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BioC 2.13: CHECK report for CNVrd2 on zin1

This page was generated on 2014-04-05 09:48:55 -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: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings CNVrd2_1.0.0.tar.gz
StartedAt: 2014-04-05 00:28:29 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 00:31:44 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 195.0 seconds
RetCode: 0
Status:  OK 
CheckDir: CNVrd2.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/CNVrd2.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (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 ... [19s/19s] 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’ ‘Rsamtools’ ‘VariantAnnotation’ ‘ggplot2’ ‘gridExtra’
  ‘methods’ ‘rjags’
  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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [17s/18s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
calculateLDSNPandCNV 5.54  1.396   7.522
* 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
  ‘/home/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-class0.0040.0000.006
calculateLDSNPandCNV5.5401.3967.522
clusteringCNVs-class0.0040.0000.004
countReadInWindow-methods0.0040.0000.001
countReadInWindow0.0000.0040.004
emnormalCNV0.1080.0200.128
groupBayesianCNVs0.0080.0040.012
groupCNVs0.1120.0040.116
identifyPolymorphicRegion0.0040.0000.003
plotCNVrd20.0480.0040.051
plotPolymorphicRegion0.0000.0040.003
segmentSamples0.0080.0000.008