Back to the "Multiple platform build/check report" A  B  C [D] E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.1: CHECK report for dyebias on moscato2

This page was generated on 2015-10-09 09:28:30 -0700 (Fri, 09 Oct 2015).

Package 279/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dyebias 1.26.0
Philip Lijnzaad
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/dyebias
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: dyebias
Version: 1.26.0
Command: rm -rf dyebias.buildbin-libdir dyebias.Rcheck && mkdir dyebias.buildbin-libdir dyebias.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=dyebias.buildbin-libdir dyebias_1.26.0.tar.gz >dyebias.Rcheck\00install.out 2>&1 && cp dyebias.Rcheck\00install.out dyebias-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=dyebias.buildbin-libdir --install="check:dyebias-install.out" --force-multiarch --no-vignettes --timings dyebias_1.26.0.tar.gz
StartedAt: 2015-10-09 01:23:22 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 01:24:43 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 81.7 seconds
RetCode: 0
Status:  OK  
CheckDir: dyebias.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf dyebias.buildbin-libdir dyebias.Rcheck && mkdir dyebias.buildbin-libdir dyebias.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=dyebias.buildbin-libdir dyebias_1.26.0.tar.gz >dyebias.Rcheck\00install.out 2>&1 && cp dyebias.Rcheck\00install.out dyebias-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=dyebias.buildbin-libdir --install="check:dyebias-install.out" --force-multiarch --no-vignettes --timings dyebias_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/dyebias.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'dyebias/DESCRIPTION' ... OK
* this is package 'dyebias' version '1.26.0'
* 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 whether package 'dyebias' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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' calls in package code:
  'limma' 'methods'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Biobase' 'marray'
  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
.check.reporter.labels: no visible global function definition for
  'maLabels'
.check.reporter.labels: no visible global function definition for
  'maGnames'
.check.reporter.labels: no visible global function definition for
  'maNspots'
.check.slide.labels: no visible global function definition for
  'maNsamples'
.check.slide.labels: no visible global function definition for
  'maLabels'
.check.slide.labels: no visible global function definition for
  'maTargets'
.limma.to.dataframe: no visible global function definition for 'eBayes'
.merge.dyebias: no visible global function definition for 'maLabels'
.merge.dyebias: no visible global function definition for 'maGnames'
.monotonicity: no visible global function definition for 'maNsamples'
.monotonicity : <anonymous>: no visible global function definition for
  'maM'
.set.design: no visible global function definition for 'modelMatrix'
.set.design : <anonymous>: no visible global function definition for
  'modelMatrix'
.slide.bias: no visible global function definition for 'maNsamples'
.slide.bias: no visible global function definition for 'maLabels'
.slide.bias: no visible global function definition for 'maTargets'
.slide.bias: no visible global function definition for 'maM'
dyebias.application.subset: no visible global function definition for
  'maInfo'
dyebias.application.subset: no visible global function definition for
  'maTargets'
dyebias.application.subset: no visible global function definition for
  'maNspots'
dyebias.application.subset: no visible global function definition for
  'maNsamples'
dyebias.application.subset: no visible global function definition for
  'maRb'
dyebias.application.subset: no visible global function definition for
  'maGb'
dyebias.application.subset: no visible global function definition for
  'maRf'
dyebias.application.subset: no visible global function definition for
  'maGf'
dyebias.apply.correction: no visible global function definition for
  'maM'
dyebias.apply.correction: no visible global function definition for
  'maNspots'
dyebias.apply.correction: no visible global function definition for
  'maNsamples'
dyebias.apply.correction: no visible global function definition for
  'maLabels'
dyebias.apply.correction: no visible global function definition for
  'maGnames'
dyebias.apply.correction: no visible global function definition for
  'maInfo'
dyebias.apply.correction: no visible global function definition for
  'maTargets'
dyebias.apply.correction: no visible global function definition for
  'maA'
dyebias.apply.correction: no visible global function definition for
  'maM<-'
dyebias.apply.correction: no visible global function definition for
  'maA<-'
dyebias.apply.correction: no visible global function definition for
  'maR<-'
dyebias.apply.correction: no visible global function definition for
  'maG<-'
dyebias.boxplot: no visible global function definition for 'maNsamples'
dyebias.estimate.iGSDBs: no visible global function definition for
  'maLabels'
dyebias.estimate.iGSDBs: no visible global function definition for
  'maGnames'
dyebias.estimate.iGSDBs: no visible global function definition for
  'maNspots'
dyebias.estimate.iGSDBs: no visible global function definition for
  'maNsamples'
dyebias.estimate.iGSDBs: no visible global function definition for
  'maM'
dyebias.estimate.iGSDBs: no visible global function definition for
  'maA'
dyebias.estimate.iGSDBs: no visible global function definition for
  'maInfo'
dyebias.estimate.iGSDBs: no visible global function definition for
  'maTargets'
dyebias.estimate.iGSDBs: no visible global function definition for
  'lmFit'
dyebias.estimate.iGSDBs: no visible global function definition for
  'eBayes'
dyebias.maplot: no visible global function definition for 'maM'
dyebias.maplot: no visible global function definition for 'maA'
dyebias.rgplot: no visible global function definition for 'maA'
dyebias.rgplot: no visible global function definition for 'maM'
dyebias.trendplot: no visible global function definition for
  'maNsamples'
dyebias.trendplot : <anonymous>: no visible global function definition
  for 'maM'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [17s] OK
** running examples for arch 'x64' ... [18s] 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: 4 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/dyebias.Rcheck/00check.log'
for details.


dyebias.Rcheck/00install.out:


install for i386

* installing *source* package 'dyebias' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'dyebias' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'dyebias' as dyebias_1.26.0.zip
* DONE (dyebias)

dyebias.Rcheck/examples_i386/dyebias-Ex.timings:

nameusersystemelapsed
dyebias.application.subset2.290.033.51
dyebias.apply.correction2.340.022.35
dyebias.boxplot2.450.012.47
dyebias.estimate.iGSDBs1.390.031.42
dyebias.monotonicity000
dyebias.monotonicityplot000
dyebias.rgplot3.830.003.84
dyebias.trendplot2.660.042.68

dyebias.Rcheck/examples_x64/dyebias-Ex.timings:

nameusersystemelapsed
dyebias.application.subset3.060.053.10
dyebias.apply.correction2.450.012.47
dyebias.boxplot2.670.022.68
dyebias.estimate.iGSDBs1.820.001.83
dyebias.monotonicity000
dyebias.monotonicityplot000
dyebias.rgplot3.780.033.80
dyebias.trendplot2.930.022.95