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BioC experimental data: CHECK report for MAQCsubset on perceval

This page was generated on 2015-08-22 17:44:36 -0700 (Sat, 22 Aug 2015).

Package 152/246HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MAQCsubset 1.7.0
VJ Carey
Snapshot Date: 2015-08-22 06:15:25 -0700 (Sat, 22 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/MAQCsubset
Last Changed Rev: 3281 / Revision: 3391
Last Changed Date: 2015-04-16 13:20:43 -0700 (Thu, 16 Apr 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
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 

Summary

Package: MAQCsubset
Version: 1.7.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MAQCsubset_1.7.0.tar.gz
StartedAt: 2015-08-22 09:36:45 -0700 (Sat, 22 Aug 2015)
EndedAt: 2015-08-22 09:44:27 -0700 (Sat, 22 Aug 2015)
EllapsedTime: 462.5 seconds
RetCode: 0
Status:  OK 
CheckDir: MAQCsubset.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MAQCsubset_1.7.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-data-experiment/meat/MAQCsubset.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 ‘MAQCsubset/DESCRIPTION’ ... OK
* this is package ‘MAQCsubset’ version ‘1.7.0’
* 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 ‘MAQCsubset’ can be installed ... [34s/43s] OK
* checking installed package size ... NOTE
  installed size is 64.4Mb
  sub-directories of 1Mb or more:
    data  64.1Mb
* 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 ‘genefilter’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘affy’ ‘Biobase’ ‘lumi’ ‘methods’
  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
proboscis: no visible global function definition for ‘rowttests’
proboscis: no visible global function definition for ‘exprs’
* 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 ... [25s/32s] 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-data-experiment/meat/MAQCsubset.Rcheck/00check.log’
for details.


MAQCsubset.Rcheck/00install.out:

* installing *source* package ‘MAQCsubset’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
Creating a generic function for ‘lines’ from package ‘graphics’ in package ‘MAQCsubset’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
* DONE (MAQCsubset)

MAQCsubset.Rcheck/MAQCsubset-Ex.timings:

nameusersystemelapsed
MAQCsubset1.7080.0702.252
gehMAQCsubDef0.4120.0290.537
gnfCerebHi0.0110.0010.012
proboStruct-class3.2290.0914.203
proboscis2.1820.1062.924