BioC 2.13: CHECK report for tRanslatome on perceval

Package: tRanslatome

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch tRanslatome_1.0.0.tar.gz

StartedAt: 2014-04-05 04:49:19 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:55:38 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 379.7 seconds

RetCode: 0

Status:  OK

CheckDir: tRanslatome.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/tRanslatome.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.0.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ... [33s/34s] 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 ... 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 ... [71s/75s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
GOEnrichment 42.393   2.56  45.771
* 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 was 1 note.
See
  ‘/Users/biocbuild/bbs-2.13-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	0.079	0.013	0.100
DEGs	0.021	0.002	0.024
DEGs.table	0.205	0.142	0.403
EnrichedSets	0.014	0.002	0.038
FC.threshold	0.056	0.009	0.065
GOComparison	1.646	0.122	1.904
GOEnrichment	42.393	2.560	45.771
GOsets	0.023	0.002	0.025
GOsims	0.026	0.003	0.028
Heatmap	0.135	0.017	0.152
Histogram	0.111	0.015	0.125
IdentityPlot	0.078	0.015	0.093
MAplot	0.086	0.014	0.100
Radar	0.109	0.016	0.125
RegulatoryEnrichment	2.128	0.124	2.235
SDplot	0.086	0.012	0.098
Scatterplot	0.122	0.022	0.145
SimilarityPlot	0.051	0.011	0.062
TranslatomeDataset	0.006	0.007	0.013
average.similarity.scores	0.049	0.015	0.065
computeDEGs	0.750	0.078	0.821
enriched.table	0.080	0.019	0.097
getConditionA	0.059	0.010	0.069
getConditionB	0.060	0.016	0.076
getConditionC	0.054	0.016	0.069
getConditionD	0.048	0.012	0.061
getConditionLabels	0.067	0.015	0.083
getDEGs	0.067	0.012	0.079
getDEGsMethod	0.049	0.011	0.061
getDataType	0.064	0.018	0.082
getExprMatrix	0.126	0.076	0.201
getLevelLabels	0.061	0.013	0.075
identity.matrix	0.062	0.015	0.076
label.condition	0.048	0.020	0.068
label.level.DEGs	0.050	0.017	0.068
label.level.enriched	0.049	0.014	0.063
newTranslatomeDataset	0.078	0.023	0.101
significance.threshold	0.061	0.015	0.075
similarity.matrix	0.061	0.014	0.074
tRanslatomeSampleData	0.064	0.010	0.075