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BioC 3.0: CHECK report for riboSeqR on perceval

This page was generated on 2015-04-10 09:59:58 -0700 (Fri, 10 Apr 2015).

Package 750/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
riboSeqR 1.0.5
Thomas J. Hardcastle
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/riboSeqR
Last Changed Rev: 102248 / Revision: 102249
Last Changed Date: 2015-04-09 16:15:26 -0700 (Thu, 09 Apr 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: riboSeqR
Version: 1.0.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch riboSeqR_1.0.5.tar.gz
StartedAt: 2015-04-10 05:44:45 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 05:48:49 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 244.0 seconds
RetCode: 0
Status:  OK 
CheckDir: riboSeqR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch riboSeqR_1.0.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/riboSeqR.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘riboSeqR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘riboSeqR’ version ‘1.0.5’
* 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 ‘riboSeqR’ can be installed ... [15s/15s] 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 ... NOTE
.readAlignments : <anonymous>: no visible global function definition
  for ‘IRanges’
.tableOverlaps: no visible global function definition for ‘seqlevels’
findCDS: no visible global function definition for ‘IRanges’
plotCDS : <anonymous> : <anonymous>: no visible global function
  definition for ‘seqlevels’
* 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 ... [76s/77s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
rnaCounts      10.256  0.147  10.507
filterHits      9.409  0.150   9.573
plotCDS         8.455  0.140   8.731
plotTranscript  8.302  0.138   8.558
frameCounting   8.321  0.115   8.436
frameShift      8.252  0.117   8.581
sliceCounts     7.506  0.103   7.668
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [7s/7s]
 [8s/8s] 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
* DONE

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/riboSeqR.Rcheck/00check.log’
for details.

riboSeqR.Rcheck/00install.out:

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

riboSeqR.Rcheck/riboSeqR-Ex.timings:

nameusersystemelapsed
filterHits9.4090.1509.573
findCDS0.2520.0020.253
frameCounting8.3210.1158.436
frameShift8.2520.1178.581
lengthDist3.4620.0973.618
plotCDS8.4550.1408.731
plotTranscript8.3020.1388.558
readRibodata3.4510.0843.548
rnaCounts10.256 0.14710.507
sliceCounts7.5060.1037.668