BioC 3.0: CHECK report for riboSeq on perceval

Package: riboSeq

Version: 0.99.14

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch riboSeq_0.99.14.tar.gz

StartedAt: 2014-09-11 02:57:50 -0700 (Thu, 11 Sep 2014)

EndedAt: 2014-09-11 03:01:46 -0700 (Thu, 11 Sep 2014)

EllapsedTime: 236.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: riboSeq.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 --no-multiarch riboSeq_0.99.14.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/riboSeq.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘riboSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘riboSeq’ version ‘0.99.14’
* 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 ‘riboSeq’ can be installed ... [14s/14s] 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 ... 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 ... WARNING
Undocumented code objects:
  ‘lengthDist’
All user-level objects in a package should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [73s/82s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
rnaCounts      11.699  0.160  11.869
plotTranscript  9.300  0.153   9.467
filterHits      9.132  0.168  12.960
frameCounting   8.335  0.113   8.524
plotCDS         8.155  0.114   8.318
sliceCounts     7.765  0.107   7.889
frameShift      7.721  0.105   7.858
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [7s/7s]
 [7s/7s] OK
* 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

WARNING: There was 1 warning.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/riboSeq.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
filterHits	9.132	0.168	12.960
findCDS	0.298	0.001	0.300
frameCounting	8.335	0.113	8.524
frameShift	7.721	0.105	7.858
plotCDS	8.155	0.114	8.318
plotTranscript	9.300	0.153	9.467
readRibodata	3.275	0.100	3.379
rnaCounts	11.699	0.160	11.869
sliceCounts	7.765	0.107	7.889