BioC 3.2: CHECK report for tRanslatome on linux1.bioconductor.org

Package: tRanslatome

Version: 1.8.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings tRanslatome_1.8.0.tar.gz

StartedAt: 2015-10-27 08:50:19 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:53:03 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 163.8 seconds

RetCode: 0

Status:  OK

CheckDir: tRanslatome.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings tRanslatome_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-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 ‘1.8.0’
* 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 ... [14s/14s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [30s/30s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
GOEnrichment 16.454  0.116  16.577
* 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-3.2-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	0.071	0.000	0.070
DEGs	0.001	0.000	0.002
DEGs.table	0.070	0.048	0.120
EnrichedSets	0.001	0.000	0.001
FC.threshold	0.048	0.000	0.048
GOComparison	1.385	0.005	1.401
GOEnrichment	16.454	0.116	16.577
GOsets	0.001	0.000	0.001
GOsims	0.001	0.000	0.002
Heatmap	0.107	0.004	0.111
Histogram	0.087	0.000	0.088
IdentityPlot	0.067	0.000	0.067
MAplot	0.083	0.000	0.083
Radar	0.088	0.000	0.088
RegulatoryEnrichment	2.706	0.011	2.726
SDplot	0.077	0.000	0.077
Scatterplot	0.059	0.000	0.059
SimilarityPlot	0.050	0.000	0.049
TranslatomeDataset	0.001	0.000	0.001
average.similarity.scores	0.044	0.004	0.048
computeDEGs	0.467	0.000	0.468
enriched.table	0.071	0.004	0.075
getConditionA	0.058	0.004	0.061
getConditionB	0.049	0.000	0.049
getConditionC	0.041	0.008	0.050
getConditionD	0.049	0.000	0.049
getConditionLabels	0.044	0.004	0.049
getDEGs	0.05	0.00	0.05
getDEGsMethod	0.049	0.000	0.049
getDataType	0.045	0.004	0.050
getExprMatrix	0.060	0.024	0.084
getLevelLabels	0.057	0.000	0.057
identity.matrix	0.048	0.000	0.049
label.condition	0.048	0.000	0.048
label.level.DEGs	0.046	0.000	0.050
label.level.enriched	0.049	0.000	0.049
newTranslatomeDataset	0.046	0.004	0.050
significance.threshold	0.048	0.000	0.048
similarity.matrix	0.047	0.004	0.051
tRanslatomeSampleData	0.049	0.000	0.049