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BioC 3.5: CHECK report for MIGSA on veracruz2

This page was generated on 2017-08-16 13:35:31 -0400 (Wed, 16 Aug 2017).

Package 817/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MIGSA 1.0.1
Juan C. Rodriguez
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/MIGSA
Last Changed Rev: 130633 / Revision: 131943
Last Changed Date: 2017-06-23 10:16:08 -0400 (Fri, 23 Jun 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
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

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: 2017-08-16 05:22:47 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 05:27:20 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 272.1 seconds
RetCode: 0
Status:  OK 
CheckDir: MIGSA.Rcheck
Warnings: 0

Command output

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


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MIGSA.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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  8.033  0.235   8.499
Genesets-enrichr 4.216  0.060   6.502
* 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-class0.0090.0010.009
FitOptions-class0.0090.0000.009
GSEAparams-class0.0020.0000.002
Genesets-as.Genesets0.0070.0000.007
Genesets-enrichr4.2160.0606.502
Genesets-geneSetsFromFile0.0200.0010.021
Genesets-loadGo8.0330.2358.499
IGSAinput-class0.6630.0060.696
IGSAinput-getDEGenes0.0570.0010.058
IGSAinput-getterSetters0.0180.0010.025
MIGSA0.2300.0010.234
MIGSAmGSZ0.0080.0000.008
MIGSAres-GoAnalysis0.3890.0120.417
MIGSAres-common0.5910.0450.528
MIGSAres-genesManipulation1.0680.0690.816
MIGSAres-getAdditionalInfo0.0250.0080.030
MIGSAres-plots4.5300.1254.410
MIGSAres-setEnrCutoff0.0430.0150.060
SEAparams-class0.0040.0000.004
summaryFunctions0.9320.0130.977