Back to the "Multiple platform build/check report" A  B  C  D  E  F [G] H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.2: CHECK report for GeneExpressionSignature on windows1.bioconductor.org

This page was generated on 2015-10-27 17:29:39 -0400 (Tue, 27 Oct 2015).

Package 398/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneExpressionSignature 1.16.0
Yang Cao , Fei Li ,Lu Han
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/GeneExpressionSignature
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GeneExpressionSignature
Version: 1.16.0
Command: rm -rf GeneExpressionSignature.buildbin-libdir GeneExpressionSignature.Rcheck && mkdir GeneExpressionSignature.buildbin-libdir GeneExpressionSignature.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneExpressionSignature.buildbin-libdir GeneExpressionSignature_1.16.0.tar.gz >GeneExpressionSignature.Rcheck\00install.out 2>&1 && cp GeneExpressionSignature.Rcheck\00install.out GeneExpressionSignature-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=GeneExpressionSignature.buildbin-libdir --install="check:GeneExpressionSignature-install.out" --force-multiarch --no-vignettes --timings GeneExpressionSignature_1.16.0.tar.gz
StartedAt: 2015-10-27 01:58:45 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 02:01:04 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 138.8 seconds
RetCode: 0
Status:  OK  
CheckDir: GeneExpressionSignature.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GeneExpressionSignature.buildbin-libdir GeneExpressionSignature.Rcheck && mkdir GeneExpressionSignature.buildbin-libdir GeneExpressionSignature.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneExpressionSignature.buildbin-libdir GeneExpressionSignature_1.16.0.tar.gz >GeneExpressionSignature.Rcheck\00install.out 2>&1 && cp GeneExpressionSignature.Rcheck\00install.out GeneExpressionSignature-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=GeneExpressionSignature.buildbin-libdir --install="check:GeneExpressionSignature-install.out" --force-multiarch --no-vignettes --timings GeneExpressionSignature_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/GeneExpressionSignature.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneExpressionSignature/DESCRIPTION' ... OK
* this is package 'GeneExpressionSignature' version '1.16.0'
* 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 'GeneExpressionSignature' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  'Biobase' 'PGSEA'
  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
RankMerging: no visible global function definition for 'exprs'
RankMerging: no visible global function definition for 'phenoData'
ScoreGSEA : PRL.Distance: no visible global function definition for
  'exprs'
ScoreGSEA: no visible global function definition for 'exprs'
ScorePGSEA: no visible global function definition for 'exprs'
ScorePGSEA: no visible global function definition for 'PGSEA'
integratePRL: no visible global function definition for 'phenoData'
integratePRL: no visible global function definition for 'exprs'
* 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' ... [31s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
ScoreGSEA         8.83   0.03    8.86
SignatureDistance 7.77   0.02    7.78
RankMerging       5.61   0.06    5.67
ScorePGSEA        5.09   0.06    5.16
** running examples for arch 'x64' ... [32s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
ScoreGSEA         8.72   0.06    8.78
SignatureDistance 7.90   0.01    7.92
ScorePGSEA        5.53   0.13    5.66
RankMerging       5.11   0.01    5.13
* 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: 2 NOTEs
See
  'C:/biocbld/bbs-3.2-bioc/meat/GeneExpressionSignature.Rcheck/00check.log'
for details.


GeneExpressionSignature.Rcheck/00install.out:


install for i386

* installing *source* package 'GeneExpressionSignature' ...
** 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 'GeneExpressionSignature' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneExpressionSignature' as GeneExpressionSignature_1.16.0.zip
* DONE (GeneExpressionSignature)

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

nameusersystemelapsed
RankMerging5.610.065.67
ScoreGSEA8.830.038.86
ScorePGSEA5.090.065.16
SignatureDistance7.770.027.78
exampleSet0.280.000.28
getRLs0.440.000.44

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

nameusersystemelapsed
RankMerging5.110.015.13
ScoreGSEA8.720.068.78
ScorePGSEA5.530.135.66
SignatureDistance7.900.017.92
exampleSet0.300.000.29
getRLs0.440.020.46