SeqGSEA 1.2.1
Xi Wang
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/SeqGSEA | | Last Changed Rev: 86303 / Revision: 88450 | | Last Changed Date: 2014-02-10 15:33:01 -0800 (Mon, 10 Feb 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/SeqGSEA.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SeqGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqGSEA’ version ‘1.2.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘SeqGSEA’ can be installed ... [11s/11s] 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 dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘estiExonProbVar’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DENBStatPermut4GSEA: no visible binding for global variable ‘i’
DSpermute4GSEA : <anonymous>: no visible binding for global variable
‘i’
calES.perm: no visible binding for global variable ‘i’
calES.perm: no visible binding for global variable ‘j’
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
‘SeqGSEA.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [257s/282s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
runSeqGSEA 30.878 0.068 38.665
DSresultExonTable 21.293 0.012 21.358
normFactor 20.986 0.016 21.131
scoreNormalization 20.925 0.024 20.990
DSresultGeneTable 20.773 0.008 20.856
DSpermutePval 20.722 0.036 20.788
topDSExons 20.581 0.000 20.620
topDSGenes 20.229 0.012 20.274
DSpermute4GSEA 19.181 0.016 19.231
genpermuteMat 18.689 0.236 18.974
loadGenesets 2.112 0.020 7.286
convertEnsembl2Symbol 0.248 0.016 6.639
convertSymbol2Ensembl 0.232 0.000 5.958
* 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
NOTE: There were 3 notes.
See
‘/home/biocbuild/bbs-2.13-bioc/meat/SeqGSEA.Rcheck/00check.log’
for details.
* installing *source* package ‘SeqGSEA’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘DESeq::plotDispEsts’ when loading ‘SeqGSEA’
Warning: replacing previous import by ‘DESeq::plotMA’ when loading ‘SeqGSEA’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘DESeq::plotDispEsts’ when loading ‘SeqGSEA’
Warning: replacing previous import by ‘DESeq::plotMA’ when loading ‘SeqGSEA’
* DONE (SeqGSEA)