BioC 3.5: CHECK report for YAPSA on oaxaca

Package: YAPSA

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings YAPSA_1.1.0.tar.gz

StartedAt: 2017-03-04 10:31:30 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 10:40:09 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 519.2 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_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/YAPSA.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.1.0’
* 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 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
Examples with CPU or elapsed time > 5s
                                   user system elapsed
run_SMC                           6.784  0.157   6.943
create_mutation_catalogue_from_VR 5.081  0.098   5.182
* 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	0.188	0.005	0.206
LCD_complex_cutoff	0.000	0.000	0.001
add_annotation	0.000	0.001	0.001
add_as_fist_to_list	0	0	0
aggregate_exposures_by_category	0	0	0
annotate_intermut_dist_PID	0.362	0.040	0.402
annotate_intermut_dist_cohort	0.106	0.003	0.109
annotation_exposures_barplot	0.000	0.000	0.001
annotation_heatmap_exposures	0.001	0.001	0.000
attribute_nucleotide_exchanges	0.003	0.000	0.004
build_gene_list_for_pathway	0.001	0.000	0.000
compare_SMCs	0.000	0.000	0.001
compare_exposures	0.001	0.000	0.000
compare_sets	0.009	0.000	0.010
compare_to_catalogues	0.001	0.000	0.000
complex_heatmap_exposures	3.588	0.013	3.602
compute_comparison_stat_df	0.000	0.000	0.001
cosineDist	0.001	0.001	0.000
create_mutation_catalogue_from_VR	5.081	0.098	5.182
create_mutation_catalogue_from_df	1.215	0.072	1.287
cut_breaks_as_intervals	1.902	0.009	1.951
exampleYAPSA	0.109	0.012	0.120
exposures_barplot	2.062	0.070	2.135
extract_names_from_gene_list	0	0	0
find_affected_PIDs	0.000	0.000	0.001
get_extreme_PIDs	0.042	0.002	0.044
hclust_exposures	0.011	0.001	0.013
makeVRangesFromDataFrame	0.099	0.006	0.104
make_catalogue_strata_df	0.000	0.000	0.001
make_comparison_matrix	0.129	0.007	0.136
make_strata_df	0.001	0.000	0.000
make_subgroups_df	0.064	0.008	0.071
melt_exposures	0.001	0.000	0.001
merge_exposures	0.001	0.000	0.000
normalizeMotifs_otherRownames	0.001	0.000	0.000
normalize_df_per_dim	0.018	0.001	0.018
plotExchangeSpectra	0.001	0.000	0.001
plot_SMC	0.001	0.000	0.001
plot_exposures	2.292	0.011	2.304
plot_strata	0.001	0.001	0.001
repeat_df	0.005	0.000	0.004
run_SMC	6.784	0.157	6.943
run_annotate_vcf_pl	0.001	0.000	0.001
run_comparison_catalogues	0.001	0.000	0.000
run_comparison_general	0.000	0.000	0.001
run_kmer_frequency_correction	0.001	0.000	0.000
run_kmer_frequency_normalization	0	0	0
run_plot_strata_general	0.001	0.000	0.000
shapiro_if_possible	0.001	0.000	0.001
split_exposures_by_subgroups	0.000	0.000	0.001
stat_plot_subgroups	0.001	0.000	0.000
stat_test_SMC	0.001	0.000	0.000
stat_test_subgroups	0.000	0.000	0.001
stderrmean	0.001	0.000	0.001
sum_over_list_of_df	0.004	0.000	0.004
test_exposureAffected	0.000	0.000	0.001
test_gene_list_in_exposures	0.000	0.000	0.001
transform_rownames_R_to_MATLAB	0	0	0
translate_to_hg19	0.008	0.000	0.009
trellis_rainfall_plot	4.071	0.026	4.118