRanslatome on morelia

Package: tRanslatome

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings tRanslatome_1.9.0.tar.gz

StartedAt: 2015-10-22 12:11:36 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 12:14:23 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 167.1 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 tRanslatome_1.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/tRanslatome.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.9.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘tRanslatome’ can be installed ... [12s/13s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
methodLimma: no visible global function definition for ‘lmFit’
GOEnrichment,DEGs: no visible global function definition for ‘toTable’
Undefined global functions or variables:
  lmFit toTable
* 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 ... [30s/30s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
GOEnrichment 18.007  0.145  18.318
* 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-3.3-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	0.062	0.009	0.070
DEGs	0.002	0.000	0.002
DEGs.table	0.168	0.089	0.258
EnrichedSets	0.002	0.000	0.002
FC.threshold	0.047	0.008	0.055
GOComparison	1.343	0.025	1.422
GOEnrichment	18.007	0.145	18.318
GOsets	0.001	0.000	0.001
GOsims	0.001	0.000	0.001
Heatmap	0.086	0.005	0.092
Histogram	0.050	0.003	0.053
IdentityPlot	0.049	0.003	0.052
MAplot	0.053	0.003	0.055
Radar	0.056	0.004	0.061
RegulatoryEnrichment	1.914	0.018	1.933
SDplot	0.053	0.003	0.056
Scatterplot	0.056	0.003	0.059
SimilarityPlot	0.048	0.003	0.051
TranslatomeDataset	0.001	0.000	0.001
average.similarity.scores	0.047	0.003	0.049
computeDEGs	0.351	0.014	0.365
enriched.table	0.050	0.003	0.053
getConditionA	0.049	0.003	0.053
getConditionB	0.054	0.004	0.059
getConditionC	0.053	0.003	0.056
getConditionD	0.046	0.002	0.050
getConditionLabels	0.046	0.003	0.049
getDEGs	0.050	0.003	0.053
getDEGsMethod	0.049	0.003	0.052
getDataType	0.049	0.003	0.052
getExprMatrix	0.075	0.027	0.102
getLevelLabels	0.047	0.002	0.049
identity.matrix	0.047	0.003	0.049
label.condition	0.049	0.003	0.053
label.level.DEGs	0.050	0.003	0.054
label.level.enriched	0.048	0.003	0.052
newTranslatomeDataset	0.048	0.003	0.051
significance.threshold	0.047	0.003	0.049
similarity.matrix	0.049	0.003	0.053
tRanslatomeSampleData	0.047	0.004	0.050