BioC 3.5: CHECK report for PureCN on veracruz2

Package: PureCN

Version: 1.6.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PureCN_1.6.3.tar.gz

StartedAt: 2017-10-18 07:38:34 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 07:55:26 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 1012.3 seconds

RetCode: 0

Status:  OK

CheckDir: PureCN.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PureCN_1.6.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/PureCN.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.6.3’
* 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 ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.7Mb
* 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   144.998  1.255 150.270
runAbsoluteCN        34.101  0.575  34.541
filterTargets        31.400  0.467  32.001
findFocal            21.112  0.419  21.247
segmentationCBS      18.673  0.422  18.721
correctCoverageBias  13.997  0.208  14.623
findBestNormal       10.181  0.069  10.523
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/PureCN.Rcheck/00check.log’
for details.

* installing *source* package ‘PureCN’ ...
** R
** data
** inst
** byte-compile and prepare 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
bootstrapResults	1.339	0.044	1.428
calculateBamCoverageByInterval	0.367	0.031	0.414
calculateGCContentByInterval	0.409	0.023	0.453
calculateLogRatio	1.015	0.017	1.063
calculatePowerDetectSomatic	1.854	0.013	1.920
callAlterations	0.118	0.008	0.129
callAlterationsFromSegmentation	1.009	0.063	0.898
callLOH	0.181	0.007	0.192
centromeres	0.002	0.003	0.005
correctCoverageBias	13.997	0.208	14.623
createCurationFile	0.319	0.012	0.344
createNormalDatabase	1.776	0.011	1.833
createSNPBlacklist	0.001	0.000	0.001
createTargetWeights	1.188	0.010	1.225
filterTargets	31.400	0.467	32.001
filterVcfBasic	0.914	0.013	0.954
filterVcfMuTect	0.493	0.005	0.509
findBestNormal	10.181	0.069	10.523
findFocal	21.112	0.419	21.247
getSexFromCoverage	0.191	0.002	0.201
getSexFromVcf	0.269	0.009	0.289
plotAbs	0.971	0.013	1.014
plotBestNormal	2.455	0.022	2.554
poolCoverage	2.920	0.026	3.039
predictSomatic	0.328	0.007	0.344
readCoverageFile	0.224	0.003	0.237
readCurationFile	0.207	0.008	0.221
runAbsoluteCN	34.101	0.575	34.541
segmentationCBS	18.673	0.422	18.721
segmentationPSCBS	144.998	1.255	150.270
setMappingBiasVcf	0.221	0.011	0.236
setPriorVcf	0.147	0.004	0.152