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 2.13: CHECK report for Risa on moscato1

This page was generated on 2014-04-05 09:51:00 -0700 (Sat, 05 Apr 2014).

Package 605/750HostnameOS / ArchBUILDCHECKBUILD BIN
Risa 1.4.1
Alejandra Gonzalez-Beltran, ISA Team
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/Risa
Last Changed Rev: 86057 / Revision: 88450
Last Changed Date: 2014-02-04 10:03:14 -0800 (Tue, 04 Feb 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: Risa
Version: 1.4.1
Command: rm -rf Risa.buildbin-libdir && mkdir Risa.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Risa.buildbin-libdir Risa_1.4.1.tar.gz >Risa-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=Risa.buildbin-libdir --install="check:Risa-install.out" --force-multiarch --no-vignettes --timings Risa_1.4.1.tar.gz && mv Risa.buildbin-libdir/* Risa.Rcheck/ && rmdir Risa.buildbin-libdir
StartedAt: 2014-04-05 06:21:28 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 06:26:29 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 301.4 seconds
RetCode: 0
Status:  OK  
CheckDir: Risa.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/Risa.Rcheck'
* using R version 3.0.3 (2014-03-06)
* 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 '1.4.1'
* 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 '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
* 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' 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'Risa.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [92s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
processAssayXcmsSet.1factor 41.54   0.30   41.87
processAssayXcmsSet         39.50   0.29   39.81
** running examples for arch 'x64' ... [83s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
processAssayXcmsSet         37.66   0.25   37.90
processAssayXcmsSet.1factor 36.66   0.17   37.16
* 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 3 notes.
See
  'D:/biocbld/bbs-2.13-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_1.4.1.zip
* DONE (Risa)

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

nameusersystemelapsed
AssayTab-class0.020.000.02
ISAtab-class0.080.000.08
Risa-package0.350.133.06
getAnnotatedDataFrameAssay0.250.030.61
getExpressionSet0.140.020.17
getMIAMEMetadata0.200.000.21
getMSAssayFilenames0.070.010.08
getMicroarrayAssayFilenames0.160.000.16
getStudyFilename0.080.000.07
isMSAssay0.060.000.07
isMicroarrayAssay0.160.000.16
processAssayXcmsSet.1factor41.54 0.3041.87
processAssayXcmsSet39.50 0.2939.81
readISAtab0.150.061.19
updateAssayMetadata0.170.020.18
write.assay.file0.080.000.08
write.investigation.file0.070.000.06
write.isatab0.060.020.08
write.study.file0.080.000.08

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

nameusersystemelapsed
AssayTab-class000
ISAtab-class000
Risa-package0.220.080.31
getAnnotatedDataFrameAssay0.220.020.24
getExpressionSet0.130.000.12
getMIAMEMetadata0.090.040.14
getMSAssayFilenames0.090.000.10
getMicroarrayAssayFilenames0.160.000.46
getStudyFilename0.090.000.10
isMSAssay0.080.000.08
isMicroarrayAssay0.160.000.15
processAssayXcmsSet.1factor36.66 0.1737.16
processAssayXcmsSet37.66 0.2537.90
readISAtab0.130.080.21
updateAssayMetadata0.120.020.14
write.assay.file0.050.000.04
write.investigation.file0.040.000.05
write.isatab0.050.000.04
write.study.file0.050.000.05