tRanslatome 1.4.0
Toma Tebaldi , Erik Dassi
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/tRanslatome | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ OK ] | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch tRanslatome_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/tRanslatome.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.4.0’
* 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’
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 ... [31s/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 loading without being on the library search path ... 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
comparisonBetweenTwoLists: no visible global function definition for
‘goSim’
createspecifictable: no visible global function definition for
‘annFUN.org’
createspecifictable: no visible global function definition for
‘inverseList’
createspecifictable: no visible binding for global variable
‘annFUN.gene2GO’
createspecifictable: no visible global function definition for
‘runTest’
createspecifictable: no visible global function definition for ‘score’
createspecifictable: no visible global function definition for
‘GenTable’
methodANOTA: no visible global function definition for ‘anotaPerformQc’
methodANOTA: no visible global function definition for
‘anotaGetSigGenes’
methodDESeq: no visible global function definition for
‘newCountDataSet’
methodDESeq: no visible global function definition for
‘estimateSizeFactors’
methodDESeq: no visible global function definition for
‘estimateDispersions’
methodDESeq: no visible global function definition for ‘nbinomTest’
methodEdgeR: no visible global function definition for ‘DGEList’
methodEdgeR: no visible global function definition for
‘calcNormFactors’
methodEdgeR: no visible global function definition for
‘estimateCommonDisp’
methodEdgeR: no visible global function definition for
‘estimateTagwiseDisp’
methodEdgeR: no visible global function definition for ‘exactTest’
methodLimma: no visible global function definition for ‘lmFit’
methodLimma: no visible global function definition for ‘makeContrasts’
methodLimma: no visible global function definition for ‘contrasts.fit’
methodLimma: no visible global function definition for ‘eBayes’
methodSAM: no visible global function definition for ‘samr’
methodSAM: no visible global function definition for
‘samr.pvalues.from.perms’
methodTTest: no visible global function definition for ‘calcTStatFast’
newTranslatomeDataset: no visible global function definition for
‘exprs’
GOEnrichment,DEGs: no visible global function definition for ‘toTable’
GOEnrichment,DEGs: no visible binding for global variable
‘org.Hs.egSYMBOL’
* 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 ... [61s/61s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
GOEnrichment 37.37 0.248 37.633
* 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
NOTE: There were 3 notes.
See
‘/Users/biocbuild/bbs-3.0-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)