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BioC 3.0: CHECK report for baySeq on moscato1

This page was generated on 2015-04-10 09:45:59 -0700 (Fri, 10 Apr 2015).

Package 71/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
baySeq 2.0.50
Thomas J. Hardcastle
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/baySeq
Last Changed Rev: 95677 / Revision: 102249
Last Changed Date: 2014-10-17 04:38:16 -0700 (Fri, 17 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: baySeq
Version: 2.0.50
Command: rm -rf baySeq.buildbin-libdir baySeq.Rcheck && mkdir baySeq.buildbin-libdir baySeq.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=baySeq.buildbin-libdir baySeq_2.0.50.tar.gz >baySeq.Rcheck\00install.out 2>&1 && cp baySeq.Rcheck\00install.out baySeq-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=baySeq.buildbin-libdir --install="check:baySeq-install.out" --force-multiarch --no-vignettes --timings baySeq_2.0.50.tar.gz
StartedAt: 2015-04-09 22:50:08 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:00:19 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 611.4 seconds
RetCode: 0
Status:  OK  
CheckDir: baySeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf baySeq.buildbin-libdir baySeq.Rcheck && mkdir baySeq.buildbin-libdir baySeq.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=baySeq.buildbin-libdir baySeq_2.0.50.tar.gz >baySeq.Rcheck\00install.out 2>&1 && cp baySeq.Rcheck\00install.out baySeq-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=baySeq.buildbin-libdir --install="check:baySeq-install.out" --force-multiarch --no-vignettes --timings baySeq_2.0.50.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/baySeq.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'baySeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'baySeq' version '2.0.50'
* 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 'baySeq' 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' call to 'edgeR' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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
getLibsizes : estLibs: no visible global function definition for
  'DGEList'
getLibsizes : estLibs: no visible global function definition for
  'calcNormFactors'
getLikelihoods: no visible global function definition for 'clusterCall'
getLikelihoods: no visible global function definition for 'parLapply'
getLikelihoods: no visible global function definition for
  'clusterEvalQ'
getPosteriors: no visible global function definition for 'clusterCall'
getPosteriors: no visible global function definition for 'parRapply'
getPriors: no visible global function definition for 'clusterCall'
getPriors: no visible global function definition for 'parLapply'
getPriors: no visible global function definition for 'clusterEvalQ'
getPriors.NB: no visible global function definition for 'parApply'
getPriors.NB: no visible global function definition for 'clusterEvalQ'
* 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' ... [212s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
baySeq-package 105.86   0.02  105.88
getPriors       76.70   0.00   76.71
getLikelihoods  21.23   0.01   21.24
** running examples for arch 'x64' ... [242s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
baySeq-package 116.61   0.01  116.62
getPriors       93.71   0.02   93.73
getLikelihoods  24.90   0.00   24.91
* 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

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/baySeq.Rcheck/00check.log'
for details.

baySeq.Rcheck/00install.out:


install for i386

* installing *source* package 'baySeq' ...
** 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 'baySeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'baySeq' as baySeq_2.0.50.zip
* DONE (baySeq)

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

nameusersystemelapsed
allModels1.230.011.25
baySeq-classes0.040.000.03
baySeq-package105.86 0.02105.88
bimodalSep0.010.000.01
densityFunction000
getLibsizes0.020.000.02
getLikelihoods21.23 0.0121.24
getPosteriors000
getPriors76.70 0.0076.71
getTPs000
makeOrderings0.080.000.07
plotMA.CD0.020.000.02
plotPosteriors0.010.000.01
plotPriors0.020.000.02
selectTop0.030.000.03
summarisePosteriors0.010.000.02
topCounts0.030.000.03

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

nameusersystemelapsed
allModels0.960.000.97
baySeq-classes0.040.000.03
baySeq-package116.61 0.01116.62
bimodalSep0.010.000.02
densityFunction000
getLibsizes000
getLikelihoods24.90 0.0024.91
getPosteriors0.010.000.01
getPriors93.71 0.0293.73
getTPs0.020.000.02
makeOrderings0.040.010.06
plotMA.CD0.020.000.01
plotPosteriors0.010.000.02
plotPriors0.020.000.02
selectTop0.010.020.03
summarisePosteriors000
topCounts0.030.010.05