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Package 56/609HostnameOS / ArchBUILDCHECKBUILD BIN
beadarraySNP 1.24.0
Jan Oosting
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/beadarraySNP
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: beadarraySNP
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch beadarraySNP_1.24.0.tar.gz
StartedAt: 2013-03-24 22:39:29 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 22:40:44 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 74.5 seconds
RetCode: 0
Status:  OK 
CheckDir: beadarraySNP.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/beadarraySNP.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'beadarraySNP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'beadarraySNP' version '1.24.0'
* 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 whether package 'beadarraySNP' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 for unstated 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
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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/beadarraySNP.Rcheck/00check.log'
for details.

beadarraySNP.Rcheck/00install.out:

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

* DONE (beadarraySNP)

beadarraySNP.Rcheck/beadarraySNP-Ex.timings:

nameusersystemelapsed
GenomicReports3.8560.4724.558
PolarTransforms0.0200.0050.024
SnpSetSegments-class0.0010.0000.002
backgroundCorrect.SNP0.0000.0010.001
calculateQCarray0.0000.0000.001
compareGenotypes0.0060.0010.008
dist.GT0.0960.0140.111
heterozygosity0.0380.0020.040
heterozygousSNPs0.0950.0040.099
normalizeBetweenAlleles.SNP0.0570.0060.064
normalizeBetweenSubsamples.SNP0.0390.0050.045
normalizeLoci.SNP0.0270.0050.032
normalizeWithinArrays.SNP0.0260.0030.029
pdfChromosomesSmoothCopyNumber000
plotQC0.0060.0020.007
read.SnpSetIllumina0.7840.0180.804
removeLowQualitySamples0.0410.0040.047
reportSamplePanelQC-methods0.0110.0030.014
standardNormalization0.1070.0130.120