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BioC 2.13: CHECK report for beadarraySNP on moscato1

This page was generated on 2014-04-05 09:49:22 -0700 (Sat, 05 Apr 2014).

Package 66/750HostnameOS / ArchBUILDCHECKBUILD BIN
beadarraySNP 1.28.0
Jan Oosting
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/beadarraySNP
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: beadarraySNP
Version: 1.28.0
Command: rm -rf beadarraySNP.buildbin-libdir && mkdir beadarraySNP.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=beadarraySNP.buildbin-libdir beadarraySNP_1.28.0.tar.gz >beadarraySNP-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=beadarraySNP.buildbin-libdir --install="check:beadarraySNP-install.out" --force-multiarch --no-vignettes --timings beadarraySNP_1.28.0.tar.gz && mv beadarraySNP.buildbin-libdir/* beadarraySNP.Rcheck/ && rmdir beadarraySNP.buildbin-libdir
StartedAt: 2014-04-05 02:25:04 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 02:26:43 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 99.0 seconds
RetCode: 0
Status:  OK  
CheckDir: beadarraySNP.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/beadarraySNP.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'beadarraySNP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'beadarraySNP' version '1.28.0'
* 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 'beadarraySNP' 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 ... NOTE
Package in Depends field not imported from: 'methods'
  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:
  'getMidMaxIdx'
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
plotQC,QCIllumina: warning in rgb(0, 0:255, 0, max = 255): partial
  argument match of 'max' to 'maxColorValue'
plotQC,QCIllumina: warning in rgb(0:255, 0, 0, max = 255): partial
  argument match of 'max' to 'maxColorValue'
reportSamplePanelQC,QCIllumina: warning in rgb(r = 0, b = 0, g =
  colstart:colend, maxColorValue = colend): partial argument match of
  'r' to 'red'
reportSamplePanelQC,QCIllumina: warning in rgb(r = 0, b = 0, g =
  colstart:colend, maxColorValue = colend): partial argument match of
  'g' to 'green'
reportSamplePanelQC,QCIllumina: warning in rgb(r = 0, b = 0, g =
  colstart:colend, maxColorValue = colend): partial argument match of
  'b' to 'blue'
reportSamplePanelQC,QCIllumina: warning in rgb(r = colstart:colend, b =
  0, g = 0, maxColorValue = colend): partial argument match of 'r' to
  'red'
reportSamplePanelQC,QCIllumina: warning in rgb(r = colstart:colend, b =
  0, g = 0, maxColorValue = colend): partial argument match of 'g' to
  'green'
reportSamplePanelQC,QCIllumina: warning in rgb(r = colstart:colend, b =
  0, g = 0, maxColorValue = colend): partial argument match of 'b' to
  'blue'
read.SnpSetIllumina: no visible global function definition for
  'createBeadSummaryData'
* 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 installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'beadarraySNP.rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [11s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
GenomicReports 4.19   0.11    5.43
** running examples for arch 'x64' ... [8s] 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

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/beadarraySNP.Rcheck/00check.log'
for details.

beadarraySNP.Rcheck/00install.out:


install for i386

* installing *source* package 'beadarraySNP' ...
** R
** data
** 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 'beadarraySNP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'beadarraySNP' as beadarraySNP_1.28.0.zip
* DONE (beadarraySNP)

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

nameusersystemelapsed
GenomicReports4.190.115.43
PolarTransforms0.030.000.03
SnpSetSegments-class0.020.000.02
backgroundCorrect.SNP000
calculateQCarray000
compareGenotypes0.010.000.02
dist.GT0.080.000.07
heterozygosity0.030.000.03
heterozygousSNPs0.080.000.08
normalizeBetweenAlleles.SNP0.050.000.05
normalizeBetweenSubsamples.SNP0.050.000.05
normalizeLoci.SNP0.030.000.03
normalizeWithinArrays.SNP0.030.000.03
pdfChromosomesSmoothCopyNumber0.010.000.02
plotQC0.020.000.01
read.SnpSetIllumina2.430.022.45
removeLowQualitySamples0.040.000.03
reportSamplePanelQC-methods0.060.000.06
standardNormalization0.130.000.12

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

nameusersystemelapsed
GenomicReports3.560.023.99
PolarTransforms0.030.000.03
SnpSetSegments-class000
backgroundCorrect.SNP0.010.000.02
calculateQCarray000
compareGenotypes0.020.000.01
dist.GT0.080.000.08
heterozygosity0.030.000.03
heterozygousSNPs0.160.000.15
normalizeBetweenAlleles.SNP0.090.000.10
normalizeBetweenSubsamples.SNP0.070.010.07
normalizeLoci.SNP0.030.020.05
normalizeWithinArrays.SNP0.120.000.13
pdfChromosomesSmoothCopyNumber000
plotQC0.020.000.02
read.SnpSetIllumina1.650.021.67
removeLowQualitySamples0.020.010.03
reportSamplePanelQC-methods0.010.000.01
standardNormalization0.10.00.1