Package: decompTumor2Sig

Version: 1.99.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings decompTumor2Sig_1.99.1.tar.gz

StartedAt: 2019-04-09 00:20:32 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:27:23 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 410.7 seconds

RetCode: 0

Status:  OK

CheckDir: decompTumor2Sig.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings decompTumor2Sig_1.99.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/decompTumor2Sig.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘decompTumor2Sig/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decompTumor2Sig’ version ‘1.99.1’
* package encoding: UTF-8
* 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 ‘decompTumor2Sig’ 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 ... NOTE
File
  inst/LICENSE
will install at top-level and is not mentioned in the DESCRIPTION file.
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
plotExplainedVariance     100.352  0.220 104.299
convertGenomesFromVRanges   8.721  0.684   9.504
decomposeTumorGenomes       3.973  0.414   5.175
* 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-3.9-bioc/meat/decompTumor2Sig.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL decompTumor2Sig
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘decompTumor2Sig’ ...
** R
** 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 (decompTumor2Sig)

name	user	system	elapsed
composeGenomesFromExposures	0.914	0.018	1.751
computeExplainedVariance	0.272	0.009	1.097
convertAlexandrov2Shiraishi	0.080	0.003	0.892
convertGenomesFromVRanges	8.721	0.684	9.504
decomposeTumorGenomes	3.973	0.414	5.175
determineSignatureDistances	0.080	0.003	0.760
downgradeShiraishiSignatures	0.011	0.002	0.015
evaluateDecompositionQuality	0.236	0.006	0.958
getGenomesFromMutFeatData	1.515	0.011	1.539
getSignaturesFromEstParam	0.245	0.005	0.252
isAlexandrovSet	0.036	0.002	0.718
isExposureSet	3.812	0.422	4.950
isShiraishiSet	0.061	0.002	0.772
isSignatureSet	0.028	0.003	0.764
mapSignatureSets	0.138	0.003	0.875
plotDecomposedContribution	0.505	0.011	1.235
plotExplainedVariance	100.352	0.220	104.299
plotMutationDistribution	2.165	0.023	2.935
readAlexandrovSignatures	0.050	0.002	0.832
readGenomesFromMPF	3.359	0.360	3.768
readGenomesFromVCF	3.719	0.365	4.138
readShiraishiSignatures	0.005	0.000	0.006
sameSignatureFormat	0.091	0.002	0.877