BioC 3.5: CHECK report for MutationalPatterns on toluca2

Package: MutationalPatterns

Version: 1.1.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MutationalPatterns_1.1.4.tar.gz

StartedAt: 2017-04-23 07:12:00 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 07:19:27 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 447.0 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_1.1.4.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 r72187)
* 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 ‘1.1.4’
* 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 20.083  1.009  21.362
read_vcfs_as_granges 15.721  3.345   6.431
mut_matrix_stranded  11.761  3.078   4.725
mut_matrix            8.547  2.587   4.101
plot_spectrum         9.341  0.177   9.602
mut_type_occurrences  6.760  0.247   7.056
* 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	0.010	0.000	0.011
enrichment_depletion_test	0.159	0.007	0.167
extract_signatures	0.001	0.000	0.002
fit_to_signatures	0.191	0.017	0.209
genomic_distribution	20.083	1.009	21.362
mut_matrix	8.547	2.587	4.101
mut_matrix_stranded	11.761	3.078	4.725
mut_type_occurrences	6.760	0.247	7.056
mutation_context	0.940	0.027	0.972
mutation_types	0.031	0.002	0.034
mutations_from_vcf	0.027	0.000	0.027
plot_192_profile	2.794	0.013	2.828
plot_96_profile	2.372	0.006	2.397
plot_compare_profiles	1.322	0.005	1.341
plot_contribution	1.869	0.006	1.904
plot_enrichment_depletion	3.188	0.007	3.214
plot_rainfall	1.498	0.006	1.518
plot_signature_strand_bias	0.562	0.002	0.575
plot_spectrum	9.341	0.177	9.602
plot_strand	0.289	0.004	0.294
plot_strand_bias	0.741	0.006	0.750
read_vcfs_as_granges	15.721	3.345	6.431
strand_bias_test	0.372	0.048	0.421
strand_from_vcf	0.314	0.014	0.332
strand_occurrences	0.208	0.005	0.221
type_context	0.991	0.029	1.040