BioC 3.5: CHECK report for MutationalPatterns on veracruz2

Package: MutationalPatterns

Version: 1.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MutationalPatterns_1.2.1.tar.gz

StartedAt: 2017-08-16 05:47:31 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 05:53:47 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 376.2 seconds

RetCode: 0

Status:  OK

CheckDir: MutationalPatterns.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MutationalPatterns_1.2.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MutationalPatterns.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 sizes of PDF files under ‘inst/doc’ ... 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 17.429  0.844  18.806
read_vcfs_as_granges 11.845  3.033   4.611
mut_matrix_stranded   8.390  2.905   3.358
mut_matrix            6.201  2.410   3.114
plot_spectrum         7.870  0.150   8.250
mut_type_occurrences  6.331  0.211   6.741
* 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	0.009	0.000	0.009
enrichment_depletion_test	0.160	0.012	0.174
extract_signatures	0.002	0.000	0.002
fit_to_signatures	0.175	0.012	0.192
genomic_distribution	17.429	0.844	18.806
mut_matrix	6.201	2.410	3.114
mut_matrix_stranded	8.390	2.905	3.358
mut_type_occurrences	6.331	0.211	6.741
mutation_context	0.862	0.022	0.910
mutation_types	0.030	0.002	0.036
mutations_from_vcf	0.022	0.000	0.022
plot_192_profile	2.411	0.011	2.507
plot_96_profile	2.199	0.005	2.256
plot_compare_profiles	1.161	0.004	1.195
plot_contribution	1.576	0.007	1.640
plot_enrichment_depletion	2.866	0.008	2.973
plot_rainfall	1.305	0.005	1.347
plot_signature_strand_bias	0.532	0.002	0.552
plot_spectrum	7.87	0.15	8.25
plot_strand	0.267	0.004	0.274
plot_strand_bias	0.680	0.008	0.694
read_vcfs_as_granges	11.845	3.033	4.611
strand_bias_test	0.286	0.040	0.337
strand_from_vcf	0.252	0.013	0.271
strand_occurrences	0.179	0.004	0.184
type_context	0.841	0.021	0.886