BioC 3.1: CHECK report for tRanslatome on petty

Package: tRanslatome

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings tRanslatome_1.6.0.tar.gz

StartedAt: 2015-10-09 02:26:00 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 02:31:28 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 327.6 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_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/tRanslatome.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.6.0’
* 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 ... [25s/25s] 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 ... [68s/69s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
GOEnrichment 45.807  0.256  46.115
* 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-3.1-bioc/meat/tRanslatome.Rcheck/00check.log’
for details.

* installing *source* package ‘tRanslatome’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’

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

name	user	system	elapsed
CVplot	0.106	0.008	0.114
DEGs	0.003	0.000	0.003
DEGs.table	0.224	0.123	0.348
EnrichedSets	0.002	0.000	0.002
FC.threshold	0.077	0.006	0.083
GOComparison	1.834	0.044	1.989
GOEnrichment	45.807	0.256	46.115
GOsets	0.002	0.000	0.003
GOsims	0.002	0.000	0.002
Heatmap	0.141	0.011	0.153
Histogram	0.077	0.009	0.086
IdentityPlot	0.075	0.008	0.083
MAplot	0.136	0.009	0.146
Radar	0.102	0.009	0.113
RegulatoryEnrichment	4.344	0.053	4.398
SDplot	0.075	0.010	0.086
Scatterplot	0.099	0.012	0.166
SimilarityPlot	0.076	0.011	0.087
TranslatomeDataset	0.003	0.000	0.004
average.similarity.scores	0.095	0.011	0.107
computeDEGs	0.704	0.013	0.718
enriched.table	0.084	0.010	0.094
getConditionA	0.072	0.010	0.081
getConditionB	0.073	0.011	0.084
getConditionC	0.074	0.010	0.085
getConditionD	0.075	0.010	0.086
getConditionLabels	0.080	0.011	0.090
getDEGs	0.073	0.011	0.083
getDEGsMethod	0.080	0.011	0.091
getDataType	0.076	0.010	0.086
getExprMatrix	0.150	0.068	0.263
getLevelLabels	0.082	0.012	0.092
identity.matrix	0.081	0.010	0.091
label.condition	0.079	0.010	0.089
label.level.DEGs	0.068	0.010	0.077
label.level.enriched	0.065	0.009	0.074
newTranslatomeDataset	0.063	0.009	0.072
significance.threshold	0.076	0.010	0.085
similarity.matrix	0.079	0.011	0.091
tRanslatomeSampleData	0.077	0.012	0.089