BioC 3.4: CHECK report for MutationalPatterns on malbec1

Package: MutationalPatterns

Version: 1.0.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MutationalPatterns_1.0.0.tar.gz

StartedAt: 2017-04-15 00:04:17 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:08:54 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 277.1 seconds

RetCode: 0

Status:  OK

CheckDir: MutationalPatterns.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MutationalPatterns_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/MutationalPatterns.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.0.0’
* 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 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     196.960  8.520  19.859
genomic_distribution  13.976  0.080  14.077
read_vcfs_as_granges   8.268  0.100   8.375
plot_spectrum          6.952  0.068   7.028
mut_type_occurrences   5.024  0.104   5.131
mut_matrix_stranded    4.948  0.092   5.045
* 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	0.008	0.000	0.006
enrichment_depletion_test	0.528	0.004	0.531
extract_signatures	0.004	0.000	0.001
fit_to_signatures	0.032	0.000	0.034
genomic_distribution	13.976	0.080	14.077
mut_matrix	4.608	0.108	4.720
mut_matrix_stranded	4.948	0.092	5.045
mut_type_occurrences	5.024	0.104	5.131
mutation_context	0.632	0.012	0.643
mutation_types	0.020	0.000	0.022
mutations_from_vcf	0.020	0.000	0.016
plot_192_profile	196.960	8.520	19.859
plot_96_profile	0.892	0.000	0.890
plot_compare_profiles	0.744	0.000	0.743
plot_contribution	0.908	0.000	0.910
plot_enrichment_depletion	1.944	0.000	1.946
plot_rainfall	0.868	0.000	0.869
plot_signature_strand_bias	0.360	0.000	0.361
plot_spectrum	6.952	0.068	7.028
plot_strand	0.152	0.000	0.153
plot_strand_bias	0.532	0.000	0.535
read_vcfs_as_granges	8.268	0.100	8.375
strand_bias_test	0.156	0.012	0.169
strand_from_vcf	0.184	0.004	0.189
strand_occurrences	0.148	0.000	0.146
type_context	0.788	0.012	0.801