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BioC 3.0: CHECK report for iPAC on perceval

This page was generated on 2015-04-10 09:57:10 -0700 (Fri, 10 Apr 2015).

Package 463/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iPAC 1.10.0
Gregory Ryslik
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/iPAC
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: iPAC
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch iPAC_1.10.0.tar.gz
StartedAt: 2015-04-10 02:56:24 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 03:06:00 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 575.4 seconds
RetCode: 0
Status:  OK 
CheckDir: iPAC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch iPAC_1.10.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/iPAC.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 ‘iPAC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iPAC’ version ‘1.10.0’
* 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 ‘iPAC’ can be installed ... [16s/17s] 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Biostrings’ ‘gdata’ ‘multtest’ ‘scatterplot3d’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
get.AlignedPositions: no visible global function definition for
  ‘PhredQuality’
get.AlignedPositions: no visible global function definition for
  ‘pairwiseAlignment’
nmc: no visible global function definition for ‘mt.rawp2adjp’
plotLinear: no visible global function definition for ‘scatterplot3d’
plotMDS: no visible global function definition for ‘scatterplot3d’
* 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 ... [428s/433s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
ClusterFind          214.267  0.631 215.787
get.Positions        121.402  7.400 130.801
nmc                   43.759  0.076  43.921
Plot.Protein.Linear   19.316  0.334  20.177
get.AlignedPositions   6.664  0.404   7.576
get.Remapped.Order     5.314  0.456   6.285
* 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 were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/iPAC.Rcheck/00check.log’
for details.

iPAC.Rcheck/00install.out:

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

iPAC.Rcheck/iPAC-Ex.timings:

nameusersystemelapsed
ClusterFind214.267 0.631215.787
KRAS.Mutations0.0060.0070.014
PIK3CA.Mutations0.0250.0360.061
Plot.Protein.Linear19.316 0.33420.177
get.AASeq0.0020.0010.163
get.AlignedPositions6.6640.4047.576
get.Positions121.402 7.400130.801
get.Remapped.Order5.3140.4566.285
get.SingleLetterCode0.0010.0000.001
iPAC-package0.0010.0010.001
nmc43.759 0.07643.921