BioC 3.5: CHECK report for MIGSA on oaxaca

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

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### Running command:
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###   /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

* 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)

name	user	system	elapsed
ExprData-class	0.008	0.001	0.008
FitOptions-class	0.007	0.000	0.009
GSEAparams-class	0.001	0.000	0.002
Genesets-as.Genesets	0.006	0.000	0.006
Genesets-enrichr	4.324	0.058	7.108
Genesets-geneSetsFromFile	0.016	0.000	0.018
Genesets-loadGo	13.680	0.679	14.366
IGSAinput-class	0.685	0.008	0.693
IGSAinput-getDEGenes	0.090	0.002	0.093
IGSAinput-getterSetters	0.020	0.001	0.021
MIGSA	0.285	0.002	0.287
MIGSAmGSZ	0.010	0.002	0.011
MIGSAres-GoAnalysis	0.429	0.013	0.442
MIGSAres-common	0.471	0.013	0.485
MIGSAres-genesManipulation	0.733	0.010	0.743
MIGSAres-getAdditionalInfo	0.027	0.005	0.033
MIGSAres-plots	4.591	0.041	4.665
MIGSAres-setEnrCutoff	0.031	0.004	0.036
SEAparams-class	0.021	0.000	0.021
summaryFunctions	0.783	0.006	0.790