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: 2017-08-16 06:51:12 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 07:07:07 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 955.4 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 3.4.1 (2017-06-30)
* 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   144.826  0.697 149.227
runAbsoluteCN        32.776  0.807  32.427
filterTargets        29.428  0.356  30.127
findFocal            20.673  0.269  20.976
segmentationCBS      17.664  0.256  17.993
correctCoverageBias  13.284  0.189  13.899
findBestNormal        9.936  0.041  10.331
* 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	1.197	0.037	1.285
calculateBamCoverageByInterval	0.310	0.024	0.337
calculateGCContentByInterval	0.349	0.018	0.374
calculateLogRatio	0.849	0.012	0.886
calculatePowerDetectSomatic	1.633	0.006	1.676
callAlterations	0.122	0.007	0.128
callAlterationsFromSegmentation	0.830	0.038	0.810
callLOH	0.165	0.005	0.183
centromeres	0.001	0.002	0.004
correctCoverageBias	13.284	0.189	13.899
createCurationFile	0.322	0.011	0.346
createNormalDatabase	1.692	0.005	1.743
createSNPBlacklist	0.000	0.000	0.001
createTargetWeights	1.106	0.006	1.152
filterTargets	29.428	0.356	30.127
filterVcfBasic	0.766	0.008	0.814
filterVcfMuTect	0.456	0.003	0.471
findBestNormal	9.936	0.041	10.331
findFocal	20.673	0.269	20.976
getSexFromCoverage	0.198	0.002	0.200
getSexFromVcf	0.227	0.008	0.242
plotAbs	1.021	0.013	1.077
plotBestNormal	2.369	0.013	2.465
poolCoverage	2.245	0.009	2.337
predictSomatic	0.344	0.010	0.378
readCoverageFile	0.220	0.001	0.226
readCurationFile	0.211	0.013	0.238
runAbsoluteCN	32.776	0.807	32.427
segmentationCBS	17.664	0.256	17.993
segmentationPSCBS	144.826	0.697	149.227
setMappingBiasVcf	0.207	0.010	0.218
setPriorVcf	0.186	0.003	0.195