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BioC 2.12: CHECK report for HiTC on george2

This page was generated on 2013-10-09 09:37:52 -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: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings HiTC_1.4.0.tar.gz
StartedAt: 2013-10-09 02:33:05 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 02:40:16 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 431.0 seconds
RetCode: 0
Status:  OK 
CheckDir: HiTC.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/HiTC.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... [29s/29s] 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [127s/128s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
mapC              22.314  1.696  24.210
HTCexp-class      22.837  0.168  23.089
CQC               22.750  0.188  23.127
getExpectedCounts 16.521  0.168  16.833
intervalsDist      7.912  0.236   8.253
binningC           5.081  0.012   5.095
* 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
CQC22.750 0.18823.127
HTCexp-class22.837 0.16823.089
HTClist-class0.0240.0000.024
Nora_5C0.6960.0040.700
binningC5.0810.0125.095
discretize0.0000.0120.011
export.my5C0.0040.0080.010
exportC0.0200.0040.023
extractRegion0.7720.0040.775
getExpectedCounts16.521 0.16816.833
import.my5C1.1360.0001.283
importC0.0080.0000.009
intervalsDist7.9120.2368.253
mapC22.314 1.69624.210
pca.hic4.760.004.79
removeIntervals0.4200.0040.424
setIntervalScale3.4040.0123.423