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BioC experimental data: CHECK report for pumadata on moscato2

This page was generated on 2014-10-04 17:41:15 -0700 (Sat, 04 Oct 2014).

Package 159/197HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pumadata 2.0.0
Richard Pearson
Snapshot Date: 2014-10-04 07:15:22 -0700 (Sat, 04 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_14/experiment/pkgs/pumadata
Last Changed Rev: 2799 / Revision: 3055
Last Changed Date: 2014-04-11 14:27:08 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: pumadata
Version: 2.0.0
Command: rm -rf pumadata.buildbin-libdir && mkdir pumadata.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pumadata.buildbin-libdir pumadata_2.0.0.tar.gz >pumadata-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=pumadata.buildbin-libdir --install="check:pumadata-install.out" --force-multiarch --no-vignettes --timings pumadata_2.0.0.tar.gz
StartedAt: 2014-10-04 10:51:01 -0700 (Sat, 04 Oct 2014)
EndedAt: 2014-10-04 10:55:03 -0700 (Sat, 04 Oct 2014)
EllapsedTime: 241.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: pumadata.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   rm -rf pumadata.buildbin-libdir && mkdir pumadata.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pumadata.buildbin-libdir pumadata_2.0.0.tar.gz >pumadata-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=pumadata.buildbin-libdir --install="check:pumadata-install.out" --force-multiarch --no-vignettes --timings pumadata_2.0.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-2.14-data-experiment/meat/pumadata.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pumadata/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pumadata' version '2.0.0'
* 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 'pumadata' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 100.6Mb
  sub-directories of 1Mb or more:
    data  100.5Mb
* 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 ... WARNING
Invalid citation information in 'inst/CITATION':
  Error in utils::readCitationFile(cfile, meta): attempt to set an attribute on NULL
* 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
'library' or 'require' call to 'Biobase' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Biobase' 'affy' 'oligo' 'puma'
  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
File 'pumadata/R/zzz.R':
  .onLoad calls:
    require(Biobase)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.
* 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 ... NOTE
  Error in inDL(x, as.logical(local), as.logical(now), ...) : 
    in_param memory allocation failed: out of memory?
  Error in .requirePackage(package) : 
    unable to find required package 'puma'
  Calls: <Anonymous> ... .findInheritedMethods -> getClass -> getClassDef -> .requirePackage
  Execution halted
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [7s] OK
** running examples for arch 'x64' ... [7s] OK
* 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

WARNING: There was 1 warning.
NOTE: There were 4 notes.
See
  'E:/biocbld/bbs-2.14-data-experiment/meat/pumadata.Rcheck/00check.log'
for details.

pumadata.Rcheck/00install.out:


install for i386

* installing *source* package 'pumadata' ...
** 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 'pumadata' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pumadata' as pumadata_2.0.0.zip
* DONE (pumadata)

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

nameusersystemelapsed
eset_estrogen_comb0.140.000.14
eset_estrogen_mmgmos0.390.020.40
eset_estrogen_pmmmgmos0.260.000.27
eset_estrogen_rma0.030.000.03
pumapca_estrogen000

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

nameusersystemelapsed
eset_estrogen_comb0.130.000.13
eset_estrogen_mmgmos0.290.000.29
eset_estrogen_pmmmgmos0.130.000.13
eset_estrogen_rma0.030.000.03
pumapca_estrogen0.020.000.01