SeqGSEA 1.4.2
Xi Wang
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/SeqGSEA | | Last Changed Rev: 93946 / Revision: 95116 | | Last Changed Date: 2014-09-09 13:40:29 -0700 (Tue, 09 Sep 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ OK ] | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SeqGSEA_1.4.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/SeqGSEA.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.4.2’
* 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 ... [23s/25s] 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
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
calES.perm: no visible binding for global variable ‘i’
calES.perm: no visible binding for global variable ‘j’
DENBStatPermut4GSEA: no visible binding for global variable ‘i’
DSpermute4GSEA : <anonymous>: no visible binding for global variable
‘i’
* 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 ... [287s/334s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
runSeqGSEA 33.216 0.296 44.691
topDSExons 20.907 0.074 21.889
scoreNormalization 20.687 0.074 21.217
normFactor 20.300 0.092 21.195
DSresultExonTable 20.248 0.111 21.994
DSpermutePval 20.194 0.094 20.987
topDSGenes 20.145 0.070 21.060
DSresultGeneTable 19.952 0.087 21.099
DSpermute4GSEA 18.436 0.079 18.896
genpermuteMat 18.345 0.069 20.068
plotES 5.609 0.028 5.947
writeSigGeneSet 5.472 0.020 5.656
plotSigGeneSet 5.413 0.018 5.593
plotSig 5.236 0.021 5.481
topGeneSets 5.222 0.019 5.509
calES.perm 5.148 0.015 5.315
GSEnrichAnalyze 5.005 0.021 5.521
loadGenesets 2.264 0.031 5.510
convertEnsembl2Symbol 0.250 0.016 17.743
* 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 2 notes.
See
‘/Users/biocbuild/bbs-2.14-bioc/meat/SeqGSEA.Rcheck/00check.log’
for details.