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BioC experimental data: CHECK report for pumadata on moscato2

This page was generated on 2015-10-07 16:21:09 -0700 (Wed, 07 Oct 2015).

Package 185/241HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pumadata 2.4.1
Richard Pearson
Snapshot Date: 2015-10-07 07:15:35 -0700 (Wed, 07 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_1/experiment/pkgs/pumadata
Last Changed Rev: 3401 / Revision: 3442
Last Changed Date: 2015-09-13 03:31:17 -0700 (Sun, 13 Sep 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK YES, new version is higher than in internal repository
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 

Summary

Package: pumadata
Version: 2.4.1
Command: rm -rf pumadata.buildbin-libdir pumadata.Rcheck && mkdir pumadata.buildbin-libdir pumadata.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pumadata.buildbin-libdir pumadata_2.4.1.tar.gz >pumadata.Rcheck\00install.out 2>&1 && cp pumadata.Rcheck\00install.out pumadata-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=pumadata.buildbin-libdir --install="check:pumadata-install.out" --force-multiarch --no-vignettes --timings pumadata_2.4.1.tar.gz
StartedAt: 2015-10-07 11:35:20 -0700 (Wed, 07 Oct 2015)
EndedAt: 2015-10-07 11:38:40 -0700 (Wed, 07 Oct 2015)
EllapsedTime: 199.6 seconds
RetCode: 0
Status:  OK  
CheckDir: pumadata.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf pumadata.buildbin-libdir pumadata.Rcheck && mkdir pumadata.buildbin-libdir pumadata.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pumadata.buildbin-libdir pumadata_2.4.1.tar.gz >pumadata.Rcheck\00install.out 2>&1 && cp pumadata.Rcheck\00install.out pumadata-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=pumadata.buildbin-libdir --install="check:pumadata-install.out" --force-multiarch --no-vignettes --timings pumadata_2.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-data-experiment/meat/pumadata.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-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 '2.4.1'
* 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 ... 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
'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.
* 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 ... OK
* 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' ... [6s] OK
** running examples for arch 'x64' ... [6s] 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
* DONE

Status: 3 NOTEs
See
  'E:/biocbld/bbs-3.1-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
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'pumadata' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'pumadata' as pumadata_2.4.1.zip
* DONE (pumadata)

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

nameusersystemelapsed
eset_estrogen_comb0.140.000.15
eset_estrogen_mmgmos0.290.000.29
eset_estrogen_pmmmgmos0.280.000.28
eset_estrogen_rma0.030.000.03
pumapca_estrogen0.020.000.01

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

nameusersystemelapsed
eset_estrogen_comb0.100.000.11
eset_estrogen_mmgmos0.130.000.13
eset_estrogen_pmmmgmos0.140.000.14
eset_estrogen_rma0.030.000.03
pumapca_estrogen0.20.00.2