BioC 3.1: CHECK report for NOISeq on petty

Package: NOISeq

Version: 2.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings NOISeq_2.14.0.tar.gz

StartedAt: 2015-10-09 00:50:38 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:54:14 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 215.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: NOISeq.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings NOISeq_2.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/NOISeq.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘2.14.0’
* 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 ‘NOISeq’ can be installed ... [9s/9s] 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, ...): argument is missing, with no default
* 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 ... [103s/104s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
noiseq    47.555  9.166  56.761
noiseqbio 22.946  0.110  23.071
QCreport  11.421  0.238  11.666
ARSyNSeq   4.935  0.076   5.183
* 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-3.1-bioc/meat/NOISeq.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
ARSyNSeq	4.935	0.076	5.183
DE.plot	0.468	0.025	0.518
PCA.GENES	0.021	0.000	0.021
QCreport	11.421	0.238	11.666
dat	0.303	0.007	0.312
dat2save	0.225	0.001	0.230
degenes	0.123	0.002	0.125
explo.plot	0.319	0.005	0.324
filter.low.counts	1.026	0.001	1.028
noiseq	47.555	9.166	56.761
noiseqbio	22.946	0.110	23.071
normalization	0.006	0.000	0.007
readData	0.240	0.005	0.245