BioC 3.5: CHECK report for MutationalPatterns on tokay2

Package: MutationalPatterns

Version: 1.2.1

Command: rm -rf MutationalPatterns.buildbin-libdir MutationalPatterns.Rcheck && mkdir MutationalPatterns.buildbin-libdir MutationalPatterns.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MutationalPatterns.buildbin-libdir MutationalPatterns_1.2.1.tar.gz >MutationalPatterns.Rcheck\00install.out 2>&1 && cp MutationalPatterns.Rcheck\00install.out MutationalPatterns-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MutationalPatterns.buildbin-libdir --install="check:MutationalPatterns-install.out" --force-multiarch --no-vignettes --timings MutationalPatterns_1.2.1.tar.gz

StartedAt: 2017-08-16 01:30:35 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:42:30 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 715.4 seconds

RetCode: 0

Status:  OK

CheckDir: MutationalPatterns.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MutationalPatterns.buildbin-libdir MutationalPatterns.Rcheck && mkdir MutationalPatterns.buildbin-libdir MutationalPatterns.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MutationalPatterns.buildbin-libdir MutationalPatterns_1.2.1.tar.gz >MutationalPatterns.Rcheck\00install.out 2>&1 && cp MutationalPatterns.Rcheck\00install.out MutationalPatterns-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MutationalPatterns.buildbin-libdir --install="check:MutationalPatterns-install.out" --force-multiarch --no-vignettes --timings MutationalPatterns_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/MutationalPatterns.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
genomic_distribution 17.98   0.57   18.55
read_vcfs_as_granges  8.92   0.28    9.20
plot_spectrum         7.48   0.16    7.64
mut_matrix            7.11   0.33    7.44
mut_matrix_stranded   6.49   0.23    6.72
mut_type_occurrences  5.37   0.28    5.65
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
genomic_distribution 15.17   0.43   15.61
read_vcfs_as_granges 11.00   0.17   11.18
plot_spectrum         8.47   0.22    8.68
mut_matrix_stranded   5.95   0.13    6.07
mut_matrix            5.70   0.21    5.92
mut_type_occurrences  5.08   0.19    5.27
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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

install for i386

* 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

install for x64

* installing *source* package 'MutationalPatterns' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MutationalPatterns' as MutationalPatterns_1.2.1.zip
* DONE (MutationalPatterns)

name	user	system	elapsed
binomial_test	0.02	0.00	0.02
enrichment_depletion_test	0.11	0.00	0.11
extract_signatures	0	0	0
fit_to_signatures	0.13	0.01	0.14
genomic_distribution	17.98	0.57	18.55
mut_matrix	7.11	0.33	7.44
mut_matrix_stranded	6.49	0.23	6.72
mut_type_occurrences	5.37	0.28	5.65
mutation_context	0.89	0.05	0.94
mutation_types	0.03	0.00	0.03
mutations_from_vcf	0.04	0.00	0.03
plot_192_profile	1.84	0.01	1.86
plot_96_profile	1.89	0.00	1.89
plot_compare_profiles	0.86	0.00	0.86
plot_contribution	1.19	0.00	1.19
plot_enrichment_depletion	2.20	0.03	2.23
plot_rainfall	0.98	0.00	0.99
plot_signature_strand_bias	0.38	0.02	0.39
plot_spectrum	7.48	0.16	7.64
plot_strand	0.18	0.01	0.19
plot_strand_bias	0.53	0.00	0.53
read_vcfs_as_granges	8.92	0.28	9.20
strand_bias_test	0.27	0.00	0.27
strand_from_vcf	0.18	0.02	0.20
strand_occurrences	0.14	0.00	0.14
type_context	0.61	0.11	0.72

name	user	system	elapsed
binomial_test	0	0	0
enrichment_depletion_test	0.11	0.00	0.11
extract_signatures	0	0	0
fit_to_signatures	0.09	0.00	0.09
genomic_distribution	15.17	0.43	15.61
mut_matrix	5.70	0.21	5.92
mut_matrix_stranded	5.95	0.13	6.07
mut_type_occurrences	5.08	0.19	5.27
mutation_context	1.05	0.06	1.11
mutation_types	0.03	0.00	0.03
mutations_from_vcf	0.03	0.00	0.03
plot_192_profile	2.52	0.01	2.53
plot_96_profile	1.87	0.00	1.88
plot_compare_profiles	1.25	0.00	1.25
plot_contribution	1.8	0.0	1.8
plot_enrichment_depletion	2.47	0.00	2.47
plot_rainfall	1.15	0.02	1.17
plot_signature_strand_bias	0.47	0.00	0.47
plot_spectrum	8.47	0.22	8.68
plot_strand	0.23	0.00	0.24
plot_strand_bias	0.66	0.00	0.65
read_vcfs_as_granges	11.00	0.17	11.18
strand_bias_test	0.21	0.00	0.22
strand_from_vcf	0.22	0.00	0.22
strand_occurrences	0.14	0.00	0.14
type_context	0.64	0.09	0.73