BioC 3.5: CHECK report for MutationalPatterns on malbec2

Package: MutationalPatterns

Version: 1.2.1

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings MutationalPatterns_1.2.1.tar.gz

StartedAt: 2017-10-18 01:05:06 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:10:03 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 297.2 seconds

RetCode: 0

Status:  OK

CheckDir: MutationalPatterns.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings MutationalPatterns_1.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/MutationalPatterns.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.2.1’
* 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 ‘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
read_vcfs_as_granges 12.252  1.764   2.058
genomic_distribution 12.516  0.084  12.610
mut_matrix_stranded   8.092  1.608   1.702
mut_matrix            6.536  1.452   6.835
plot_spectrum         6.516  0.120   6.643
* 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	0.004	0.000	0.007
enrichment_depletion_test	0.128	0.000	0.129
extract_signatures	0.004	0.000	0.002
fit_to_signatures	0.596	0.008	0.605
genomic_distribution	12.516	0.084	12.610
mut_matrix	6.536	1.452	6.835
mut_matrix_stranded	8.092	1.608	1.702
mut_type_occurrences	4.756	0.120	4.879
mutation_context	0.632	0.016	0.648
mutation_types	0.024	0.000	0.025
mutations_from_vcf	0.020	0.000	0.019
plot_192_profile	2.436	0.000	2.436
plot_96_profile	1.780	0.004	1.787
plot_compare_profiles	0.796	0.000	0.799
plot_contribution	1.180	0.000	1.178
plot_enrichment_depletion	1.960	0.000	1.961
plot_rainfall	0.964	0.000	0.963
plot_signature_strand_bias	0.360	0.004	0.365
plot_spectrum	6.516	0.120	6.643
plot_strand	0.200	0.000	0.202
plot_strand_bias	0.552	0.000	0.555
read_vcfs_as_granges	12.252	1.764	2.058
strand_bias_test	0.240	0.012	0.251
strand_from_vcf	0.232	0.016	0.247
strand_occurrences	0.144	0.000	0.146
type_context	0.672	0.004	0.679