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BioC 3.2: CHECK report for compcodeR on moscato1

This page was generated on 2016-04-23 10:20:13 -0700 (Sat, 23 Apr 2016).

Package 214/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
compcodeR 1.6.0
Charlotte Soneson
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/compcodeR
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  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: compcodeR
Version: 1.6.0
Command: rm -rf compcodeR.buildbin-libdir compcodeR.Rcheck && mkdir compcodeR.buildbin-libdir compcodeR.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=compcodeR.buildbin-libdir compcodeR_1.6.0.tar.gz >compcodeR.Rcheck\00install.out 2>&1 && cp compcodeR.Rcheck\00install.out compcodeR-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=compcodeR.buildbin-libdir --install="check:compcodeR-install.out" --force-multiarch --no-vignettes --timings compcodeR_1.6.0.tar.gz
StartedAt: 2016-04-23 01:02:17 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 01:14:21 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 724.7 seconds
RetCode: 0
Status:  OK  
CheckDir: compcodeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf compcodeR.buildbin-libdir compcodeR.Rcheck && mkdir compcodeR.buildbin-libdir compcodeR.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=compcodeR.buildbin-libdir compcodeR_1.6.0.tar.gz >compcodeR.Rcheck\00install.out 2>&1 && cp compcodeR.Rcheck\00install.out compcodeR-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=compcodeR.buildbin-libdir --install="check:compcodeR-install.out" --force-multiarch --no-vignettes --timings compcodeR_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/compcodeR.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 'compcodeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'compcodeR' version '1.6.0'
* 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 ... NOTE
'library' or 'require' call to 'rpanel' 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 ... 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' ... [329s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
DESeq.nbinom.createRmd 122.71   1.34  124.11
NBPSeq.createRmd        88.35   0.63   89.17
EBSeq.createRmd         18.47   0.03   19.28
DESeq.GLM.createRmd     12.31   0.10   14.39
show-compData-method    10.57   0.01   10.59
convertcompDataToList    9.41   0.03    9.44
baySeq.createRmd         8.08   0.08    8.57
DESeq2.createRmd         7.70   0.09    7.80
runComparison            4.15   0.11    6.50
** running examples for arch 'x64' ... [300s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
DESeq.nbinom.createRmd   111.62   1.64  113.25
NBPSeq.createRmd          75.62   0.59   76.32
EBSeq.createRmd           14.57   0.05   14.86
DESeq.GLM.createRmd       14.13   0.20   15.05
convertcompDataToList     10.16   0.89   11.05
show-compData-method       9.54   0.87   10.40
DESeq2.createRmd           9.18   0.05    9.22
baySeq.createRmd           8.25   0.05    8.29
NOISeq.prenorm.createRmd   5.25   0.02    5.27
runComparison              4.02   0.06    5.85
* 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: 2 NOTEs
See
  'D:/biocbld/bbs-3.2-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_1.6.0.zip
* DONE (compcodeR)

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

nameusersystemelapsed
DESeq.GLM.createRmd12.31 0.1014.39
DESeq.nbinom.createRmd122.71 1.34124.11
DESeq2.createRmd7.700.097.80
DSS.createRmd2.700.143.35
EBSeq.createRmd18.47 0.0319.28
NBPSeq.createRmd88.35 0.6389.17
NOISeq.prenorm.createRmd4.820.114.93
SAMseq.createRmd2.060.032.85
TCC.createRmd3.230.044.18
baySeq.createRmd8.080.088.57
checkDataObject0.410.000.41
checkTableConsistency1.760.072.01
check_compData0.620.000.63
check_compData_results1.140.031.17
compData0.020.000.01
convertListTocompData0.010.000.02
convertcompDataToList9.410.039.44
edgeR.GLM.createRmd1.900.033.22
edgeR.exact.createRmd1.190.031.22
generateCodeHTMLs0.840.021.03
generateSyntheticData0.360.000.36
listcreateRmd0.020.000.02
logcpm.limma.createRmd0.850.010.95
runComparison4.150.116.50
runComparisonGUI000
runDiffExp0.860.020.89
show-compData-method10.57 0.0110.59
sqrtcpm.limma.createRmd0.560.020.58
summarizeSyntheticDataSet1.760.173.36
ttest.createRmd0.640.000.64
voom.limma.createRmd0.910.000.90
voom.ttest.createRmd0.870.031.81
vst.limma.createRmd1.230.001.23
vst.ttest.createRmd0.990.000.99

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

nameusersystemelapsed
DESeq.GLM.createRmd14.13 0.2015.05
DESeq.nbinom.createRmd111.62 1.64113.25
DESeq2.createRmd9.180.059.22
DSS.createRmd2.170.042.28
EBSeq.createRmd14.57 0.0514.86
NBPSeq.createRmd75.62 0.5976.32
NOISeq.prenorm.createRmd5.250.025.27
SAMseq.createRmd2.170.112.39
TCC.createRmd3.550.063.96
baySeq.createRmd8.250.058.29
checkDataObject0.360.000.36
checkTableConsistency1.530.031.64
check_compData0.370.000.37
check_compData_results0.940.020.97
compData000
convertListTocompData000
convertcompDataToList10.16 0.8911.05
edgeR.GLM.createRmd1.960.032.71
edgeR.exact.createRmd0.920.050.97
generateCodeHTMLs0.820.010.83
generateSyntheticData0.350.000.36
listcreateRmd0.020.000.01
logcpm.limma.createRmd0.620.020.64
runComparison4.020.065.85
runComparisonGUI0.020.000.01
runDiffExp0.760.032.05
show-compData-method 9.54 0.8710.40
sqrtcpm.limma.createRmd0.710.030.75
summarizeSyntheticDataSet2.140.162.89
ttest.createRmd0.700.021.29
voom.limma.createRmd0.970.061.03
voom.ttest.createRmd0.620.030.66
vst.limma.createRmd0.890.050.93
vst.ttest.createRmd0.910.031.28