BioC 3.5: CHECK report for MIGSA on veracruz2

Package: MIGSA

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MIGSA_1.0.1.tar.gz

StartedAt: 2017-10-18 06:09:39 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 06:14:25 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 286.3 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_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MIGSA.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.0.1’
* 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 ‘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  7.796  0.235   8.247
Genesets-enrichr 4.627  0.080   6.519
* 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	0.009	0.001	0.009
FitOptions-class	0.008	0.000	0.008
GSEAparams-class	0.002	0.000	0.002
Genesets-as.Genesets	0.009	0.000	0.010
Genesets-enrichr	4.627	0.080	6.519
Genesets-geneSetsFromFile	0.022	0.001	0.023
Genesets-loadGo	7.796	0.235	8.247
IGSAinput-class	0.691	0.010	0.727
IGSAinput-getDEGenes	0.061	0.001	0.064
IGSAinput-getterSetters	0.020	0.001	0.022
MIGSA	0.265	0.003	0.277
MIGSAmGSZ	0.009	0.000	0.010
MIGSAres-GoAnalysis	0.406	0.014	0.432
MIGSAres-common	0.577	0.041	0.524
MIGSAres-genesManipulation	1.062	0.066	0.791
MIGSAres-getAdditionalInfo	0.031	0.006	0.034
MIGSAres-plots	4.670	0.134	4.557
MIGSAres-setEnrCutoff	0.035	0.005	0.040
SEAparams-class	0.003	0.000	0.004
summaryFunctions	0.884	0.011	0.914