Package: decompTumor2Sig

Version: 2.0.0

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_2.0.0.tar.gz

StartedAt: 2019-10-16 01:00:25 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 01:07:09 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 404.4 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_2.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/decompTumor2Sig.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘2.0.0’
* 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     95.376  0.011  95.415
convertGenomesFromVRanges  8.408  0.208   8.626
* 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	0.398	0.032	1.186
computeExplainedVariance	0.380	0.008	1.038
convertAlexandrov2Shiraishi	0.162	0.008	0.813
convertGenomesFromVRanges	8.408	0.208	8.626
decomposeTumorGenomes	2.764	0.136	3.588
determineSignatureDistances	0.164	0.008	0.927
downgradeShiraishiSignatures	0.008	0.004	0.020
evaluateDecompositionQuality	0.310	0.001	0.961
getGenomesFromMutFeatData	0.570	0.000	0.577
getSignaturesFromEstParam	0.247	0.000	0.254
isAlexandrovSet	0.132	0.000	0.881
isExposureSet	3.767	0.124	4.545
isShiraishiSet	0.157	0.004	0.747
isSignatureSet	0.100	0.004	0.690
mapSignatureSets	0.252	0.012	0.925
plotDecomposedContribution	0.605	0.008	1.264
plotExplainedVariance	95.376	0.011	95.415
plotMutationDistribution	1.996	0.004	2.671
readAlexandrovSignatures	0.132	0.000	0.788
readGenomesFromMPF	2.631	0.116	2.757
readGenomesFromVCF	3.104	0.080	3.183
readShiraishiSignatures	0.005	0.000	0.004
sameSignatureFormat	0.120	0.012	0.893