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BioC 2.14: CHECK report for compcodeR on moscato2

This page was generated on 2014-10-08 08:56:46 -0700 (Wed, 08 Oct 2014).

Package 183/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
compcodeR 1.0.0
Charlotte Soneson
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/compcodeR
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: compcodeR
Version: 1.0.0
Command: rm -rf compcodeR.buildbin-libdir && mkdir compcodeR.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=compcodeR.buildbin-libdir compcodeR_1.0.0.tar.gz >compcodeR-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=compcodeR.buildbin-libdir --install="check:compcodeR-install.out" --force-multiarch --no-vignettes --timings compcodeR_1.0.0.tar.gz
StartedAt: 2014-10-08 00:09:46 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 00:18:36 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 530.7 seconds
RetCode: 0
Status:  OK  
CheckDir: compcodeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf compcodeR.buildbin-libdir && mkdir compcodeR.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=compcodeR.buildbin-libdir compcodeR_1.0.0.tar.gz >compcodeR-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=compcodeR.buildbin-libdir --install="check:compcodeR-install.out" --force-multiarch --no-vignettes --timings compcodeR_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/compcodeR.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 'compcodeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'compcodeR' version '1.0.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'rpanel'
* 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 'compcodeR' 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 ... 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' ... [221s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
DESeq.nbinom.createRmd 112.08   1.28  113.38
EBSeq.createRmd         15.21   0.08   15.32
DESeq.GLM.createRmd     14.79   0.17   14.98
show-compData-method    13.71   0.80   14.52
convertcompDataToList   10.59   0.81   11.40
DESeq2.createRmd         5.29   0.06    5.36
baySeq.createRmd         5.04   0.02    5.05
** running examples for arch 'x64' ... [216s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
DESeq.nbinom.createRmd 96.50   1.25   97.78
show-compData-method   15.90   2.60   18.51
DESeq.GLM.createRmd    15.55   0.20   15.96
convertcompDataToList  11.87   1.70   13.57
EBSeq.createRmd        11.36   0.02   12.27
baySeq.createRmd        6.44   0.10    6.54
DESeq2.createRmd        5.48   0.03    5.52
* 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 was 1 note.
See
  'E:/biocbld/bbs-2.14-bioc/meat/compcodeR.Rcheck/00check.log'
for details.

compcodeR.Rcheck/00install.out:


install for i386

* installing *source* package 'compcodeR' ...
** 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 'compcodeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'compcodeR' as compcodeR_1.0.0.zip
* DONE (compcodeR)

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

nameusersystemelapsed
DESeq.GLM.createRmd14.79 0.1714.98
DESeq.nbinom.createRmd112.08 1.28113.38
DESeq2.createRmd5.290.065.36
DSS.createRmd1.340.051.62
EBSeq.createRmd15.21 0.0815.32
HTSDiff.createRmd3.900.084.03
NBPSeq.createRmd0.790.040.86
NOISeq.prenorm.createRmd4.030.004.02
SAMseq.createRmd2.030.032.07
TCC.createRmd2.990.033.03
baySeq.createRmd5.040.025.05
checkDataObject0.360.000.36
checkTableConsistency1.620.031.65
check_compData0.650.000.66
check_compData_results1.030.021.04
compData0.020.000.02
convertListTocompData000
convertcompDataToList10.59 0.8111.40
edgeR.GLM.createRmd2.540.012.58
edgeR.exact.createRmd1.220.001.21
generateCodeHTMLs0.970.031.06
generateSyntheticData0.340.020.36
listcreateRmd0.020.000.02
logcpm.limma.createRmd0.670.020.69
runComparison3.090.073.37
runComparisonGUI000
runDiffExp0.950.000.95
show-compData-method13.71 0.8014.52
sqrtcpm.limma.createRmd0.890.020.91
summarizeSyntheticDataSet1.350.061.45
ttest.createRmd0.80.00.8
voom.limma.createRmd1.440.011.45
voom.ttest.createRmd1.090.051.42
vst.limma.createRmd1.100.061.17
vst.ttest.createRmd0.970.020.98

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

nameusersystemelapsed
DESeq.GLM.createRmd15.55 0.2015.96
DESeq.nbinom.createRmd96.50 1.2597.78
DESeq2.createRmd5.480.035.52
DSS.createRmd1.610.032.26
EBSeq.createRmd11.36 0.0212.27
HTSDiff.createRmd3.010.033.04
NBPSeq.createRmd0.750.011.60
NOISeq.prenorm.createRmd4.300.034.34
SAMseq.createRmd1.760.052.38
TCC.createRmd3.220.063.53
baySeq.createRmd6.440.106.54
checkDataObject0.420.000.42
checkTableConsistency1.720.001.71
check_compData0.470.000.47
check_compData_results0.950.030.98
compData000
convertListTocompData0.010.000.02
convertcompDataToList11.87 1.7013.57
edgeR.GLM.createRmd1.810.011.83
edgeR.exact.createRmd1.110.041.34
generateCodeHTMLs1.190.011.20
generateSyntheticData0.430.000.44
listcreateRmd000
logcpm.limma.createRmd0.860.010.88
runComparison4.570.084.74
runComparisonGUI000
runDiffExp1.950.051.99
show-compData-method15.90 2.6018.51
sqrtcpm.limma.createRmd1.250.001.24
summarizeSyntheticDataSet2.280.022.81
ttest.createRmd1.230.001.24
voom.limma.createRmd1.340.011.35
voom.ttest.createRmd0.740.040.78
vst.limma.createRmd1.060.011.07
vst.ttest.createRmd1.370.061.44