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: 2017-10-18 01:36:50 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:48:13 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 683.3 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-3.5-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
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/MutationalPatterns.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 15.16   0.45   15.61
plot_spectrum         8.07   0.36    8.42
read_vcfs_as_granges  8.25   0.10    8.36
mut_matrix            5.11   0.24    5.34
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
genomic_distribution 15.46   0.42   15.87
read_vcfs_as_granges  9.72   0.11    9.83
plot_spectrum         7.98   0.22    8.20
mut_matrix_stranded   7.04   0.28    7.33
mut_matrix            7.03   0.25    7.28
mut_type_occurrences  5.39   0.17    5.57
* 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	0.03	0.00	0.03
enrichment_depletion_test	0.22	0.00	0.22
extract_signatures	0	0	0
fit_to_signatures	0.20	0.03	0.23
genomic_distribution	15.16	0.45	15.61
mut_matrix	5.11	0.24	5.34
mut_matrix_stranded	4.67	0.20	4.88
mut_type_occurrences	4.47	0.20	4.67
mutation_context	0.92	0.02	0.94
mutation_types	0.03	0.00	0.03
mutations_from_vcf	0.03	0.00	0.03
plot_192_profile	2	0	2
plot_96_profile	2.58	0.00	2.58
plot_compare_profiles	1.11	0.00	1.11
plot_contribution	1.11	0.00	1.11
plot_enrichment_depletion	1.87	0.00	1.87
plot_rainfall	0.90	0.00	0.89
plot_signature_strand_bias	0.35	0.01	0.38
plot_spectrum	8.07	0.36	8.42
plot_strand	0.31	0.00	0.31
plot_strand_bias	0.68	0.04	0.72
read_vcfs_as_granges	8.25	0.10	8.36
strand_bias_test	0.27	0.00	0.26
strand_from_vcf	0.19	0.00	0.19
strand_occurrences	0.09	0.03	0.13
type_context	0.62	0.05	0.67

name	user	system	elapsed
binomial_test	0.02	0.00	0.02
enrichment_depletion_test	0.15	0.00	0.15
extract_signatures	0	0	0
fit_to_signatures	0.06	0.02	0.08
genomic_distribution	15.46	0.42	15.87
mut_matrix	7.03	0.25	7.28
mut_matrix_stranded	7.04	0.28	7.33
mut_type_occurrences	5.39	0.17	5.57
mutation_context	0.82	0.05	0.85
mutation_types	0.03	0.00	0.04
mutations_from_vcf	0.01	0.00	0.01
plot_192_profile	2.02	0.00	2.01
plot_96_profile	1.90	0.00	1.91
plot_compare_profiles	1.03	0.00	1.03
plot_contribution	1.38	0.00	1.38
plot_enrichment_depletion	2.33	0.00	2.32
plot_rainfall	1.18	0.00	1.19
plot_signature_strand_bias	0.49	0.00	0.49
plot_spectrum	7.98	0.22	8.20
plot_strand	0.19	0.01	0.20
plot_strand_bias	0.60	0.02	0.62
read_vcfs_as_granges	9.72	0.11	9.83
strand_bias_test	0.28	0.01	0.30
strand_from_vcf	0.22	0.00	0.22
strand_occurrences	0.16	0.00	0.16
type_context	0.88	0.03	0.91