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BioC 3.1: CHECK report for beadarraySNP on zin2

This page was generated on 2015-10-09 09:23:10 -0700 (Fri, 09 Oct 2015).

Package 76/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
beadarraySNP 1.34.0
Jan Oosting
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/beadarraySNP
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: beadarraySNP
Version: 1.34.0
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings beadarraySNP_1.34.0.tar.gz
StartedAt: 2015-10-08 22:41:41 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 22:42:46 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 64.4 seconds
RetCode: 0
Status:  OK 
CheckDir: beadarraySNP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings beadarraySNP_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/beadarraySNP.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘beadarraySNP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘beadarraySNP’ version ‘1.34.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘beadarraySNP’ can be installed ... [5s/5s] 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [6s/6s] 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-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
** testing if installed package can be loaded
* DONE (beadarraySNP)

beadarraySNP.Rcheck/beadarraySNP-Ex.timings:

nameusersystemelapsed
GenomicReports2.3410.0242.363
PolarTransforms0.0150.0000.016
SnpSetSegments-class0.0020.0000.001
backgroundCorrect.SNP000
calculateQCarray0.0010.0000.001
compareGenotypes0.0050.0000.005
dist.GT0.0380.0000.038
heterozygosity0.020.000.02
heterozygousSNPs0.0540.0000.054
normalizeBetweenAlleles.SNP0.0360.0000.036
normalizeBetweenSubsamples.SNP0.0240.0000.024
normalizeLoci.SNP0.0140.0000.014
normalizeWithinArrays.SNP0.0140.0040.018
pdfChromosomesSmoothCopyNumber000
plotQC0.0050.0000.006
read.SnpSetIllumina0.6260.0070.633
removeLowQualitySamples0.0190.0040.023
reportSamplePanelQC-methods0.0080.0000.008
standardNormalization0.060.000.06