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BioC 3.2: CHECK report for compcodeR on oaxaca

This page was generated on 2016-04-23 10:27:47 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings compcodeR_1.6.0.tar.gz
StartedAt: 2016-04-22 23:03:30 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 23:07:57 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 266.1 seconds
RetCode: 0
Status:  OK 
CheckDir: compcodeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings compcodeR_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/compcodeR.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘compcodeR’ can be installed ... [4s/5s] 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [205s/211s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
DESeq.nbinom.createRmd   54.133  2.783  56.972
NBPSeq.createRmd         35.510  2.382  39.434
DESeq.GLM.createRmd      14.777  1.115  15.767
convertcompDataToList     9.333  6.135  15.393
show-compData-method      9.857  5.486  15.268
EBSeq.createRmd           9.926  0.480  14.084
baySeq.createRmd          7.656  0.601   8.178
DESeq2.createRmd          7.371  0.795   8.118
NOISeq.prenorm.createRmd  5.920  0.555   6.400
* 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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/compcodeR.Rcheck/00check.log’
for details.


compcodeR.Rcheck/00install.out:

* 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
* DONE (compcodeR)

compcodeR.Rcheck/compcodeR-Ex.timings:

nameusersystemelapsed
DESeq.GLM.createRmd14.777 1.11515.767
DESeq.nbinom.createRmd54.133 2.78356.972
DESeq2.createRmd7.3710.7958.118
DSS.createRmd2.1070.1792.550
EBSeq.createRmd 9.926 0.48014.084
NBPSeq.createRmd35.510 2.38239.434
NOISeq.prenorm.createRmd5.9200.5556.400
SAMseq.createRmd1.7070.2161.956
TCC.createRmd2.5840.2082.982
baySeq.createRmd7.6560.6018.178
checkDataObject0.4070.0670.469
checkTableConsistency1.3550.1331.475
check_compData0.7790.0590.833
check_compData_results0.8960.0971.387
compData0.0040.0000.004
convertListTocompData0.0080.0010.008
convertcompDataToList 9.333 6.13515.393
edgeR.GLM.createRmd1.5190.1331.636
edgeR.exact.createRmd0.8800.0840.955
generateCodeHTMLs0.8990.1031.059
generateSyntheticData0.4010.0500.445
listcreateRmd0.010.000.01
logcpm.limma.createRmd0.6170.0750.686
runComparison3.5800.3113.932
runComparisonGUI0.0010.0000.001
runDiffExp1.3110.1031.403
show-compData-method 9.857 5.48615.268
sqrtcpm.limma.createRmd0.6700.0770.746
summarizeSyntheticDataSet2.1920.1872.407
ttest.createRmd0.7380.0790.816
voom.limma.createRmd0.8630.0820.936
voom.ttest.createRmd0.7460.0780.821
vst.limma.createRmd0.9710.0861.050
vst.ttest.createRmd0.9160.0770.986