BioC 3.1: CHECK report for tRanslatome on morelia

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 07:01:45 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 07:04:59 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 194.0 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 (2015-08-14)
* 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 ‘1.6.0’
* 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 ... [15s/16s] 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 ... [34s/34s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
GOEnrichment 18.699  0.808  19.518
* 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	0.074	0.006	0.080
DEGs	0.003	0.000	0.003
DEGs.table	0.146	0.097	0.242
EnrichedSets	0.002	0.001	0.003
FC.threshold	0.055	0.005	0.059
GOComparison	1.122	0.070	1.253
GOEnrichment	18.699	0.808	19.518
GOsets	0.001	0.000	0.002
GOsims	0.002	0.000	0.003
Heatmap	0.098	0.009	0.108
Histogram	0.051	0.016	0.068
IdentityPlot	0.053	0.025	0.078
MAplot	0.066	0.018	0.083
Radar	0.068	0.020	0.089
RegulatoryEnrichment	2.573	0.133	2.707
SDplot	0.054	0.007	0.060
Scatterplot	0.089	0.011	0.100
SimilarityPlot	0.049	0.007	0.055
TranslatomeDataset	0.001	0.000	0.001
average.similarity.scores	0.051	0.007	0.058
computeDEGs	0.529	0.084	0.613
enriched.table	0.057	0.010	0.068
getConditionA	0.045	0.006	0.052
getConditionB	0.046	0.006	0.052
getConditionC	0.043	0.006	0.049
getConditionD	0.054	0.008	0.061
getConditionLabels	0.047	0.008	0.054
getDEGs	0.058	0.009	0.068
getDEGsMethod	0.054	0.008	0.061
getDataType	0.067	0.008	0.075
getExprMatrix	0.100	0.079	0.179
getLevelLabels	0.057	0.023	0.081
identity.matrix	0.053	0.024	0.078
label.condition	0.059	0.031	0.090
label.level.DEGs	0.053	0.026	0.080
label.level.enriched	0.057	0.010	0.067
newTranslatomeDataset	0.050	0.007	0.057
significance.threshold	0.053	0.013	0.066
similarity.matrix	0.053	0.016	0.069
tRanslatomeSampleData	0.054	0.012	0.066