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BioC 3.2: CHECK report for OGSA on zin1

This page was generated on 2015-08-24 10:50:42 -0700 (Mon, 24 Aug 2015).

Package 698/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OGSA 0.99.7
Michael F. Ochs
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OGSA
Last Changed Rev: 106497 / Revision: 107696
Last Changed Date: 2015-07-16 12:09:19 -0700 (Thu, 16 Jul 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / 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 UNNEEDED, same version exists in internal repository

Summary

Package: OGSA
Version: 0.99.7
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings OGSA_0.99.7.tar.gz
StartedAt: 2015-08-24 02:15:09 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 02:17:11 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 121.7 seconds
RetCode: 0
Status:  OK 
CheckDir: OGSA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings OGSA_0.99.7.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/OGSA.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OGSA/DESCRIPTION’ ... OK
* this is package ‘OGSA’ version ‘0.99.7’
* 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 ‘OGSA’ can be installed ... [2s/2s] 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 ... [93s/94s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
copaStat 73.674  0.423  74.305
* 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

OGSA.Rcheck/00install.out:

* installing *source* package ‘OGSA’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (OGSA)

OGSA.Rcheck/OGSA-Ex.timings:

nameusersystemelapsed
copaInt2.2470.0212.266
copaIntE2.4670.0042.469
copaStat73.674 0.42374.305
expressionSetDataSet0.0930.0000.093
expressionSetPheno0.0950.0000.095
outCallRank1.5210.0081.530
outCallRankE1.5760.0001.592
outCallTib2.1820.0002.186
outCallTibE2.2870.0002.287
outCount2.0920.0002.092
outMap2.1400.0042.151
outRank1.4900.0001.495
testGScogps0.0010.0000.001