BioC 3.5: CHECK report for YAPSA on tokay2

Package: YAPSA

Version: 1.2.0

Command: rm -rf YAPSA.buildbin-libdir YAPSA.Rcheck && mkdir YAPSA.buildbin-libdir YAPSA.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=YAPSA.buildbin-libdir YAPSA_1.2.0.tar.gz >YAPSA.Rcheck\00install.out 2>&1 && cp YAPSA.Rcheck\00install.out YAPSA-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=YAPSA.buildbin-libdir --install="check:YAPSA-install.out" --force-multiarch --no-vignettes --timings YAPSA_1.2.0.tar.gz

StartedAt: 2017-10-18 03:39:53 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 03:48:52 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 539.3 seconds

RetCode: 0

Status:  OK

CheckDir: YAPSA.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf YAPSA.buildbin-libdir YAPSA.Rcheck && mkdir YAPSA.buildbin-libdir YAPSA.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=YAPSA.buildbin-libdir YAPSA_1.2.0.tar.gz >YAPSA.Rcheck\00install.out 2>&1 && cp YAPSA.Rcheck\00install.out YAPSA-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=YAPSA.buildbin-libdir --install="check:YAPSA-install.out" --force-multiarch --no-vignettes --timings YAPSA_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/YAPSA.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 'YAPSA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'YAPSA' version '1.2.0'
* 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 'YAPSA' 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
run_SMC 5.42   0.11    5.53
* 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 'YAPSA' ...
** R
** data
** 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 'YAPSA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'YAPSA' as YAPSA_1.2.0.zip
* DONE (YAPSA)

name	user	system	elapsed
LCD	0.62	0.00	0.66
LCD_complex_cutoff	0	0	0
add_annotation	0	0	0
add_as_fist_to_list	0	0	0
aggregate_exposures_by_category	0	0	0
annotate_intermut_dist_PID	0.19	0.00	0.19
annotate_intermut_dist_cohort	0.08	0.00	0.08
annotation_exposures_barplot	0	0	0
annotation_heatmap_exposures	0	0	0
attribute_nucleotide_exchanges	0.01	0.00	0.01
build_gene_list_for_pathway	0	0	0
compare_SMCs	0	0	0
compare_exposures	0	0	0
compare_sets	0.03	0.00	0.03
compare_to_catalogues	0	0	0
complex_heatmap_exposures	1.78	0.00	1.79
compute_comparison_stat_df	0	0	0
cosineDist	0	0	0
create_mutation_catalogue_from_VR	2.62	0.14	2.77
create_mutation_catalogue_from_df	0.74	0.06	0.79
cut_breaks_as_intervals	1.22	0.00	1.22
exampleYAPSA	0.09	0.02	0.11
exposures_barplot	1.14	0.06	1.21
extract_names_from_gene_list	0	0	0
find_affected_PIDs	0	0	0
get_extreme_PIDs	0.01	0.00	0.02
hclust_exposures	0.00	0.01	0.01
makeVRangesFromDataFrame	0.08	0.02	0.10
make_catalogue_strata_df	0	0	0
make_comparison_matrix	0.11	0.00	0.11
make_strata_df	0	0	0
make_subgroups_df	0.05	0.01	0.06
melt_exposures	0	0	0
merge_exposures	0	0	0
normalizeMotifs_otherRownames	0	0	0
normalize_df_per_dim	0.01	0.00	0.01
plotExchangeSpectra	0	0	0
plot_SMC	0	0	0
plot_exposures	1.32	0.04	1.35
plot_strata	0	0	0
repeat_df	0	0	0
run_SMC	4.70	0.26	4.97
run_annotate_vcf_pl	0	0	0
run_comparison_catalogues	0	0	0
run_comparison_general	0	0	0
run_kmer_frequency_correction	0	0	0
run_kmer_frequency_normalization	0	0	0
run_plot_strata_general	0	0	0
shapiro_if_possible	0	0	0
split_exposures_by_subgroups	0	0	0
stat_plot_subgroups	0	0	0
stat_test_SMC	0	0	0
stat_test_subgroups	0	0	0
stderrmean	0	0	0
sum_over_list_of_df	0.02	0.00	0.02
test_exposureAffected	0	0	0
test_gene_list_in_exposures	0	0	0
transform_rownames_R_to_MATLAB	0	0	0
translate_to_hg19	0	0	0
trellis_rainfall_plot	2.84	0.02	2.90

name	user	system	elapsed
LCD	0.09	0.00	0.09
LCD_complex_cutoff	0	0	0
add_annotation	0	0	0
add_as_fist_to_list	0	0	0
aggregate_exposures_by_category	0	0	0
annotate_intermut_dist_PID	0.2	0.0	0.2
annotate_intermut_dist_cohort	0.06	0.00	0.06
annotation_exposures_barplot	0	0	0
annotation_heatmap_exposures	0	0	0
attribute_nucleotide_exchanges	0	0	0
build_gene_list_for_pathway	0	0	0
compare_SMCs	0	0	0
compare_exposures	0	0	0
compare_sets	0.01	0.00	0.01
compare_to_catalogues	0	0	0
complex_heatmap_exposures	1.88	0.01	1.89
compute_comparison_stat_df	0	0	0
cosineDist	0	0	0
create_mutation_catalogue_from_VR	2.89	0.06	2.96
create_mutation_catalogue_from_df	0.80	0.05	0.84
cut_breaks_as_intervals	0.78	0.00	0.78
exampleYAPSA	0.11	0.00	0.11
exposures_barplot	1.78	0.02	1.80
extract_names_from_gene_list	0	0	0
find_affected_PIDs	0	0	0
get_extreme_PIDs	0.04	0.00	0.04
hclust_exposures	0.01	0.00	0.01
makeVRangesFromDataFrame	0.1	0.0	0.1
make_catalogue_strata_df	0	0	0
make_comparison_matrix	0.12	0.00	0.12
make_strata_df	0	0	0
make_subgroups_df	0.05	0.00	0.05
melt_exposures	0	0	0
merge_exposures	0	0	0
normalizeMotifs_otherRownames	0	0	0
normalize_df_per_dim	0.01	0.00	0.01
plotExchangeSpectra	0	0	0
plot_SMC	0	0	0
plot_exposures	1.53	0.00	1.53
plot_strata	0	0	0
repeat_df	0.02	0.00	0.02
run_SMC	5.42	0.11	5.53
run_annotate_vcf_pl	0	0	0
run_comparison_catalogues	0	0	0
run_comparison_general	0	0	0
run_kmer_frequency_correction	0	0	0
run_kmer_frequency_normalization	0	0	0
run_plot_strata_general	0	0	0
shapiro_if_possible	0	0	0
split_exposures_by_subgroups	0	0	0
stat_plot_subgroups	0	0	0
stat_test_SMC	0	0	0
stat_test_subgroups	0	0	0
stderrmean	0	0	0
sum_over_list_of_df	0	0	0
test_exposureAffected	0	0	0
test_gene_list_in_exposures	0	0	0
transform_rownames_R_to_MATLAB	0	0	0
translate_to_hg19	0	0	0
trellis_rainfall_plot	3.25	0.03	3.28