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Package 152/516HostnameOS / ArchBUILDCHECKBUILD BIN
eisa 1.6.0
Gabor Csardi
Snapshot Date: 2012-01-08 18:22:44 -0800 (Sun, 08 Jan 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/eisa
Last Changed Rev: 59920 / Revision: 61898
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: eisa
Version: 1.6.0
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch eisa_1.6.0.tar.gz
StartedAt: 2012-01-09 02:56:13 -0800 (Mon, 09 Jan 2012)
EndedAt: 2012-01-09 03:00:51 -0800 (Mon, 09 Jan 2012)
EllapsedTime: 278.1 seconds
RetCode: 0
Status:  OK  
CheckDir: eisa.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/eisa.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'eisa/DESCRIPTION' ... OK
* this is package 'eisa' version '1.6.0'
* 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 whether package 'eisa' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 ... NOTE
annotate: no visible binding for global variable 'ALL'
* 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 ... NOTE
'library' or 'require' calls not declared from:
  'org.Hs.eg.db' 'targetscan.Hs.eg.db'
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
  'affy' 'targetscan.Hs.eg.db'
* 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
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "connection" in package 'graph' seems equivalent to one from package 'IRanges' and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "file" in package 'graph' seems equivalent to one from package 'IRanges' and is not turning on duplicate class definitions for this class
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 ...
*** tangling vignette sources ...
   'EISA_biclust.Rnw' 
   'EISA_tutorial.Rnw' 
** testing if installed package can be loaded

* DONE (eisa)

eisa.Rcheck/eisa-Ex.timings:

nameusersystemelapsed
ALLModules0.060.000.06
ISA.CHR1.360.041.57
ISA.GO 6.00 0.1115.17
ISA.KEGG2.120.012.25
ISA27.05 0.2527.67
ISA.html15.13 0.7517.59
ISA.iterate7.980.168.24
ISA.miRNA0.020.010.03
ISA.normalize5.810.145.95
ISA.sweep12.80 0.2513.07
ISA.unique6.920.117.03
ISA2heatmap2.040.052.09
ISAExpressionSet5.330.125.52
ISAModules-class0.020.000.01
ListHyperGParams-class3.90.14.0
ListHyperGResult-class4.740.114.84
cond.plot2.830.042.87
eisa.biclust5.170.085.25
enrichment0.470.020.49
exp.plot2.90.02.9
gograph5.220.115.36
mnplot2.830.062.89
overlap1.110.271.37
profilePlot2.050.032.08
robustness3.450.033.50