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BioC 2.13: CHECK report for sSeq on perceval

This page was generated on 2014-04-05 09:53:06 -0700 (Sat, 05 Apr 2014).

Package 691/750HostnameOS / ArchBUILDCHECKBUILD BIN
sSeq 1.0.0
Danni Yu
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/sSeq
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: sSeq
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch sSeq_1.0.0.tar.gz
StartedAt: 2014-04-05 04:37:24 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 04:44:07 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 403.1 seconds
RetCode: 0
Status:  OK 
CheckDir: sSeq.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/sSeq.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sSeq’ version ‘1.0.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘sSeq’ can be installed ... [2s/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 dependencies in R code ... NOTE
‘library’ or ‘require’ call to ‘caTools’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘caTools’ ‘RColorBrewer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘sSeq.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [367s/373s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
nbTestSH       108.863 10.586 121.407
getTgroup      107.298  8.542 117.372
sSeq-package   102.994  9.163 114.238
plotDispersion   6.301  0.750   7.204
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/sSeq.Rcheck/00check.log’
for details.

sSeq.Rcheck/00install.out:

* installing *source* package ‘sSeq’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (sSeq)

sSeq.Rcheck/sSeq-Ex.timings:

nameusersystemelapsed
Hammer2months0.0910.0080.099
Sultan0.0860.0070.092
Tuch0.0670.0070.073
countsTable0.0380.0050.043
drawMA_vol0.4440.0090.461
ecdfAUC0.0800.0050.086
equalSpace0.5270.0140.549
exactNBtest10.0040.0000.005
getAdjustDisp0.5790.0070.620
getNormFactor0.0310.0050.035
getQ4.4610.1284.645
getT3.5530.3013.908
getTgroup107.298 8.542117.372
nbTestSH108.863 10.586121.407
plotDispersion6.3010.7507.204
rnbinomMV0.0050.0040.009
rowVars0.0020.0040.006
sSeq-package102.994 9.163114.238
sim0.9750.0841.201