BioC 3.3: CHECK report for PureCN on zin2

Package: PureCN

Version: 1.0.4

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings PureCN_1.0.4.tar.gz

StartedAt: 2016-10-13 05:31:15 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 05:37:41 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 385.9 seconds

RetCode: 0

Status:  OK

CheckDir: PureCN.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings PureCN_1.0.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/PureCN.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PureCN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PureCN’ version ‘1.0.4’
* 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 ‘PureCN’ can be installed ... 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
segmentationPSCBS 103.103  0.203 103.493
runAbsoluteCN      27.645  0.004  27.692
findFocal          27.202  0.036  27.221
segmentationCBS    21.652  0.004  21.651
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: OK

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

name	user	system	elapsed
chr.hash	0.003	0.000	0.003
correctCoverageBias	0.472	0.016	0.488
createCurationFile	0.237	0.004	0.243
createExonWeightFile	0.803	0.011	0.816
createNormalDatabase	1.115	0.004	1.120
createSNPBlacklist	0.001	0.000	0.000
filterVcfBasic	0.814	0.008	0.825
filterVcfMuTect	0.350	0.016	0.365
findBestNormal	1.172	0.024	1.195
findFocal	27.202	0.036	27.221
getSexFromCoverage	0.095	0.004	0.098
plotAbs	0.127	0.000	0.127
plotBestNormal	1.357	0.004	1.361
poolCoverage	1.393	0.004	1.396
predictSomatic	0.103	0.008	0.110
readCoverageGatk	0.113	0.004	0.117
readCurationFile	0.162	0.004	0.165
runAbsoluteCN	27.645	0.004	27.692
segmentationCBS	21.652	0.004	21.651
segmentationPSCBS	103.103	0.203	103.493
setPriorVcf	0.146	0.008	0.154