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BioC 3.0: CHECK report for beadarraySNP on moscato1

This page was generated on 2015-04-10 09:44:24 -0700 (Fri, 10 Apr 2015).

Package 74/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
beadarraySNP 1.32.0
Jan Oosting
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/beadarraySNP
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: beadarraySNP
Version: 1.32.0
Command: rm -rf beadarraySNP.buildbin-libdir beadarraySNP.Rcheck && mkdir beadarraySNP.buildbin-libdir beadarraySNP.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=beadarraySNP.buildbin-libdir beadarraySNP_1.32.0.tar.gz >beadarraySNP.Rcheck\00install.out 2>&1 && cp beadarraySNP.Rcheck\00install.out beadarraySNP-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=beadarraySNP.buildbin-libdir --install="check:beadarraySNP-install.out" --force-multiarch --no-vignettes --timings beadarraySNP_1.32.0.tar.gz
StartedAt: 2015-04-09 22:52:24 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 22:53:55 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 90.7 seconds
RetCode: 0
Status:  OK  
CheckDir: beadarraySNP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf beadarraySNP.buildbin-libdir beadarraySNP.Rcheck && mkdir beadarraySNP.buildbin-libdir beadarraySNP.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=beadarraySNP.buildbin-libdir beadarraySNP_1.32.0.tar.gz >beadarraySNP.Rcheck\00install.out 2>&1 && cp beadarraySNP.Rcheck\00install.out beadarraySNP-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=beadarraySNP.buildbin-libdir --install="check:beadarraySNP-install.out" --force-multiarch --no-vignettes --timings beadarraySNP_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/beadarraySNP.Rcheck'
* using R version 3.1.3 (2015-03-09)
* 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 '1.32.0'
* 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
** 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 ... NOTE
'library' or 'require' calls in package code:
  'DNAcopy' 'aCGH' 'affy' 'beadarray' 'limma' 'snapCGH'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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
backgroundCorrect.SNP: no visible global function definition for
  'normexp.fit'
backgroundCorrect.SNP: no visible global function definition for
  'normexp.signal'
backgroundCorrect.SNP: no visible binding for global variable
  'bg.adjust'
convert2aCGH: no visible global function definition for 'create.aCGH'
normalizeBetweenAlleles.SNP: no visible global function definition for
  'normalizeQuantiles'
normalizeBetweenSubsamples.SNP: no visible global function definition
  for 'normalizeQuantiles'
read.SnpSetIllumina: no visible global function definition for
  'readIllumina'
read.SnpSetIllumina: no visible global function definition for
  'summarize'
segmentate: no visible global function definition for 'smooth.CNA'
segmentate: no visible global function definition for 'CNA'
segmentate.old: no visible global function definition for 'runDNAcopy'
segmentate.old: no visible global function definition for 'runHomHMM'
segmentate.old: no visible global function definition for 'runBioHMM'
segmentate.old: no visible global function definition for 'runGLAD'
segmentate.old: no visible global function definition for 'mergeStates'
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [7s] OK
** running examples for arch 'x64' ... [9s] 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

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-3.0-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_1.32.0.zip
* DONE (beadarraySNP)

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

nameusersystemelapsed
GenomicReports3.100.053.42
PolarTransforms0.010.000.02
SnpSetSegments-class000
backgroundCorrect.SNP000
calculateQCarray000
compareGenotypes000
dist.GT0.030.010.05
heterozygosity0.020.000.02
heterozygousSNPs0.050.000.05
normalizeBetweenAlleles.SNP0.040.000.04
normalizeBetweenSubsamples.SNP0.030.000.03
normalizeLoci.SNP0.020.000.02
normalizeWithinArrays.SNP0.010.000.01
pdfChromosomesSmoothCopyNumber000
plotQC0.020.000.02
read.SnpSetIllumina1.860.001.86
removeLowQualitySamples0.030.000.03
reportSamplePanelQC-methods000
standardNormalization0.090.000.09

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

nameusersystemelapsed
GenomicReports3.860.014.13
PolarTransforms0.020.000.02
SnpSetSegments-class000
backgroundCorrect.SNP000
calculateQCarray000
compareGenotypes000
dist.GT0.030.020.05
heterozygosity0.030.000.03
heterozygousSNPs0.080.000.14
normalizeBetweenAlleles.SNP0.070.000.08
normalizeBetweenSubsamples.SNP0.030.000.03
normalizeLoci.SNP0.030.000.03
normalizeWithinArrays.SNP0.030.000.03
pdfChromosomesSmoothCopyNumber000
plotQC000
read.SnpSetIllumina1.750.011.76
removeLowQualitySamples0.010.000.02
reportSamplePanelQC-methods0.020.000.02
standardNormalization0.090.000.09