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BioC 3.1: CHECK report for cogena on petty

This page was generated on 2015-10-09 09:37:32 -0700 (Fri, 09 Oct 2015).

Package 199/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cogena 1.0.0
Zhilong Jia
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/cogena
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cogena
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cogena_1.0.0.tar.gz
StartedAt: 2015-10-08 22:15:25 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 22:18:44 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 199.1 seconds
RetCode: 0
Status:  OK 
CheckDir: cogena.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cogena_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/cogena.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cogena/DESCRIPTION’ ... OK
* this is package ‘cogena’ version ‘1.0.0’
* package encoding: UTF-8
* 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 ‘cogena’ can be installed ... [4s/5s] 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 R/sysdata.rda ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [45s/140s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
hubgeneInCluster 3.708  0.305  10.549
heatmapPEI       3.720  0.270  10.845
heatmapCluster   3.585  0.253  10.536
geneExpInCluster 3.343  0.369  10.737
cogena           3.410  0.287  15.763
heatmapPEI2      3.344  0.220  10.752
optCluster       3.264  0.272  20.810
geneInCluster    3.221  0.277  10.142
corInCluster     3.091  0.277  13.460
enrichment       3.041  0.261  10.000
cogena_methods   3.034  0.266  10.037
* 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

cogena.Rcheck/00install.out:

* installing *source* package ‘cogena’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘summary’ from package ‘base’ in package ‘cogena’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cogena)

cogena.Rcheck/cogena-Ex.timings:

nameusersystemelapsed
cogena 3.410 0.28715.763
cogena_methods 3.034 0.26610.037
corInCluster 3.091 0.27713.460
enrichment 3.041 0.26110.000
gene2set0.1000.0070.381
geneExpInCluster 3.343 0.36910.737
geneInCluster 3.221 0.27710.142
gmt2list0.0660.0010.067
heatmapCluster 3.585 0.25310.536
heatmapPEI 3.720 0.27010.845
heatmapPEI2 3.344 0.22010.752
hubgeneInCluster 3.708 0.30510.549
optCluster 3.264 0.27220.810
sota3.5270.0644.049