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BioC 3.5: CHECK report for MIGSA on oaxaca

This page was generated on 2017-03-04 16:54:01 -0500 (Sat, 04 Mar 2017).

Package 788/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MIGSA 0.99.907
Juan C. Rodriguez
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MIGSA
Last Changed Rev: 127042 / Revision: 127142
Last Changed Date: 2017-03-01 02:58:07 -0500 (Wed, 01 Mar 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: MIGSA
Version: 0.99.907
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MIGSA_0.99.907.tar.gz
StartedAt: 2017-03-04 05:49:20 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 05:53:52 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 271.9 seconds
RetCode: 0
Status:  OK 
CheckDir: MIGSA.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MIGSA_0.99.907.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MIGSA.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MIGSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MIGSA’ version ‘0.99.907’
* 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 ‘MIGSA’ can be installed ... 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 ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
Genesets-loadGo  13.680  0.679  14.366
Genesets-enrichr  4.324  0.058   7.108
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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

MIGSA.Rcheck/00install.out:

* installing *source* package ‘MIGSA’ ...
** 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 (MIGSA)

MIGSA.Rcheck/MIGSA-Ex.timings:

nameusersystemelapsed
ExprData-class0.0080.0010.008
FitOptions-class0.0070.0000.009
GSEAparams-class0.0010.0000.002
Genesets-as.Genesets0.0060.0000.006
Genesets-enrichr4.3240.0587.108
Genesets-geneSetsFromFile0.0160.0000.018
Genesets-loadGo13.680 0.67914.366
IGSAinput-class0.6850.0080.693
IGSAinput-getDEGenes0.0900.0020.093
IGSAinput-getterSetters0.0200.0010.021
MIGSA0.2850.0020.287
MIGSAmGSZ0.0100.0020.011
MIGSAres-GoAnalysis0.4290.0130.442
MIGSAres-common0.4710.0130.485
MIGSAres-genesManipulation0.7330.0100.743
MIGSAres-getAdditionalInfo0.0270.0050.033
MIGSAres-plots4.5910.0414.665
MIGSAres-setEnrCutoff0.0310.0040.036
SEAparams-class0.0210.0000.021
summaryFunctions0.7830.0060.790