BioC 3.1: CHECK report for tRanslatome on zin2

Package: tRanslatome

Version: 1.6.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings tRanslatome_1.6.0.tar.gz

StartedAt: 2015-10-09 06:07:24 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 06:10:01 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 156.3 seconds

RetCode: 0

Status:  OK

CheckDir: tRanslatome.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings tRanslatome_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/tRanslatome.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ... [13s/13s] 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 ... [28s/28s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
GOEnrichment 16.148  0.051  16.231
* 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
  ‘/home/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	0.066	0.000	0.065
DEGs	0.001	0.000	0.002
DEGs.table	0.105	0.048	0.152
EnrichedSets	0.001	0.000	0.001
FC.threshold	0.043	0.004	0.047
GOComparison	1.055	0.016	1.089
GOEnrichment	16.148	0.051	16.231
GOsets	0.001	0.000	0.001
GOsims	0.001	0.000	0.001
Heatmap	0.081	0.000	0.082
Histogram	0.054	0.000	0.053
IdentityPlot	0.049	0.000	0.050
MAplot	0.057	0.000	0.058
Radar	0.061	0.000	0.061
RegulatoryEnrichment	2.301	0.004	2.308
SDplot	0.055	0.004	0.059
Scatterplot	0.059	0.004	0.063
SimilarityPlot	0.051	0.000	0.051
TranslatomeDataset	0.001	0.000	0.001
average.similarity.scores	0.063	0.000	0.062
computeDEGs	0.478	0.000	0.477
enriched.table	0.054	0.004	0.058
getConditionA	0.054	0.000	0.055
getConditionB	0.054	0.000	0.054
getConditionC	0.054	0.000	0.054
getConditionD	0.054	0.000	0.055
getConditionLabels	0.054	0.000	0.055
getDEGs	0.055	0.000	0.055
getDEGsMethod	0.054	0.000	0.054
getDataType	0.067	0.000	0.066
getExprMatrix	0.091	0.020	0.113
getLevelLabels	0.050	0.004	0.055
identity.matrix	0.052	0.000	0.052
label.condition	0.048	0.000	0.048
label.level.DEGs	0.049	0.000	0.048
label.level.enriched	0.049	0.000	0.049
newTranslatomeDataset	0.05	0.00	0.05
significance.threshold	0.045	0.004	0.049
similarity.matrix	0.049	0.000	0.049
tRanslatomeSampleData	0.049	0.000	0.049