BioC 3.6: CHECK report for MutationalPatterns on tokay1

Package: MutationalPatterns

Version: 1.3.0

Command: rm -rf MutationalPatterns.buildbin-libdir MutationalPatterns.Rcheck && mkdir MutationalPatterns.buildbin-libdir MutationalPatterns.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MutationalPatterns.buildbin-libdir MutationalPatterns_1.3.0.tar.gz >MutationalPatterns.Rcheck\00install.out 2>&1 && cp MutationalPatterns.Rcheck\00install.out MutationalPatterns-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=MutationalPatterns.buildbin-libdir --install="check:MutationalPatterns-install.out" --force-multiarch --no-vignettes --timings MutationalPatterns_1.3.0.tar.gz

StartedAt: 2017-08-16 01:07:12 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:17:56 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 643.7 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-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MutationalPatterns.buildbin-libdir MutationalPatterns_1.3.0.tar.gz >MutationalPatterns.Rcheck\00install.out 2>&1 && cp MutationalPatterns.Rcheck\00install.out MutationalPatterns-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=MutationalPatterns.buildbin-libdir --install="check:MutationalPatterns-install.out" --force-multiarch --no-vignettes --timings MutationalPatterns_1.3.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-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 '1.3.0'
* 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 13.22   0.28   13.50
read_vcfs_as_granges  7.45   0.13    7.57
plot_spectrum         5.66   0.20    5.86
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
genomic_distribution 14.99   0.49   15.47
read_vcfs_as_granges  9.39   0.11    9.50
plot_spectrum         7.17   0.19    7.36
mut_matrix_stranded   5.03   0.24    5.27
mut_matrix            5.04   0.12    5.17
* 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_1.3.0.zip
* DONE (MutationalPatterns)

name	user	system	elapsed
binomial_test	0	0	0
enrichment_depletion_test	0.06	0.04	0.11
extract_signatures	0.00	0.02	0.02
fit_to_signatures	0.08	0.00	0.08
genomic_distribution	13.22	0.28	13.50
mut_matrix	4.26	0.27	4.53
mut_matrix_stranded	4.11	0.26	4.37
mut_type_occurrences	3.64	0.24	3.88
mutation_context	0.55	0.00	0.55
mutation_types	0.03	0.00	0.03
mutations_from_vcf	0.02	0.00	0.01
plot_192_profile	1.57	0.01	1.60
plot_96_profile	1.44	0.00	1.43
plot_compare_profiles	0.85	0.00	0.85
plot_contribution	1.01	0.02	1.03
plot_enrichment_depletion	1.78	0.00	1.78
plot_rainfall	0.83	0.00	0.83
plot_signature_strand_bias	0.33	0.00	0.33
plot_spectrum	5.66	0.20	5.86
plot_strand	0.15	0.00	0.15
plot_strand_bias	0.49	0.00	0.49
read_vcfs_as_granges	7.45	0.13	7.57
strand_bias_test	0.18	0.00	0.17
strand_from_vcf	0.18	0.00	0.18
strand_occurrences	0.10	0.03	0.13
type_context	0.58	0.08	0.66

name	user	system	elapsed
binomial_test	0.02	0.00	0.01
enrichment_depletion_test	0.12	0.00	0.13
extract_signatures	0	0	0
fit_to_signatures	0.08	0.00	0.08
genomic_distribution	14.99	0.49	15.47
mut_matrix	5.04	0.12	5.17
mut_matrix_stranded	5.03	0.24	5.27
mut_type_occurrences	4.56	0.15	4.72
mutation_context	0.71	0.00	0.70
mutation_types	0.03	0.00	0.03
mutations_from_vcf	0.03	0.00	0.03
plot_192_profile	2.03	0.00	2.03
plot_96_profile	1.78	0.00	1.79
plot_compare_profiles	0.97	0.00	0.96
plot_contribution	1.33	0.00	1.33
plot_enrichment_depletion	2.36	0.00	2.36
plot_rainfall	1.06	0.00	1.06
plot_signature_strand_bias	0.39	0.00	0.39
plot_spectrum	7.17	0.19	7.36
plot_strand	0.19	0.00	0.19
plot_strand_bias	0.64	0.00	0.64
read_vcfs_as_granges	9.39	0.11	9.50
strand_bias_test	0.23	0.02	0.25
strand_from_vcf	0.22	0.00	0.22
strand_occurrences	0.15	0.00	0.16
type_context	0.84	0.01	0.86