BioC 3.4: CHECK report for MutationalPatterns on tokay1

Package: MutationalPatterns

Version: 1.0.0

Command: rm -rf MutationalPatterns.buildbin-libdir MutationalPatterns.Rcheck && mkdir MutationalPatterns.buildbin-libdir MutationalPatterns.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MutationalPatterns.buildbin-libdir MutationalPatterns_1.0.0.tar.gz >MutationalPatterns.Rcheck\00install.out 2>&1 && cp MutationalPatterns.Rcheck\00install.out MutationalPatterns-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=MutationalPatterns.buildbin-libdir --install="check:MutationalPatterns-install.out" --force-multiarch --no-vignettes --timings MutationalPatterns_1.0.0.tar.gz

StartedAt: 2017-04-14 23:45:18 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:52:55 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 456.8 seconds

RetCode: 0

Status:  OK

CheckDir: MutationalPatterns.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf MutationalPatterns.buildbin-libdir MutationalPatterns.Rcheck && mkdir MutationalPatterns.buildbin-libdir MutationalPatterns.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MutationalPatterns.buildbin-libdir MutationalPatterns_1.0.0.tar.gz >MutationalPatterns.Rcheck\00install.out 2>&1 && cp MutationalPatterns.Rcheck\00install.out MutationalPatterns-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=MutationalPatterns.buildbin-libdir --install="check:MutationalPatterns-install.out" --force-multiarch --no-vignettes --timings MutationalPatterns_1.0.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/MutationalPatterns.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.0.0'
* 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 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 14.81   0.63   15.45
read_vcfs_as_granges  7.22   0.10    7.32
plot_spectrum         5.92   0.24    6.16
mut_matrix_stranded   4.87   0.17    5.04
plot_192_profile      2.43   0.07   10.22
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
genomic_distribution 14.86   0.26   15.12
read_vcfs_as_granges 10.13   0.26   10.39
plot_spectrum         8.43   0.15    8.59
mut_matrix            5.98   0.30    6.28
mut_matrix_stranded   5.54   0.13    5.68
mut_type_occurrences  5.29   0.21    5.51
plot_192_profile      3.12   0.09   13.03
* 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_1.0.0.zip
* DONE (MutationalPatterns)

name	user	system	elapsed
binomial_test	0.01	0.00	0.02
enrichment_depletion_test	0.13	0.00	0.12
extract_signatures	0	0	0
fit_to_signatures	0.06	0.01	0.08
genomic_distribution	14.81	0.63	15.45
mut_matrix	4.30	0.26	4.57
mut_matrix_stranded	4.87	0.17	5.04
mut_type_occurrences	4.15	0.21	4.35
mutation_context	0.78	0.04	0.83
mutation_types	0.03	0.00	0.03
mutations_from_vcf	0.03	0.00	0.03
plot_192_profile	2.43	0.07	10.22
plot_96_profile	1.09	0.00	1.10
plot_compare_profiles	0.80	0.00	0.79
plot_contribution	0.84	0.00	0.85
plot_enrichment_depletion	1.72	0.00	1.72
plot_rainfall	0.83	0.03	0.86
plot_signature_strand_bias	0.36	0.00	0.36
plot_spectrum	5.92	0.24	6.16
plot_strand	0.16	0.01	0.17
plot_strand_bias	0.5	0.0	0.5
read_vcfs_as_granges	7.22	0.10	7.32
strand_bias_test	0.17	0.00	0.17
strand_from_vcf	0.19	0.00	0.19
strand_occurrences	0.11	0.00	0.11
type_context	0.64	0.04	0.69

name	user	system	elapsed
binomial_test	0.02	0.00	0.01
enrichment_depletion_test	0.65	0.00	0.66
extract_signatures	0	0	0
fit_to_signatures	0.03	0.00	0.03
genomic_distribution	14.86	0.26	15.12
mut_matrix	5.98	0.30	6.28
mut_matrix_stranded	5.54	0.13	5.68
mut_type_occurrences	5.29	0.21	5.51
mutation_context	1.03	0.04	1.06
mutation_types	0.03	0.00	0.03
mutations_from_vcf	0.02	0.00	0.02
plot_192_profile	3.12	0.09	13.03
plot_96_profile	1.30	0.00	1.29
plot_compare_profiles	1.17	0.00	1.18
plot_contribution	1.25	0.00	1.25
plot_enrichment_depletion	2.26	0.00	2.27
plot_rainfall	1.03	0.02	1.05
plot_signature_strand_bias	0.47	0.00	0.47
plot_spectrum	8.43	0.15	8.59
plot_strand	0.24	0.03	0.27
plot_strand_bias	0.92	0.02	0.94
read_vcfs_as_granges	10.13	0.26	10.39
strand_bias_test	0.25	0.02	0.26
strand_from_vcf	0.38	0.00	0.37
strand_occurrences	0.31	0.00	0.32
type_context	1.30	0.03	1.32