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BioC 3.4: CHECK report for iCheck on moscato1

This page was generated on 2016-09-21 03:47:38 -0700 (Wed, 21 Sep 2016).

Package 597/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iCheck 1.3.0
Weiliang Qiu
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/iCheck
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: iCheck
Version: 1.3.0
Command: rm -rf iCheck.buildbin-libdir iCheck.Rcheck && mkdir iCheck.buildbin-libdir iCheck.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=iCheck.buildbin-libdir iCheck_1.3.0.tar.gz >iCheck.Rcheck\00install.out 2>&1 && cp iCheck.Rcheck\00install.out iCheck-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=iCheck.buildbin-libdir --install="check:iCheck-install.out" --force-multiarch --no-vignettes --timings iCheck_1.3.0.tar.gz
StartedAt: 2016-09-20 10:29:17 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 10:35:03 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 346.0 seconds
RetCode: 0
Status:  OK  
CheckDir: iCheck.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf iCheck.buildbin-libdir iCheck.Rcheck && mkdir iCheck.buildbin-libdir iCheck.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=iCheck.buildbin-libdir iCheck_1.3.0.tar.gz >iCheck.Rcheck\00install.out 2>&1 && cp iCheck.Rcheck\00install.out iCheck-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=iCheck.buildbin-libdir --install="check:iCheck-install.out" --force-multiarch --no-vignettes --timings iCheck_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/iCheck.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'iCheck/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iCheck' version '1.3.0'
* 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 'iCheck' can be installed ... 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
* 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
** checking loading without being on the library search path ... 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 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
LumiBatch2Table: no visible global function definition for
  'write.table'
myCombineIntersect: no visible global function definition for
  'capture.output'
myCombineIntersect: no visible global function definition for
  'packageDescription'
myCombineUnion: no visible global function definition for
  'capture.output'
myCombineUnion: no visible global function definition for
  'packageDescription'
readbgx: no visible global function definition for 'read.delim'
readbgx2: no visible global function definition for 'read.delim'
Undefined global functions or variables:
  capture.output packageDescription read.delim write.table
Consider adding
  importFrom("utils", "capture.output", "packageDescription",
             "read.delim", "write.table")
to your NAMESPACE file.
* 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' ... OK
** running examples for arch 'x64' ... 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: 1 NOTE
See
  'D:/biocbld/bbs-3.4-bioc/meat/iCheck.Rcheck/00check.log'
for details.


iCheck.Rcheck/00install.out:


install for i386

* installing *source* package 'iCheck' ...
** 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 'iCheck' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iCheck' as iCheck_1.3.0.zip
* DONE (iCheck)

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

nameusersystemelapsed
LumiBatch2Table0.110.000.20
R2PlotFunc0.200.010.22
genSimData.BayesNormal0.030.000.03
getPCAFunc0.060.000.07
glmWrapper0.750.000.75
lkhrWrapper0.530.020.54
lmFitPaired0.060.000.06
lmFitWrapper0.050.000.05
pca2DPlot0.060.000.06
pca3DPlot0.060.000.07
plotCurves0.050.000.04
plotQCCurves0.080.000.08
plotSamplep95p050.070.000.08
quantilePlot0.080.000.08
sortExpressionSet0.060.000.06

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

nameusersystemelapsed
LumiBatch2Table0.190.000.22
R2PlotFunc0.570.010.59
genSimData.BayesNormal0.050.000.05
getPCAFunc0.060.000.06
glmWrapper0.550.000.54
lkhrWrapper0.700.000.71
lmFitPaired0.060.000.06
lmFitWrapper0.060.000.07
pca2DPlot0.060.000.06
pca3DPlot0.080.000.08
plotCurves0.050.000.04
plotQCCurves0.100.000.09
plotSamplep95p050.080.000.08
quantilePlot0.090.000.10
sortExpressionSet0.080.000.07