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BioC 3.2: CHECK report for compcodeR on zin1

This page was generated on 2016-04-23 10:13:47 -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: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings compcodeR_1.6.0.tar.gz
StartedAt: 2016-04-22 23:29:41 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 23:33:59 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 257.4 seconds
RetCode: 0
Status:  OK 
CheckDir: compcodeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings compcodeR_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/compcodeR.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (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 ... [3s/3s] 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 ... [220s/220s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
DESeq.nbinom.createRmd 84.616  0.304  85.146
NBPSeq.createRmd       57.590  0.163  57.863
EBSeq.createRmd        11.931  0.152  12.091
DESeq.GLM.createRmd    10.644  0.364  10.934
show-compData-method    6.682  0.172   6.814
convertcompDataToList   6.612  0.165   6.730
baySeq.createRmd        5.921  0.248   6.119
DESeq2.createRmd        5.706  0.374   6.019
* 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
  ‘/home/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.createRmd10.644 0.36410.934
DESeq.nbinom.createRmd84.616 0.30485.146
DESeq2.createRmd5.7060.3746.019
DSS.createRmd1.5390.1011.626
EBSeq.createRmd11.931 0.15212.091
NBPSeq.createRmd57.590 0.16357.863
NOISeq.prenorm.createRmd3.9510.2774.177
SAMseq.createRmd1.4110.0881.515
TCC.createRmd2.5450.1002.678
baySeq.createRmd5.9210.2486.119
checkDataObject0.2870.0320.316
checkTableConsistency1.2290.1111.329
check_compData0.3090.0120.318
check_compData_results0.6700.0820.746
compData0.0040.0000.003
convertListTocompData0.0010.0040.006
convertcompDataToList6.6120.1656.730
edgeR.GLM.createRmd1.4950.0871.569
edgeR.exact.createRmd0.7990.0760.868
generateCodeHTMLs0.6840.0560.741
generateSyntheticData0.3000.0320.328
listcreateRmd0.0090.0000.009
logcpm.limma.createRmd0.5810.0490.623
runComparison3.0620.2143.254
runComparisonGUI0.0010.0000.001
runDiffExp0.7320.0610.784
show-compData-method6.6820.1726.814
sqrtcpm.limma.createRmd0.5000.0500.545
summarizeSyntheticDataSet1.4840.0521.524
ttest.createRmd0.5240.0550.573
voom.limma.createRmd0.6480.0970.738
voom.ttest.createRmd0.5320.0810.608
vst.limma.createRmd0.7840.0730.850
vst.ttest.createRmd0.7290.0600.782