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BioC 2.12: CHECK report for attract on moscato2

This page was generated on 2013-10-09 09:38:48 -0700 (Wed, 09 Oct 2013).

Package 53/671HostnameOS / ArchBUILDCHECKBUILD BIN
attract 1.12.0
Jessica Mar
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/attract
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ WARNINGS ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  WARNINGS  OK 

Summary

Package: attract
Version: 1.12.0
Command: rm -rf attract.buildbin-libdir && mkdir attract.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=attract.buildbin-libdir attract_1.12.0.tar.gz >attract-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=attract.buildbin-libdir --install="check:attract-install.out" --force-multiarch --no-vignettes --timings attract_1.12.0.tar.gz && mv attract.buildbin-libdir/* attract.Rcheck/ && rmdir attract.buildbin-libdir
StartedAt: 2013-10-09 01:02:55 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 01:08:24 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 328.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: attract.Rcheck
Warnings: 1

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/attract.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'attract/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'attract' version '1.12.0'
* 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 'attract' can be installed ... WARNING
Found the following significant warnings:
  Warning: package 'KEGG.db' was built under R version 3.1.0
  Warning: package 'KEGG.db' was built under R version 3.1.0
  Warning: package 'KEGG.db' was built under R version 3.1.0
See 'E:/biocbld/bbs-2.12-bioc/meat/attract.Rcheck/00install.out' for details.
* 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
* 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 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
plotsynexprs: warning in axis(1, at = tickMarks, lab = tickLabels):
  partial argument match of 'lab' to 'labels'
removeFlatGenes: warning in topTable(fit2, coef =
  (1:(length(my.contrasts))), adjust = "fdr", n = nrow(dat.fr)):
  partial argument match of 'n' to 'number'
removeFlatGenes: warning in topTable(fit2, coef =
  (1:(length(my.contrasts))), adjust = "fdr", n = nrow(dat.fr)):
  partial argument match of 'adjust' to 'adjust.method'
* 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' ... NOTE
The following files should probably not be installed:
  'fancyvrb.sty'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ...
** running examples for arch 'i386' ... [48s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
findCorrPartners 12.12   0.18   12.31
findAttractors   10.86   0.04   15.85
findSynexprs     10.62   0.00   10.63
** running examples for arch 'x64' ... [52s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
findSynexprs     15.92   0.05   15.97
findCorrPartners 13.12   0.09   13.22
findAttractors   12.90   0.08   12.98
* 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

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  'E:/biocbld/bbs-2.12-bioc/meat/attract.Rcheck/00check.log'
for details.

attract.Rcheck/00install.out:


install for i386

* installing *source* package 'attract' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: package 'KEGG.db' was built under R version 3.1.0
Warning: replacing previous import 'makeGOGraph' when loading 'AnnotationDbi'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: package 'KEGG.db' was built under R version 3.1.0
Warning: replacing previous import 'makeGOGraph' when loading 'AnnotationDbi'

install for x64

* installing *source* package 'attract' ...
** testing if installed package can be loaded
Warning: package 'KEGG.db' was built under R version 3.1.0
Warning: replacing previous import 'makeGOGraph' when loading 'AnnotationDbi'
* MD5 sums
packaged installation of 'attract' as attract_1.12.0.zip
* DONE (attract)