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BioC 3.2: CHECK report for rgsepd on oaxaca

This page was generated on 2016-04-23 10:28:45 -0700 (Sat, 23 Apr 2016).

Package 879/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rgsepd 1.2.0
Karl Stamm
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/rgsepd
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  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: rgsepd
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rgsepd_1.2.0.tar.gz
StartedAt: 2016-04-23 03:48:45 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 04:01:15 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 749.9 seconds
RetCode: 0
Status:  OK 
CheckDir: rgsepd.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rgsepd_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/rgsepd.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rgsepd/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rgsepd’ version ‘1.2.0’
* 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 ‘rgsepd’ can be installed ... [36s/48s] 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 ... [236s/312s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
GSEPD_DEGHeatmap 181.735 12.155 263.961
* 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

rgsepd.Rcheck/00install.out:

* installing *source* package ‘rgsepd’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
* DONE (rgsepd)

rgsepd.Rcheck/rgsepd-Ex.timings:

nameusersystemelapsed
DisplayName0.0080.0000.008
GSEPD_ChangeConditions0.6770.0190.697
GSEPD_ChangeOutput0.7640.0130.777
GSEPD_DEGHeatmap181.735 12.155263.961
GSEPD_Export_DESeq0.7860.0190.805
GSEPD_Heatmap3.5680.0373.632
GSEPD_INIT0.6450.0160.662
GSEPD_PCA_Plot3.2130.0343.250
GSEPD_PCA_Spec3.2310.0243.258
GSEPD_Process0.6060.0160.623
GSEPD_ProcessAll0.5490.0150.563
GSEPD_PullDEG2.8400.0372.934
IlluminaBodymap0.3970.0110.408
IlluminaBodymapMeta0.0130.0010.015
Name_to_RefSeq0.0010.0000.001
rgsepd-package0.5040.0160.520