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BioC 3.1: CHECK report for riboSeqR on petty

This page was generated on 2015-10-09 09:36:37 -0700 (Fri, 09 Oct 2015).

Package 822/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
riboSeqR 1.2.0
Thomas J. Hardcastle
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/riboSeqR
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: riboSeqR
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings riboSeqR_1.2.0.tar.gz
StartedAt: 2015-10-09 01:37:29 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 01:41:08 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 218.6 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 riboSeqR_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/riboSeqR.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 ‘riboSeqR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘riboSeqR’ version ‘1.2.0’
* 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 ‘riboSeqR’ can be installed ... [12s/13s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ‘scanBam’
.readAlignments : <anonymous>: no visible global function definition
  for ‘IRanges’
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 ... [81s/82s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
plotCDS        9.768  0.105  10.284
filterHits     9.584  0.124   9.712
plotTranscript 9.316  0.110   9.562
frameShift     9.303  0.091   9.412
rnaCounts      9.283  0.098   9.393
sliceCounts    9.152  0.090   9.249
frameCounting  8.855  0.090   8.952
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [6s/6s]
 [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
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/riboSeqR.Rcheck/00check.log’
for details.


riboSeqR.Rcheck/00install.out:

* installing *source* package ‘riboSeqR’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (riboSeqR)

riboSeqR.Rcheck/riboSeqR-Ex.timings:

nameusersystemelapsed
filterHits9.5840.1249.712
findCDS0.3360.0010.336
frameCounting8.8550.0908.952
frameShift9.3030.0919.412
lengthDist4.6330.0824.719
plotCDS 9.768 0.10510.284
plotTranscript9.3160.1109.562
readRibodata4.7380.0724.822
rnaCounts9.2830.0989.393
sliceCounts9.1520.0909.249