BioC 3.6: CHECK report for MutationalPatterns on malbec1

Package: MutationalPatterns

Version: 1.3.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings MutationalPatterns_1.3.0.tar.gz

StartedAt: 2017-08-16 01:00:02 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:04:45 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 282.7 seconds

RetCode: 0

Status:  OK

CheckDir: MutationalPatterns.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 MutationalPatterns_1.3.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/MutationalPatterns.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 ‘MutationalPatterns/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MutationalPatterns’ version ‘1.3.0’
* 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 ‘MutationalPatterns’ 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 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
genomic_distribution 13.048  0.104  13.162
read_vcfs_as_granges 10.548  2.144   1.919
mut_matrix_stranded   6.672  1.524   1.499
mut_matrix            5.624  1.400   1.355
plot_spectrum         6.280  0.060   6.343
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: OK

* installing *source* package ‘MutationalPatterns’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MutationalPatterns)

name	user	system	elapsed
binomial_test	0.008	0.000	0.006
enrichment_depletion_test	0.096	0.004	0.098
extract_signatures	0.000	0.000	0.002
fit_to_signatures	0.584	0.000	0.583
genomic_distribution	13.048	0.104	13.162
mut_matrix	5.624	1.400	1.355
mut_matrix_stranded	6.672	1.524	1.499
mut_type_occurrences	4.632	0.124	4.760
mutation_context	0.604	0.012	0.618
mutation_types	0.024	0.000	0.022
mutations_from_vcf	0.020	0.000	0.018
plot_192_profile	1.684	0.004	1.692
plot_96_profile	1.504	0.004	1.510
plot_compare_profiles	0.804	0.004	0.807
plot_contribution	1.140	0.004	1.145
plot_enrichment_depletion	1.96	0.00	1.96
plot_rainfall	0.928	0.008	0.935
plot_signature_strand_bias	0.360	0.000	0.361
plot_spectrum	6.280	0.060	6.343
plot_strand	0.172	0.004	0.179
plot_strand_bias	0.536	0.004	0.540
read_vcfs_as_granges	10.548	2.144	1.919
strand_bias_test	0.256	0.020	0.273
strand_from_vcf	0.228	0.016	0.248
strand_occurrences	0.156	0.004	0.160
type_context	0.716	0.008	0.724