BioC 3.2: CHECK report for tRanslatome on oaxaca

Package: tRanslatome

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings tRanslatome_1.8.0.tar.gz

StartedAt: 2016-04-23 05:04:57 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 05:08:54 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 237.1 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_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/tRanslatome.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.8.0’
* 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 ... [19s/20s] 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’
* 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 ... [40s/40s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
GOEnrichment 22.386  0.207  22.677
* 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-3.2-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	0.113	0.010	0.123
DEGs	0.002	0.000	0.003
DEGs.table	0.163	0.090	0.253
EnrichedSets	0.001	0.000	0.002
FC.threshold	0.064	0.006	0.070
GOComparison	1.331	0.027	1.419
GOEnrichment	22.386	0.207	22.677
GOsets	0.001	0.000	0.001
GOsims	0.001	0.000	0.001
Heatmap	0.102	0.006	0.109
Histogram	0.066	0.004	0.071
IdentityPlot	0.059	0.005	0.064
MAplot	0.072	0.007	0.078
Radar	0.077	0.004	0.082
RegulatoryEnrichment	3.417	0.056	3.475
SDplot	0.068	0.005	0.073
Scatterplot	0.067	0.004	0.075
SimilarityPlot	0.064	0.006	0.070
TranslatomeDataset	0.002	0.000	0.002
average.similarity.scores	0.061	0.005	0.065
computeDEGs	0.561	0.014	0.575
enriched.table	0.067	0.006	0.073
getConditionA	0.063	0.005	0.069
getConditionB	0.065	0.005	0.071
getConditionC	0.067	0.007	0.073
getConditionD	0.060	0.005	0.066
getConditionLabels	0.060	0.005	0.064
getDEGs	0.060	0.005	0.066
getDEGsMethod	0.063	0.005	0.068
getDataType	0.063	0.005	0.068
getExprMatrix	0.099	0.039	0.139
getLevelLabels	0.057	0.005	0.062
identity.matrix	0.061	0.005	0.066
label.condition	0.062	0.006	0.068
label.level.DEGs	0.066	0.006	0.071
label.level.enriched	0.062	0.006	0.067
newTranslatomeDataset	0.062	0.005	0.066
significance.threshold	0.060	0.004	0.064
similarity.matrix	0.059	0.005	0.063
tRanslatomeSampleData	0.057	0.005	0.063