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BioC 2.12: CHECK report for HiTC on petty

This page was generated on 2013-10-09 09:40:10 -0700 (Wed, 09 Oct 2013).

Package 315/671HostnameOS / ArchBUILDCHECKBUILD BIN
HiTC 1.4.0
Nicolas Servant
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/HiTC
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: HiTC
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HiTC_1.4.0.tar.gz
StartedAt: 2013-10-08 22:45:29 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 22:52:12 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 402.8 seconds
RetCode: 0
Status:  OK 
CheckDir: HiTC.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/HiTC.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'HiTC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HiTC' version '1.4.0'
* 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 'HiTC' can be installed ... [27s/28s] OK
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... OK
* 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 examples ... [121s/123s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
mapC              20.963  1.718  23.037
HTCexp-class      18.867  0.608  19.669
CQC               18.625  0.256  19.400
getExpectedCounts 15.742  0.717  16.737
intervalsDist      9.052  0.465   9.607
binningC           6.358  0.193   6.647
pca.hic            6.137  0.032   6.215
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

HiTC.Rcheck/00install.out:

* installing *source* package 'HiTC' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'HiTC'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (HiTC)

HiTC.Rcheck/HiTC-Ex.timings:

nameusersystemelapsed
CQC18.625 0.25619.400
HTCexp-class18.867 0.60819.669
HTClist-class0.0020.0040.008
Nora_5C0.7620.0240.793
binningC6.3580.1936.647
discretize0.0030.0070.011
export.my5C0.0030.0050.008
exportC0.0110.0080.018
extractRegion0.8540.0190.894
getExpectedCounts15.742 0.71716.737
import.my5C1.0300.0511.106
importC0.0040.0070.011
intervalsDist9.0520.4659.607
mapC20.963 1.71823.037
pca.hic6.1370.0326.215
removeIntervals0.6810.0150.703
setIntervalScale3.6930.0483.793