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BioC 3.3: CHECK report for arrayQualityMetrics on moscato2

This page was generated on 2016-10-13 12:48:21 -0700 (Thu, 13 Oct 2016).

Package 59/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
arrayQualityMetrics 3.28.2
Audrey Kauffmann
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/arrayQualityMetrics
Last Changed Rev: 117513 / Revision: 122332
Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: arrayQualityMetrics
Version: 3.28.2
Command: rm -rf arrayQualityMetrics.buildbin-libdir arrayQualityMetrics.Rcheck && mkdir arrayQualityMetrics.buildbin-libdir arrayQualityMetrics.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=arrayQualityMetrics.buildbin-libdir arrayQualityMetrics_3.28.2.tar.gz >arrayQualityMetrics.Rcheck\00install.out 2>&1 && cp arrayQualityMetrics.Rcheck\00install.out arrayQualityMetrics-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=arrayQualityMetrics.buildbin-libdir --install="check:arrayQualityMetrics-install.out" --force-multiarch --no-vignettes --timings arrayQualityMetrics_3.28.2.tar.gz
StartedAt: 2016-10-13 01:01:59 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 01:07:27 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 328.0 seconds
RetCode: 0
Status:  OK  
CheckDir: arrayQualityMetrics.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   rm -rf arrayQualityMetrics.buildbin-libdir arrayQualityMetrics.Rcheck && mkdir arrayQualityMetrics.buildbin-libdir arrayQualityMetrics.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=arrayQualityMetrics.buildbin-libdir arrayQualityMetrics_3.28.2.tar.gz >arrayQualityMetrics.Rcheck\00install.out 2>&1 && cp arrayQualityMetrics.Rcheck\00install.out arrayQualityMetrics-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=arrayQualityMetrics.buildbin-libdir --install="check:arrayQualityMetrics-install.out" --force-multiarch --no-vignettes --timings arrayQualityMetrics_3.28.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/arrayQualityMetrics.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 'arrayQualityMetrics/DESCRIPTION' ... OK
* this is package 'arrayQualityMetrics' version '3.28.2'
* 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 'arrayQualityMetrics' 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
aqm.outliers : bp: no visible global function definition for 'par'
aqm.outliers : bp: no visible global function definition for 'segments'
aqm.outliers : bp: no visible global function definition for 'abline'
aqm.outliers : bp: no visible global function definition for 'text'
aqm.pca: no visible global function definition for 'prcomp'
aqm.pca: no visible global function definition for 'na.omit'
aqm.pmmm : PMMM: no visible global function definition for 'lines'
aqm.probesmap: no visible binding for global variable 'hasTarget'
outliers: no visible global function definition for 'ecdf'
outliers : <anonymous>: no visible global function definition for
  'ks.test'
Undefined global functions or variables:
  abline ecdf hasTarget ks.test lines na.omit par prcomp segments text
Consider adding
  importFrom("graphics", "abline", "lines", "par", "segments", "text")
  importFrom("stats", "ecdf", "ks.test", "na.omit", "prcomp")
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 ... NONE
* 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
  'E:/biocbld/bbs-3.3-bioc/meat/arrayQualityMetrics.Rcheck/00check.log'
for details.


arrayQualityMetrics.Rcheck/00install.out:


install for i386

* installing *source* package 'arrayQualityMetrics' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'boxplot' from package 'graphics' in package 'affyPLM'
Creating a generic function for 'hist' from package 'graphics' in package 'affyPLM'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'boxplot' from package 'graphics' in package 'affyPLM'
Creating a generic function for 'hist' from package 'graphics' in package 'affyPLM'

install for x64

* installing *source* package 'arrayQualityMetrics' ...
** testing if installed package can be loaded
Creating a generic function for 'boxplot' from package 'graphics' in package 'affyPLM'
Creating a generic function for 'hist' from package 'graphics' in package 'affyPLM'
* MD5 sums
packaged installation of 'arrayQualityMetrics' as arrayQualityMetrics_3.28.2.zip
* DONE (arrayQualityMetrics)