BioC 3.4: CHECK report for MutationalPatterns on morelia

Package: MutationalPatterns

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MutationalPatterns_1.0.0.tar.gz

StartedAt: 2017-04-15 05:30:12 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 05:36:40 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 388.2 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_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/MutationalPatterns.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.0.0’
* 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 ‘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
plot_192_profile     111.943  4.802  38.588
genomic_distribution  18.509  0.880  21.942
read_vcfs_as_granges  11.799  0.149  11.961
plot_spectrum          8.628  0.167   8.804
mut_matrix_stranded    7.091  0.182   7.279
mut_matrix             6.849  0.363  32.354
mut_type_occurrences   5.830  0.153   5.991
* 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	0.006	0.001	0.006
enrichment_depletion_test	0.430	0.001	0.431
extract_signatures	0.002	0.001	0.002
fit_to_signatures	0.051	0.003	0.054
genomic_distribution	18.509	0.880	21.942
mut_matrix	6.849	0.363	32.354
mut_matrix_stranded	7.091	0.182	7.279
mut_type_occurrences	5.830	0.153	5.991
mutation_context	0.792	0.021	0.812
mutation_types	0.019	0.001	0.020
mutations_from_vcf	0.016	0.001	0.016
plot_192_profile	111.943	4.802	38.588
plot_96_profile	1.394	0.004	1.399
plot_compare_profiles	0.926	0.003	0.929
plot_contribution	1.302	0.007	1.312
plot_enrichment_depletion	2.893	0.010	2.904
plot_rainfall	1.749	0.065	1.825
plot_signature_strand_bias	0.508	0.001	0.510
plot_spectrum	8.628	0.167	8.804
plot_strand	0.263	0.006	0.270
plot_strand_bias	0.854	0.007	0.863
read_vcfs_as_granges	11.799	0.149	11.961
strand_bias_test	0.235	0.005	0.240
strand_from_vcf	0.280	0.005	0.285
strand_occurrences	0.173	0.004	0.178
type_context	1.115	0.026	1.143