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BioC 3.2: CHECK report for attract on moscato1

This page was generated on 2016-04-23 10:17:20 -0700 (Sat, 23 Apr 2016).

Package 67/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
attract 1.22.0
Jessica Mar
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/attract
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: attract
Version: 1.22.0
Command: rm -rf attract.buildbin-libdir attract.Rcheck && mkdir attract.buildbin-libdir attract.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=attract.buildbin-libdir attract_1.22.0.tar.gz >attract.Rcheck\00install.out 2>&1 && cp attract.Rcheck\00install.out attract-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=attract.buildbin-libdir --install="check:attract-install.out" --force-multiarch --no-vignettes --timings attract_1.22.0.tar.gz
StartedAt: 2016-04-22 23:44:16 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 23:50:03 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 346.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: attract.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf attract.buildbin-libdir attract.Rcheck && mkdir attract.buildbin-libdir attract.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=attract.buildbin-libdir attract_1.22.0.tar.gz >attract.Rcheck\00install.out 2>&1 && cp attract.Rcheck\00install.out attract-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=attract.buildbin-libdir --install="check:attract-install.out" --force-multiarch --no-vignettes --timings attract_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/attract.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'attract/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'attract' version '1.22.0'
* 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 'attract' can be installed ... WARNING
Found the following significant warnings:
  Warning: package 'Matrix' was built under R version 3.2.5
  Warning: replacing previous import 'GOstats::makeGOGraph' by 'AnnotationDbi::makeGOGraph' when loading 'attract'
See 'D:/biocbld/bbs-3.2-bioc/meat/attract.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'AnnotationDbi' 'KEGG.db' 'limma' 'cluster' 'GOstats' 'graphics' 'methods' 'stats'
A package should be listed in only one of these fields.
* 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:
  'GOstats' 'KEGG.db' 'cluster' 'limma'
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotsynexprs: warning in axis(1, at = tickMarks, lab = tickLabels):
  partial argument match of 'lab' to 'labels'
removeFlatGenes: warning in topTable(fit2, coef =
  (1:(length(my.contrasts))), adjust = "fdr", n = nrow(dat.fr)):
  partial argument match of 'n' to 'number'
removeFlatGenes: warning in topTable(fit2, coef =
  (1:(length(my.contrasts))), adjust = "fdr", n = nrow(dat.fr)):
  partial argument match of 'adjust' to 'adjust.method'
* 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' ... [43s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
findCorrPartners 10.66   0.12   10.78
findAttractors    9.41   0.05   13.84
findSynexprs      9.23   0.02    9.25
** running examples for arch 'x64' ... [54s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
findCorrPartners 14.28   0.08   14.35
findAttractors   14.23   0.10   14.34
findSynexprs     12.37   0.05   12.43
* 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: 1 WARNING, 3 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/attract.Rcheck/00check.log'
for details.


attract.Rcheck/00install.out:


install for i386

* installing *source* package 'attract' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: package 'Matrix' was built under R version 3.2.5
Warning: replacing previous import 'GOstats::makeGOGraph' by 'AnnotationDbi::makeGOGraph' when loading 'attract'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: package 'Matrix' was built under R version 3.2.5
Warning: replacing previous import 'GOstats::makeGOGraph' by 'AnnotationDbi::makeGOGraph' when loading 'attract'

install for x64

* installing *source* package 'attract' ...
** testing if installed package can be loaded
Warning: package 'Matrix' was built under R version 3.2.5
Warning: replacing previous import 'GOstats::makeGOGraph' by 'AnnotationDbi::makeGOGraph' when loading 'attract'
* MD5 sums
packaged installation of 'attract' as attract_1.22.0.zip
* DONE (attract)

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

nameusersystemelapsed
AttractorModuleSet-class000
SynExpressionSet-class000
attract-package000
buildCorMatrix000
buildKeggIncidenceMatrix000
calcFuncSynexprs000
calcInform000
calcModfstat000
calcRss0.020.000.02
exprs.dat0.20.00.2
findAttractors 9.41 0.0513.84
findCorrPartners10.66 0.1210.78
findOnepwaySynexprs000
findSynexprs9.230.029.25
flagPwayExists000
loring.eset0.390.030.42
plotsynexprs000
removeFlatGenes0.380.000.37
samp.info0.000.020.02
subset.loring.eset0.170.000.17

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

nameusersystemelapsed
AttractorModuleSet-class000
SynExpressionSet-class000
attract-package000
buildCorMatrix000
buildKeggIncidenceMatrix0.020.000.02
calcFuncSynexprs000
calcInform000
calcModfstat000
calcRss000
exprs.dat0.160.020.18
findAttractors14.23 0.1014.34
findCorrPartners14.28 0.0814.35
findOnepwaySynexprs000
findSynexprs12.37 0.0512.43
flagPwayExists000
loring.eset0.200.000.21
plotsynexprs000
removeFlatGenes0.290.000.28
samp.info0.010.000.02
subset.loring.eset0.130.020.14