BioC 3.2: CHECK report for tRanslatome on oaxaca

Package: tRanslatome

Version: 1.7.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings tRanslatome_1.7.2.tar.gz

StartedAt: 2015-08-24 04:29:26 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 04:33:08 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 221.4 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_1.7.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-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 ‘1.7.2’
* 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 ... [18s/18s] 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 ... [39s/39s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
GOEnrichment 22.296   0.16  22.538
* 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
Warning: replacing previous import by ‘graph::.__C__dist’ when loading ‘topGO’

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘graph::.__C__dist’ when loading ‘topGO’

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

name	user	system	elapsed
CVplot	0.098	0.008	0.107
DEGs	0.002	0.000	0.003
DEGs.table	0.17	0.09	0.26
EnrichedSets	0.002	0.000	0.002
FC.threshold	0.064	0.005	0.069
GOComparison	1.362	0.033	1.457
GOEnrichment	22.296	0.160	22.538
GOsets	0.001	0.000	0.002
GOsims	0.001	0.000	0.001
Heatmap	0.103	0.012	0.115
Histogram	0.069	0.010	0.083
IdentityPlot	0.066	0.012	0.079
MAplot	0.101	0.011	0.112
Radar	0.082	0.011	0.095
RegulatoryEnrichment	3.411	0.044	3.474
SDplot	0.076	0.011	0.088
Scatterplot	0.079	0.011	0.091
SimilarityPlot	0.069	0.011	0.080
TranslatomeDataset	0.002	0.000	0.003
average.similarity.scores	0.064	0.011	0.075
computeDEGs	0.599	0.012	0.612
enriched.table	0.069	0.011	0.080
getConditionA	0.063	0.010	0.073
getConditionB	0.061	0.011	0.072
getConditionC	0.065	0.011	0.076
getConditionD	0.065	0.010	0.075
getConditionLabels	0.065	0.011	0.076
getDEGs	0.065	0.011	0.077
getDEGsMethod	0.065	0.011	0.076
getDataType	0.064	0.011	0.076
getExprMatrix	0.111	0.050	0.161
getLevelLabels	0.064	0.011	0.074
identity.matrix	0.065	0.011	0.076
label.condition	0.063	0.010	0.073
label.level.DEGs	0.065	0.010	0.076
label.level.enriched	0.065	0.011	0.077
newTranslatomeDataset	0.067	0.010	0.077
significance.threshold	0.064	0.011	0.075
similarity.matrix	0.065	0.011	0.076
tRanslatomeSampleData	0.065	0.010	0.074