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BioC 2.13: CHECK report for gwascat on perceval

This page was generated on 2014-04-05 09:52:48 -0700 (Sat, 05 Apr 2014).

Package 335/750HostnameOS / ArchBUILDCHECKBUILD BIN
gwascat 1.6.0
VJ Carey
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/gwascat
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: gwascat
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch gwascat_1.6.0.tar.gz
StartedAt: 2014-04-05 01:55:39 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 02:06:19 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 640.5 seconds
RetCode: 0
Status:  OK 
CheckDir: gwascat.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/gwascat.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gwascat/DESCRIPTION’ ... OK
* this is package ‘gwascat’ version ‘1.6.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘SNPlocs.Hsapiens.dbSNP.20111119’
* 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 ‘gwascat’ can be installed ... [44s/45s] OK
* checking installed package size ... NOTE
  installed size is 23.7Mb
  sub-directories of 1Mb or more:
    data  20.4Mb
    obo    1.3Mb
    tab    1.1Mb
* 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
‘library’ or ‘require’ call to ‘graph’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘graph’ ‘methods’ ‘snpStats’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘fixNonASCII’ ‘gwdf2GRanges’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
chklocs: no visible global function definition for ‘getSNPlocs’
snpGenos: no visible global function definition for ‘getSNPlocs’
traitsManh: no visible binding for global variable ‘Pvalue_mlog’
traitsManh: no visible binding for global variable ‘Trait’
* 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 ... [69s/71s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
riskyAlleleCount 15.320  0.282  16.052
gwcex2gviz       12.582  0.548  13.376
traitsManh        5.721  0.274   6.369
* 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

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/gwascat.Rcheck/00check.log’
for details.

gwascat.Rcheck/00install.out:

* installing *source* package ‘gwascat’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
NOTE: input data had non-ASCII characters replaced by '*'.
* DONE (gwascat)

gwascat.Rcheck/gwascat-Ex.timings:

nameusersystemelapsed
gwascat-package0.0020.0050.007
gwaswloc-class0.0070.0070.014
gwcex2gviz12.582 0.54813.376
gwdf_2012_02_020.0020.0030.004
locon60.0380.0130.050
makeCurrentGwascat0.0030.0040.007
riskyAlleleCount15.320 0.28216.052
topTraits2.7080.2633.018
traitsManh5.7210.2746.369