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BioC 2.13: CHECK report for AffyExpress on moscato1

This page was generated on 2014-04-05 09:49:34 -0700 (Sat, 05 Apr 2014).

Package 18/750HostnameOS / ArchBUILDCHECKBUILD BIN
AffyExpress 1.28.0
Xuejun Arthur Li
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/AffyExpress
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: AffyExpress
Version: 1.28.0
Command: rm -rf AffyExpress.buildbin-libdir && mkdir AffyExpress.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AffyExpress.buildbin-libdir AffyExpress_1.28.0.tar.gz >AffyExpress-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=AffyExpress.buildbin-libdir --install="check:AffyExpress-install.out" --force-multiarch --no-vignettes --timings AffyExpress_1.28.0.tar.gz && mv AffyExpress.buildbin-libdir/* AffyExpress.Rcheck/ && rmdir AffyExpress.buildbin-libdir
StartedAt: 2014-04-05 02:01:03 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 02:04:12 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 188.4 seconds
RetCode: 0
Status:  OK  
CheckDir: AffyExpress.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/AffyExpress.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AffyExpress/DESCRIPTION' ... OK
* this is package 'AffyExpress' version '1.28.0'
* 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 whether package 'AffyExpress' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  'affy' 'limma'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'AffyExpress.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [53s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
AffyInteraction         9.84   0.11    9.97
Filter                  5.58   0.11    5.69
result2html             5.07   0.10    5.17
regress                 5.15   0.01    5.17
interaction.result2html 4.93   0.07    5.01
** running examples for arch 'x64' ... [53s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
AffyInteraction         9.61   0.16   11.44
Filter                  5.10   0.04    5.14
interaction.result2html 4.62   0.02    5.58
* 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

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/AffyExpress.Rcheck/00check.log'
for details.

AffyExpress.Rcheck/00install.out:


install for i386

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

install for x64

* installing *source* package 'AffyExpress' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AffyExpress' as AffyExpress_1.28.0.zip
* DONE (AffyExpress)

AffyExpress.Rcheck/examples_i386/AffyExpress-Ex.timings:

nameusersystemelapsed
AffyInteraction9.840.119.97
AffyQA0.020.000.01
AffyRegress4.880.084.96
Filter5.580.115.69
import.data000
interaction.result2html4.930.075.01
make.contrast0.170.000.17
make.design0.020.000.02
post.interaction4.60.04.6
pre.process4.600.024.63
regress5.150.015.17
result2html5.070.105.17
select.sig.gene4.70.04.7

AffyExpress.Rcheck/examples_x64/AffyExpress-Ex.timings:

nameusersystemelapsed
AffyInteraction 9.61 0.1611.44
AffyQA0.000.010.01
AffyRegress4.670.044.70
Filter5.100.045.14
import.data000
interaction.result2html4.620.025.58
make.contrast0.020.000.02
make.design0.010.000.02
post.interaction4.420.024.43
pre.process4.330.014.36
regress4.250.024.25
result2html4.490.034.53
select.sig.gene4.270.014.29