BioC 3.4: CHECK report for YAPSA on morelia

Package: YAPSA

Version: 0.99.10

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings YAPSA_0.99.10.tar.gz

StartedAt: 2016-09-20 14:26:46 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 14:32:22 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 335.5 seconds

RetCode: 0

Status:  OK

CheckDir: YAPSA.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings YAPSA_0.99.10.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/YAPSA.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘YAPSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘YAPSA’ version ‘0.99.10’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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

* 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
* DONE (YAPSA)

name	user	system	elapsed
LCD	0.010	0.001	0.076
LCD_complex_cutoff	0.001	0.000	0.000
add_annotation	0.000	0.000	0.001
add_as_fist_to_list	0.001	0.000	0.001
aggregate_exposures_by_category	0.000	0.000	0.001
annotate_intermut_dist_PID	0.026	0.001	0.026
annotate_intermut_dist_cohort	0.032	0.000	0.032
annotation_exposures_barplot	0.000	0.000	0.001
annotation_heatmap_exposures	0.000	0.000	0.001
attribute_nucleotide_exchanges	0.004	0.000	0.005
build_gene_list_for_pathway	0.001	0.000	0.001
compare_SMCs	0.001	0.000	0.000
compare_exposures	0	0	0
compare_sets	0.006	0.001	0.005
compare_to_catalogues	0	0	0
complex_heatmap_exposures	0.671	0.037	0.708
compute_comparison_stat_df	0.001	0.000	0.000
cosineDist	0.001	0.000	0.001
create_mutation_catalogue_from_VR	1.971	0.075	2.111
create_mutation_catalogue_from_df	0.970	0.074	1.044
cut_breaks_as_intervals	0.183	0.006	0.271
exampleYAPSA	0.081	0.008	0.089
exposures_barplot	0.613	0.004	0.635
extract_names_from_gene_list	0	0	0
find_affected_PIDs	0.001	0.000	0.000
get_extreme_PIDs	0.033	0.001	0.034
hclust_exposures	0.009	0.001	0.010
makeVRangesFromDataFrame	0.079	0.003	0.082
make_catalogue_strata_df	0.000	0.000	0.001
make_comparison_matrix	0.114	0.008	0.137
make_strata_df	0.001	0.000	0.000
make_subgroups_df	0.041	0.004	0.045
melt_exposures	0.001	0.000	0.000
merge_exposures	0.000	0.001	0.000
normalizeMotifs_otherRownames	0.000	0.000	0.001
normalize_df_per_dim	0.015	0.001	0.016
plotExchangeSpectra	0	0	0
plot_SMC	0.000	0.000	0.001
plot_exposures	0.539	0.004	0.612
plot_strata	0	0	0
repeat_df	0.004	0.000	0.003
run_SMC	4.529	0.157	4.713
run_annotate_vcf_pl	0	0	0
run_comparison_catalogues	0.001	0.000	0.001
run_comparison_general	0	0	0
run_kmer_frequency_correction	0.001	0.000	0.000
run_kmer_frequency_normalization	0.000	0.000	0.001
run_plot_strata_general	0.001	0.000	0.000
shapiro_if_possible	0.001	0.000	0.001
split_exposures_by_subgroups	0.001	0.000	0.001
stat_plot_subgroups	0.000	0.001	0.000
stat_test_SMC	0	0	0
stat_test_subgroups	0	0	0
stderrmean	0.001	0.000	0.001
sum_over_list_of_df	0.002	0.001	0.003
test_exposureAffected	0.001	0.000	0.001
test_gene_list_in_exposures	0	0	0
transform_rownames_R_to_MATLAB	0	0	0
translate_to_hg19	0.005	0.001	0.005
trellis_rainfall_plot	2.614	0.022	2.718