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BioC 2.12: CHECK report for eisa on george2

This page was generated on 2013-10-09 09:37:36 -0700 (Wed, 09 Oct 2013).

Package 204/671HostnameOS / ArchBUILDCHECKBUILD BIN
eisa 1.12.2
Gabor Csardi
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/eisa
Last Changed Rev: 81017 / Revision: 81334
Last Changed Date: 2013-10-01 13:27:00 -0700 (Tue, 01 Oct 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: eisa
Version: 1.12.2
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings eisa_1.12.2.tar.gz
StartedAt: 2013-10-09 01:33:22 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 01:41:41 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 499.3 seconds
RetCode: 0
Status:  OK 
CheckDir: eisa.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/eisa.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘eisa/DESCRIPTION’ ... OK
* this is package ‘eisa’ version ‘1.12.2’
* 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 ‘eisa’ can be installed ... [28s/28s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [235s/238s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
ISA                    62.147  0.232  63.037
ISA.html               27.986  0.648  29.057
ISA.sweep              20.713  0.104  20.906
ISA.GO                 13.613  0.424  14.144
ISA.iterate            12.585  0.212  13.211
ISA.unique             10.049  0.176  10.230
gograph                 8.716  0.152   8.959
ISA.normalize           8.445  0.180   8.630
ListHyperGResult-class  8.340  0.136   8.479
ListHyperGParams-class  7.449  0.108   7.560
ISAExpressionSet        6.812  0.232   7.047
ISA.KEGG                5.121  0.068   5.310
eisa.biclust            4.909  0.092   5.178
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

eisa.Rcheck/00install.out:

* installing *source* package ‘eisa’ ...
** R
** data
** inst
** preparing package for lazy loading
in method for ‘coerce’ with signature ‘"Biclust","ISAModules"’: no definition for class “Biclust”
in method for ‘coerce’ with signature ‘"ISAModules","Biclust"’: no definition for class “Biclust”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (eisa)

eisa.Rcheck/eisa-Ex.timings:

nameusersystemelapsed
ALLModules0.0320.0120.041
ISA.CHR2.7840.0643.055
ISA.GO13.613 0.42414.144
ISA.KEGG5.1210.0685.310
ISA62.147 0.23263.037
ISA.html27.986 0.64829.057
ISA.iterate12.585 0.21213.211
ISA.miRNA1.6120.0841.823
ISA.normalize8.4450.1808.630
ISA.sweep20.713 0.10420.906
ISA.unique10.049 0.17610.230
ISA2heatmap1.2200.0601.277
ISAExpressionSet6.8120.2327.047
ISAModules-class0.0400.0000.042
ListHyperGParams-class7.4490.1087.560
ListHyperGResult-class8.3400.1368.479
cond.plot2.7360.0562.790
eisa.biclust4.9090.0925.178
enrichment0.9840.0161.009
exp.plot2.9400.0603.005
gograph8.7160.1528.959
mnplot3.0370.0323.080
overlap1.1200.8082.034
profilePlot1.2240.0241.262
robustness3.3240.1083.443