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BioC 2.13: CHECK report for CNVrd2 on perceval

This page was generated on 2014-04-05 09:53:18 -0700 (Sat, 05 Apr 2014).

Package 160/750HostnameOS / ArchBUILDCHECKBUILD BIN
CNVrd2 1.0.0
Hoang Tan Nguyen
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/CNVrd2
Last Changed Rev: 88131 / Revision: 88450
Last Changed Date: 2014-03-29 00:39:09 -0700 (Sat, 29 Mar 2014)
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: CNVrd2
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CNVrd2_1.0.0.tar.gz
StartedAt: 2014-04-05 00:31:30 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 00:37:42 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 371.7 seconds
RetCode: 0
Status:  OK 
CheckDir: CNVrd2.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/CNVrd2.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNVrd2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNVrd2’ version ‘1.0.0’
* 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 ‘CNVrd2’ can be installed ... [31s/32s] 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘DNAcopy’ ‘ggplot2’ ‘gridExtra’ ‘methods’ ‘rjags’ ‘Rsamtools’
  ‘VariantAnnotation’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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 ... OK
* 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 ... [35s/40s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
calculateLDSNPandCNV 10.872   4.95   16.97
* 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 was 1 note.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/CNVrd2.Rcheck/00check.log’
for details.

CNVrd2.Rcheck/00install.out:

* installing *source* package ‘CNVrd2’ ...
** 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 (CNVrd2)

CNVrd2.Rcheck/CNVrd2-Ex.timings:

nameusersystemelapsed
CNVrd2-class0.5210.0040.627
calculateLDSNPandCNV10.872 4.95016.970
clusteringCNVs-class0.0110.0140.025
countReadInWindow-methods0.0020.0040.007
countReadInWindow0.0040.0070.010
emnormalCNV0.1610.0130.189
groupBayesianCNVs0.0210.0320.054
groupCNVs0.1380.0100.150
identifyPolymorphicRegion0.0030.0050.008
plotCNVrd20.0670.0230.092
plotPolymorphicRegion0.0050.0090.015
segmentSamples0.0100.0060.017