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BioC 3.2: CHECK report for beadarraySNP on perceval

This page was generated on 2015-10-27 17:33:19 -0400 (Tue, 27 Oct 2015).

Package 80/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
beadarraySNP 1.36.0
Jan Oosting
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/beadarraySNP
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: beadarraySNP
Version: 1.36.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings beadarraySNP_1.36.0.tar.gz
StartedAt: 2015-10-27 05:40:36 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 05:42:15 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 99.2 seconds
RetCode: 0
Status:  OK 
CheckDir: beadarraySNP.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings beadarraySNP_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/beadarraySNP.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.36.0’
* 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 ... [8s/8s] 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:
  ‘aCGH’ ‘affy’ ‘beadarray’ ‘DNAcopy’ ‘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 ... [8s/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

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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
GenomicReports3.1560.1193.632
PolarTransforms0.0170.0010.019
SnpSetSegments-class0.0030.0000.003
backgroundCorrect.SNP0.0010.0000.001
calculateQCarray0.0000.0000.001
compareGenotypes0.0060.0010.008
dist.GT0.0520.0040.057
heterozygosity0.0230.0010.050
heterozygousSNPs0.0640.0020.065
normalizeBetweenAlleles.SNP0.0660.0040.071
normalizeBetweenSubsamples.SNP0.0580.0030.062
normalizeLoci.SNP0.0240.0020.026
normalizeWithinArrays.SNP0.0190.0030.024
pdfChromosomesSmoothCopyNumber0.0010.0000.001
plotQC0.0070.0020.009
read.SnpSetIllumina0.9570.0140.972
removeLowQualitySamples0.0280.0050.033
reportSamplePanelQC-methods0.0100.0020.012
standardNormalization0.1030.0030.107