BioC 3.5: CHECK report for MutationalPatterns on oaxaca

Package: MutationalPatterns

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MutationalPatterns_1.1.0.tar.gz

StartedAt: 2017-03-04 06:16:46 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 06:23:30 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 404.7 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_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MutationalPatterns.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.1.0’
* 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     159.608  6.624  47.235
genomic_distribution  19.686  1.004  20.833
read_vcfs_as_granges  11.325  0.160  11.492
plot_spectrum          8.368  0.153   8.524
mut_matrix             7.000  0.337  22.444
mut_matrix_stranded    6.879  0.175   7.057
mut_type_occurrences   4.763  0.129   5.381
* 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	0.007	0.000	0.007
enrichment_depletion_test	0.132	0.006	0.139
extract_signatures	0.001	0.001	0.001
fit_to_signatures	0.137	0.014	0.151
genomic_distribution	19.686	1.004	20.833
mut_matrix	7.000	0.337	22.444
mut_matrix_stranded	6.879	0.175	7.057
mut_type_occurrences	4.763	0.129	5.381
mutation_context	0.629	0.016	0.646
mutation_types	0.030	0.001	0.031
mutations_from_vcf	0.031	0.001	0.031
plot_192_profile	159.608	6.624	47.235
plot_96_profile	2.717	0.012	2.732
plot_compare_profiles	1.242	0.006	1.249
plot_contribution	1.748	0.007	1.756
plot_enrichment_depletion	3.022	0.008	3.031
plot_rainfall	1.398	0.009	1.408
plot_signature_strand_bias	0.560	0.002	0.562
plot_spectrum	8.368	0.153	8.524
plot_strand	0.304	0.006	0.310
plot_strand_bias	0.702	0.006	0.707
read_vcfs_as_granges	11.325	0.160	11.492
strand_bias_test	0.250	0.003	0.253
strand_from_vcf	0.255	0.004	0.259
strand_occurrences	0.234	0.005	0.239
type_context	0.946	0.022	0.968