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BioC 2.14: CHECK report for DEXSeq on moscato2

This page was generated on 2014-10-08 08:54:01 -0700 (Wed, 08 Oct 2014).

Package 223/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEXSeq 1.10.8
Alejandro Reyes
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/DEXSeq
Last Changed Rev: 92125 / Revision: 95116
Last Changed Date: 2014-07-03 01:45:51 -0700 (Thu, 03 Jul 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: DEXSeq
Version: 1.10.8
Command: rm -rf DEXSeq.buildbin-libdir && mkdir DEXSeq.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DEXSeq.buildbin-libdir DEXSeq_1.10.8.tar.gz >DEXSeq-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=DEXSeq.buildbin-libdir --install="check:DEXSeq-install.out" --force-multiarch --no-vignettes --timings DEXSeq_1.10.8.tar.gz
StartedAt: 2014-10-08 00:30:40 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 00:36:23 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 342.4 seconds
RetCode: 0
Status:  OK  
CheckDir: DEXSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DEXSeq.buildbin-libdir && mkdir DEXSeq.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DEXSeq.buildbin-libdir DEXSeq_1.10.8.tar.gz >DEXSeq-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=DEXSeq.buildbin-libdir --install="check:DEXSeq-install.out" --force-multiarch --no-vignettes --timings DEXSeq_1.10.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/DEXSeq.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 'DEXSeq/DESCRIPTION' ... OK
* this is package 'DEXSeq' version '1.10.8'
* 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 'DEXSeq' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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' ... [55s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
DEXSeq                  9.19      0    9.38
estimateExonFoldChanges 8.40      0    8.39
methods-gr              6.36      0    6.36
perGeneQValue           6.21      0    6.21
DEXSeqResults           5.87      0    5.86
testForDEU              5.82      0    5.82
estimateDispersions     5.08      0    5.09
** running examples for arch 'x64' ... [60s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
DEXSeq                  10.22   0.01   10.24
estimateExonFoldChanges  9.25   0.00    9.25
perGeneQValue            6.63   0.00    6.63
methods-gr               6.43   0.03    6.46
DEXSeqResults            6.36   0.00    6.37
testForDEU               6.29   0.00    6.29
estimateDispersions      5.22   0.00    5.22
* 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

DEXSeq.Rcheck/00install.out:


install for i386

* installing *source* package 'DEXSeq' ...
** 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 'DEXSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DEXSeq' as DEXSeq_1.10.8.zip
* DONE (DEXSeq)

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

nameusersystemelapsed
DEXSeq9.190.009.38
DEXSeqDataSet000
DEXSeqHTML000
DEXSeqResults5.870.005.86
accessors0.080.000.08
counts0.020.000.01
estimateDispersions5.080.005.09
estimateExonFoldChanges8.400.008.39
methods-gr6.360.006.36
perGeneQValue6.210.006.21
plotDEXSeq000
plotMA000
testForDEU5.820.005.82

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

nameusersystemelapsed
DEXSeq10.22 0.0110.24
DEXSeqDataSet0.020.000.01
DEXSeqHTML000
DEXSeqResults6.360.006.37
accessors0.080.000.08
counts0.000.020.02
estimateDispersions5.220.005.22
estimateExonFoldChanges9.250.009.25
methods-gr6.430.036.46
perGeneQValue6.630.006.63
plotDEXSeq000
plotMA000
testForDEU6.290.006.29