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BioC 3.0: CHECK report for compcodeR on moscato1

This page was generated on 2015-04-10 09:50:26 -0700 (Fri, 10 Apr 2015).

Package 190/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
compcodeR 1.2.1
Charlotte Soneson
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/compcodeR
Last Changed Rev: 99175 / Revision: 102249
Last Changed Date: 2015-02-07 01:02:05 -0800 (Sat, 07 Feb 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: compcodeR
Version: 1.2.1
Command: rm -rf compcodeR.buildbin-libdir compcodeR.Rcheck && mkdir compcodeR.buildbin-libdir compcodeR.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=compcodeR.buildbin-libdir compcodeR_1.2.1.tar.gz >compcodeR.Rcheck\00install.out 2>&1 && cp compcodeR.Rcheck\00install.out compcodeR-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=compcodeR.buildbin-libdir --install="check:compcodeR-install.out" --force-multiarch --no-vignettes --timings compcodeR_1.2.1.tar.gz
StartedAt: 2015-04-10 00:03:23 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:12:48 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 564.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: compcodeR.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf compcodeR.buildbin-libdir compcodeR.Rcheck && mkdir compcodeR.buildbin-libdir compcodeR.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=compcodeR.buildbin-libdir compcodeR_1.2.1.tar.gz >compcodeR.Rcheck\00install.out 2>&1 && cp compcodeR.Rcheck\00install.out compcodeR-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=compcodeR.buildbin-libdir --install="check:compcodeR-install.out" --force-multiarch --no-vignettes --timings compcodeR_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/compcodeR.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 'compcodeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'compcodeR' version '1.2.1'
* 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 ... WARNING
Functions or methods with usage in documentation object 'HTSDiff.createRmd' but not in code:
  HTSDiff.createRmd

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'library' or 'require' call not declared from: 'HTSDiff'
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [245s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
DESeq.nbinom.createRmd   113.80   1.54  115.36
EBSeq.createRmd           18.05   0.08   18.13
show-compData-method      13.99   2.42   16.41
convertcompDataToList     12.99   2.41   15.40
DESeq.GLM.createRmd       15.05   0.16   15.41
baySeq.createRmd          10.07   0.06   10.12
DESeq2.createRmd           6.94   0.32    7.25
NOISeq.prenorm.createRmd   4.85   0.07    5.57
runComparison              4.82   0.10    5.41
** running examples for arch 'x64' ... [218s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
DESeq.nbinom.createRmd   98.62   1.40  100.04
DESeq.GLM.createRmd      17.05   0.20   17.52
show-compData-method     11.97   1.81   13.78
convertcompDataToList    12.09   0.84   12.94
EBSeq.createRmd          12.63   0.06   12.90
baySeq.createRmd         10.54   0.01   10.58
DESeq2.createRmd          6.82   0.16    6.97
NOISeq.prenorm.createRmd  5.02   0.04    5.07
* 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

WARNING: There were 2 warnings.
NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-3.0-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_1.2.1.zip
* DONE (compcodeR)

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

nameusersystemelapsed
DESeq.GLM.createRmd15.05 0.1615.41
DESeq.nbinom.createRmd113.80 1.54115.36
DESeq2.createRmd6.940.327.25
DSS.createRmd2.430.073.23
EBSeq.createRmd18.05 0.0818.13
HTSDiff.createRmd000
NBPSeq.createRmd0.960.031.62
NOISeq.prenorm.createRmd4.850.075.57
SAMseq.createRmd2.160.042.51
TCC.createRmd3.400.053.67
baySeq.createRmd10.07 0.0610.12
checkDataObject0.350.000.36
checkTableConsistency1.650.051.72
check_compData0.360.000.35
check_compData_results0.900.010.92
compData000
convertListTocompData000
convertcompDataToList12.99 2.4115.40
edgeR.GLM.createRmd2.250.012.29
edgeR.exact.createRmd1.870.021.88
generateCodeHTMLs1.230.041.28
generateSyntheticData0.550.000.55
listcreateRmd0.010.000.01
logcpm.limma.createRmd1.160.041.19
runComparison4.820.105.41
runComparisonGUI000
runDiffExp1.270.071.33
show-compData-method13.99 2.4216.41
sqrtcpm.limma.createRmd0.930.061.00
summarizeSyntheticDataSet1.460.141.86
ttest.createRmd1.110.061.17
voom.limma.createRmd1.530.021.54
voom.ttest.createRmd0.940.010.95
vst.limma.createRmd1.560.021.57
vst.ttest.createRmd1.400.061.54

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

nameusersystemelapsed
DESeq.GLM.createRmd17.05 0.2017.52
DESeq.nbinom.createRmd 98.62 1.40100.04
DESeq2.createRmd6.820.166.97
DSS.createRmd2.020.032.04
EBSeq.createRmd12.63 0.0612.90
HTSDiff.createRmd000
NBPSeq.createRmd1.080.061.25
NOISeq.prenorm.createRmd5.020.045.07
SAMseq.createRmd1.820.061.98
TCC.createRmd3.180.113.64
baySeq.createRmd10.54 0.0110.58
checkDataObject0.420.000.42
checkTableConsistency1.680.021.73
check_compData0.410.000.40
check_compData_results1.000.051.05
compData0.010.000.01
convertListTocompData000
convertcompDataToList12.09 0.8412.94
edgeR.GLM.createRmd1.920.031.95
edgeR.exact.createRmd1.220.001.21
generateCodeHTMLs1.040.011.10
generateSyntheticData0.720.000.72
listcreateRmd0.010.000.02
logcpm.limma.createRmd1.280.051.32
runComparison4.600.134.99
runComparisonGUI0.010.000.01
runDiffExp1.500.011.52
show-compData-method11.97 1.8113.78
sqrtcpm.limma.createRmd1.150.001.15
summarizeSyntheticDataSet1.840.073.76
ttest.createRmd0.810.070.88
voom.limma.createRmd1.060.011.07
voom.ttest.createRmd101
vst.limma.createRmd1.060.021.07
vst.ttest.createRmd0.970.061.06