BioC 3.2: CHECK report for mogsa on perceval

Package: mogsa

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mogsa_1.2.0.tar.gz

StartedAt: 2015-10-27 10:07:00 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 10:09:20 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 139.6 seconds

RetCode: 0

Status:  OK

CheckDir: mogsa.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mogsa_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/mogsa.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mogsa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mogsa’ version ‘1.2.0’
* 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 ‘mogsa’ 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 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 ... OK
* 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 ... [22s/22s] OK
* 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: OK

* installing *source* package ‘mogsa’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (mogsa)

name	user	system	elapsed
GIS	0.976	0.027	1.231
annotate.gs	0.406	0.011	0.418
bootMbpca	0.001	0.000	0.001
box.gs.feature	0.482	0.007	0.490
combine-methods	0.718	0.011	0.730
decompose.gs.group	0.394	0.008	0.453
decompose.gs.ind	0.179	0.005	0.185
distMoa	0.599	0.016	0.615
getmgsa	0.177	0.008	0.186
matpower	0.001	0.000	0.002
mbpca	4.336	0.138	4.476
mgsa-class	0.743	0.015	0.758
moGap	1.742	0.038	1.781
moa-class	0.122	0.005	0.128
moa	0.192	0.012	0.205
moa.sup-class	0.369	0.009	0.377
moaCoef	0.496	0.022	0.518
moaScore	0.489	0.018	0.508
mogsa-package	0.573	0.020	0.593
mogsa	0.564	0.011	0.575
pairwise.rv	0.024	0.001	0.024
plotGS	0.377	0.010	0.387
prepGraphite	0.179	0.013	0.238
prepMsigDB	0.004	0.000	0.004
prepSupMoa	1.730	0.048	1.777
softK	0.001	0.000	0.001
sup.moa	0.478	0.016	0.494
wsvd	0.002	0.000	0.002