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BioC 3.0: CHECK report for compcodeR on oaxaca

This page was generated on 2015-04-10 10:08:52 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch compcodeR_1.2.1.tar.gz
StartedAt: 2015-04-09 22:32:13 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 22:36:54 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 280.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: compcodeR.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch compcodeR_1.2.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/compcodeR.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.2.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘compcodeR’ can be installed ... [6s/6s] 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [187s/205s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
DESeq.nbinom.createRmd   54.559  2.972  58.359
baySeq.createRmd         18.284  1.165  24.133
DESeq.GLM.createRmd      17.170  1.126  18.451
show-compData-method     11.525  3.320  17.299
convertcompDataToList    11.214  3.475  17.508
EBSeq.createRmd          11.287  0.668  14.004
DESeq2.createRmd          7.644  0.785   8.457
NOISeq.prenorm.createRmd  5.083  0.411   6.009
* 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
  ‘/Users/biocbuild/bbs-3.0-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.createRmd17.170 1.12618.451
DESeq.nbinom.createRmd54.559 2.97258.359
DESeq2.createRmd7.6440.7858.457
DSS.createRmd2.1480.1722.434
EBSeq.createRmd11.287 0.66814.004
HTSDiff.createRmd0.0050.0000.005
NBPSeq.createRmd0.8300.0860.965
NOISeq.prenorm.createRmd5.0830.4116.009
SAMseq.createRmd2.2180.1833.115
TCC.createRmd2.8720.2163.413
baySeq.createRmd18.284 1.16524.133
checkDataObject0.4700.0640.534
checkTableConsistency1.7470.1641.918
check_compData0.4650.0530.569
check_compData_results1.0900.1011.734
compData0.0060.0010.011
convertListTocompData0.0080.0010.016
convertcompDataToList11.214 3.47517.508
edgeR.GLM.createRmd1.8420.1572.012
edgeR.exact.createRmd1.1380.0871.308
generateCodeHTMLs1.1180.0961.267
generateSyntheticData0.4880.0430.533
listcreateRmd0.0120.0010.013
logcpm.limma.createRmd0.8590.0820.948
runComparison4.0850.3194.504
runComparisonGUI0.0020.0010.002
runDiffExp1.1160.1082.040
show-compData-method11.525 3.32017.299
sqrtcpm.limma.createRmd0.8420.0860.936
summarizeSyntheticDataSet2.1820.1612.402
ttest.createRmd0.8750.0750.951
voom.limma.createRmd1.1710.0982.124
voom.ttest.createRmd0.9140.0761.016
vst.limma.createRmd1.4480.1121.567
vst.ttest.createRmd1.1300.1111.258