Package: decompTumor2Sig

Version: 1.99.1

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings decompTumor2Sig_1.99.1.tar.gz

StartedAt: 2019-04-08 23:54:05 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-09 00:00:29 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 384.4 seconds

RetCode: 0

Status:  OK

CheckDir: decompTumor2Sig.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings decompTumor2Sig_1.99.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/decompTumor2Sig.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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 ... 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 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     88.056  0.012  88.098
convertGenomesFromVRanges  8.096  0.248   8.350
* 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

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL decompTumor2Sig
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘decompTumor2Sig’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (decompTumor2Sig)

name	user	system	elapsed
composeGenomesFromExposures	1.198	0.008	2.057
computeExplainedVariance	0.355	0.004	1.132
convertAlexandrov2Shiraishi	0.115	0.020	0.929
convertGenomesFromVRanges	8.096	0.248	8.350
decomposeTumorGenomes	3.065	0.132	4.032
determineSignatureDistances	0.167	0.004	0.945
downgradeShiraishiSignatures	0.007	0.004	0.022
evaluateDecompositionQuality	0.242	0.000	0.916
getGenomesFromMutFeatData	0.409	0.000	0.417
getSignaturesFromEstParam	0.252	0.000	0.252
isAlexandrovSet	0.124	0.000	0.900
isExposureSet	3.323	0.140	4.145
isShiraishiSet	0.142	0.000	0.937
isSignatureSet	0.124	0.000	0.796
mapSignatureSets	0.251	0.000	1.025
plotDecomposedContribution	0.391	0.004	1.083
plotExplainedVariance	88.056	0.012	88.098
plotMutationDistribution	2.726	0.008	3.438
readAlexandrovSignatures	0.117	0.004	0.837
readGenomesFromMPF	3.016	0.108	3.137
readGenomesFromVCF	3.388	0.132	3.528
readShiraishiSignatures	0.007	0.000	0.008
sameSignatureFormat	0.146	0.000	0.815