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 2.14: CHECK report for Risa on moscato2

This page was generated on 2014-10-08 08:54:59 -0700 (Wed, 08 Oct 2014).

Package 665/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Risa 1.6.0
Alejandra Gonzalez-Beltran, ISA Team
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/Risa
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: Risa
Version: 1.6.0
Command: rm -rf Risa.buildbin-libdir && mkdir Risa.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Risa.buildbin-libdir Risa_1.6.0.tar.gz >Risa-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=Risa.buildbin-libdir --install="check:Risa-install.out" --force-multiarch --no-vignettes --timings Risa_1.6.0.tar.gz
StartedAt: 2014-10-08 04:39:14 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 04:43:22 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 247.3 seconds
RetCode: 0
Status:  OK  
CheckDir: Risa.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Risa.buildbin-libdir && mkdir Risa.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Risa.buildbin-libdir Risa_1.6.0.tar.gz >Risa-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=Risa.buildbin-libdir --install="check:Risa-install.out" --force-multiarch --no-vignettes --timings Risa_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/Risa.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 'Risa/DESCRIPTION' ... OK
* this is package 'Risa' version '1.6.0'
* 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 'Risa' 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
'library' or 'require' calls to packages already attached by Depends:
  'affy' 'biocViews'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Biobase' 'Rcpp' 'affy' 'biocViews' 'methods'
  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
getPackagesInBiocView: no visible binding for global variable
  'biocViewsVocab'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [70s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
processAssayXcmsSet.1factor 30.47   0.05   30.86
processAssayXcmsSet         30.01   0.02   30.03
** running examples for arch 'x64' ... [67s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
processAssayXcmsSet.1factor 30.67   0.09   31.29
processAssayXcmsSet         29.36   0.13   29.48
* 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
  'E:/biocbld/bbs-2.14-bioc/meat/Risa.Rcheck/00check.log'
for details.

Risa.Rcheck/00install.out:


install for i386

* installing *source* package 'Risa' ...
** R
** 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 'Risa' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Risa' as Risa_1.6.0.zip
* DONE (Risa)

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

nameusersystemelapsed
AssayTab-class000
ISAtab-class000
Risa-package0.240.064.52
getAnnotatedDataFrameAssay0.230.030.28
getExpressionSet0.100.020.13
getMIAMEMetadata0.120.010.14
getMSAssayFilenames0.050.000.04
getMicroarrayAssayFilenames0.110.000.11
getStudyFilename0.030.000.03
isMSAssay0.050.000.05
isMicroarrayAssay0.090.000.17
processAssayXcmsSet.1factor30.47 0.0530.86
processAssayXcmsSet30.01 0.0230.03
readISAtab0.140.040.19
updateAssayMetadata0.130.000.12
write.assay.file0.040.000.05
write.investigation.file0.030.000.03
write.isatab0.070.000.06
write.study.file0.030.000.03

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

nameusersystemelapsed
AssayTab-class0.020.000.02
ISAtab-class000
Risa-package0.190.080.28
getAnnotatedDataFrameAssay0.310.000.31
getExpressionSet0.110.010.12
getMIAMEMetadata0.140.000.14
getMSAssayFilenames0.040.000.05
getMicroarrayAssayFilenames0.100.000.09
getStudyFilename0.040.000.05
isMSAssay0.050.000.05
isMicroarrayAssay0.090.020.11
processAssayXcmsSet.1factor30.67 0.0931.29
processAssayXcmsSet29.36 0.1329.48
readISAtab0.120.060.19
updateAssayMetadata0.110.020.12
write.assay.file0.050.000.05
write.investigation.file0.060.000.06
write.isatab0.050.000.19
write.study.file0.050.000.05