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BioC 3.2: CHECK report for NOISeq on oaxaca

This page was generated on 2016-04-23 10:26:12 -0700 (Sat, 23 Apr 2016).

Package 710/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NOISeq 2.14.1
Sonia Tarazona
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/NOISeq
Last Changed Rev: 113523 / Revision: 116712
Last Changed Date: 2016-02-11 04:21:24 -0800 (Thu, 11 Feb 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: NOISeq
Version: 2.14.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings NOISeq_2.14.1.tar.gz
StartedAt: 2016-04-23 02:40:15 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 02:42:45 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 150.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: NOISeq.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings NOISeq_2.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/NOISeq.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 ‘NOISeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NOISeq’ version ‘2.14.1’
* 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 ‘NOISeq’ 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Error in bibentry(bibtype = entry, textVersion = textVersion, header = header,     footer = footer, ...): object 'e140' not found
* 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... [75s/75s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
noiseq    34.378  6.253  40.676
noiseqbio 17.124  0.081  17.245
QCreport   8.001  0.426   8.438
* 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: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/NOISeq.Rcheck/00check.log’
for details.


NOISeq.Rcheck/00install.out:

* installing *source* package ‘NOISeq’ ...
** 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 (NOISeq)

NOISeq.Rcheck/NOISeq-Ex.timings:

nameusersystemelapsed
ARSyNSeq3.3550.0523.410
DE.plot0.3210.0160.344
PCA.GENES0.0130.0000.013
QCreport8.0010.4268.438
dat0.2180.0040.222
dat2save0.1710.0020.173
degenes0.0750.0020.078
explo.plot0.2110.0020.215
filter.low.counts0.9240.0020.928
noiseq34.378 6.25340.676
noiseqbio17.124 0.08117.245
normalization0.0070.0000.006
readData0.1900.0030.193