BioC 3.6: CHECK report for PureCN on malbec1

Package: PureCN

Version: 1.7.44

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings PureCN_1.7.44.tar.gz

StartedAt: 2017-08-16 01:34:56 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:50:03 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 906.6 seconds

RetCode: 0

Status:  OK

CheckDir: PureCN.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings PureCN_1.7.44.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/PureCN.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.7.44’
* 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  6.1Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.9Mb
* 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 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   146.096  0.088 146.213
runAbsoluteCN        30.228  0.012  30.042
filterTargets        28.076  0.008  27.967
findFocal            18.856  0.008  18.757
correctCoverageBias  17.584  0.004  17.600
segmentationCBS      15.812  0.000  15.703
findBestNormal        9.148  0.000   9.150
annotateTargets       7.112  0.076   7.196
* 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
  ‘/home/biocbuild/bbs-3.6-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
annotateTargets	7.112	0.076	7.196
bootstrapResults	0.460	0.008	0.470
calculateBamCoverageByInterval	0.396	0.004	0.401
calculateGCContentByInterval	0.412	0.004	0.416
calculateLogRatio	0.868	0.012	0.884
calculatePowerDetectSomatic	1.728	0.000	1.733
callAlterations	0.144	0.000	0.143
callAlterationsFromSegmentation	1.812	0.008	1.775
callLOH	0.200	0.000	0.199
callMutationBurden	1.276	0.000	1.279
centromeres	0.000	0.004	0.002
correctCoverageBias	17.584	0.004	17.600
createCurationFile	0.388	0.000	0.388
createNormalDatabase	2.24	0.00	2.24
createTargetWeights	1.376	0.000	1.377
filterTargets	28.076	0.008	27.967
filterVcfBasic	1.34	0.00	1.34
filterVcfMuTect	0.392	0.000	0.392
filterVcfMuTect2	0.416	0.000	0.417
findBestNormal	9.148	0.000	9.150
findFocal	18.856	0.008	18.757
getSexFromCoverage	0.304	0.000	0.305
getSexFromVcf	0.176	0.000	0.175
plotAbs	0.740	0.000	0.743
plotBestNormal	2.736	0.000	2.738
poolCoverage	2.736	0.008	2.745
predictSomatic	0.424	0.012	0.437
readCoverageFile	0.312	0.004	0.316
readCurationFile	0.264	0.004	0.266
runAbsoluteCN	30.228	0.012	30.042
segmentationCBS	15.812	0.000	15.703
segmentationPSCBS	146.096	0.088	146.213
setMappingBiasVcf	0.164	0.000	0.165
setPriorVcf	0.148	0.000	0.148