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Package 18/631HostnameOS / ArchBUILDCHECKBUILD BIN
AffyExpress 1.25.0
Xuejun Arthur Li
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AffyExpress
Last Changed Rev: 70052 / Revision: 72575
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: AffyExpress
Version: 1.25.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings AffyExpress_1.25.0.tar.gz
StartedAt: 2013-01-16 00:20:19 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 00:21:46 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 86.8 seconds
RetCode: 0
Status:  OK 
CheckDir: AffyExpress.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/AffyExpress.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AffyExpress/DESCRIPTION’ ... OK
* this is package ‘AffyExpress’ version ‘1.25.0’
* 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 ‘AffyExpress’ can be installed ... 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 ... NOTE
AffyQA: warning in png(file = figure1): partial argument match of
  'file' to 'filename'
AffyQA: warning in png(file = figure1, height = 960): partial argument
  match of 'file' to 'filename'
AffyQA: warning in matrix(c(1, 3, 5, 7, 2, 4, 6, 7), nr = 4, ncol = 2):
  partial argument match of 'nr' to 'nrow'
AffyQA: warning in png(file = figure2): partial argument match of
  'file' to 'filename'
AffyQA: warning in plotAffyRNAdeg(deg, col = dum[1:size]): partial
  argument match of 'col' to 'cols'
AffyQA: warning in png(file = figure3): partial argument match of
  'file' to 'filename'
AffyQA: warning in png(file = figure4): partial argument match of
  'file' to 'filename'
AffyQA: warning in png(file = figure5): partial argument match of
  'file' to 'filename'
* 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 ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
AffyInteraction 6.864    0.1   6.993
* 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

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/AffyExpress.Rcheck/00check.log’
for details.

AffyExpress.Rcheck/00install.out:

* installing *source* package ‘AffyExpress’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘AffyExpress.Rnw’ 
** testing if installed package can be loaded

* DONE (AffyExpress)

AffyExpress.Rcheck/AffyExpress-Ex.timings:

nameusersystemelapsed
AffyInteraction6.8640.1006.993
AffyQA0.0120.0040.013
AffyRegress2.3040.0242.333
Filter2.6720.0402.716
import.data0.0160.0000.014
interaction.result2html2.6050.0242.632
make.contrast0.0360.0000.036
make.design0.0280.0000.028
post.interaction2.1480.0362.190
pre.process2.0040.0202.022
regress2.0640.0082.078
result2html2.1840.0322.218
select.sig.gene2.4480.0242.474