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BioC 2.14: CHECK report for AffyExpress on morelia

This page was generated on 2014-10-08 09:03:18 -0700 (Wed, 08 Oct 2014).

Package 19/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AffyExpress 1.30.0
Xuejun Arthur Li
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/AffyExpress
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: AffyExpress
Version: 1.30.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AffyExpress_1.30.0.tar.gz
StartedAt: 2014-10-07 21:03:24 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 21:04:40 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 76.3 seconds
RetCode: 0
Status:  OK 
CheckDir: AffyExpress.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AffyExpress_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/AffyExpress.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AffyExpress/DESCRIPTION’ ... OK
* this is package ‘AffyExpress’ version ‘1.30.0’
* 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 ... [4s/4s] 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [20s/20s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
AffyInteraction 5.121  0.092   5.216
* 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 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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
** testing if installed package can be loaded
* DONE (AffyExpress)

AffyExpress.Rcheck/AffyExpress-Ex.timings:

nameusersystemelapsed
AffyInteraction5.1210.0925.216
AffyQA0.0010.0000.001
AffyRegress1.6410.0231.665
Filter2.1160.0312.149
import.data0.0010.0000.000
interaction.result2html1.8590.0241.894
make.contrast0.0150.0000.015
make.design0.0090.0000.009
post.interaction1.4830.0131.496
pre.process1.4020.0131.415
regress1.4030.0111.415
result2html1.5510.0181.570
select.sig.gene1.1750.0111.187