BioC 3.5: CHECK report for YAPSA on veracruz2

Package: YAPSA

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings YAPSA_1.2.0.tar.gz

StartedAt: 2017-10-18 10:13:36 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 10:20:03 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 386.8 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_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/YAPSA.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.2.0’
* 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 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 4.916  0.151   5.148
* 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	0.111	0.004	0.117
LCD_complex_cutoff	0.000	0.000	0.001
add_annotation	0.001	0.001	0.000
add_as_fist_to_list	0	0	0
aggregate_exposures_by_category	0.000	0.000	0.001
annotate_intermut_dist_PID	0.248	0.035	0.285
annotate_intermut_dist_cohort	0.069	0.001	0.070
annotation_exposures_barplot	0.000	0.000	0.001
annotation_heatmap_exposures	0.000	0.000	0.001
attribute_nucleotide_exchanges	0.004	0.001	0.003
build_gene_list_for_pathway	0.000	0.000	0.001
compare_SMCs	0.001	0.000	0.001
compare_exposures	0	0	0
compare_sets	0.019	0.001	0.020
compare_to_catalogues	0.000	0.000	0.001
complex_heatmap_exposures	2.127	0.017	2.168
compute_comparison_stat_df	0.001	0.000	0.000
cosineDist	0.001	0.000	0.001
create_mutation_catalogue_from_VR	3.318	0.285	4.445
create_mutation_catalogue_from_df	0.874	0.053	0.948
cut_breaks_as_intervals	1.325	0.014	1.359
exampleYAPSA	0.07	0.01	0.08
exposures_barplot	1.356	0.049	1.430
extract_names_from_gene_list	0	0	0
find_affected_PIDs	0.000	0.000	0.001
get_extreme_PIDs	0.028	0.002	0.029
hclust_exposures	0.008	0.001	0.009
makeVRangesFromDataFrame	0.071	0.005	0.079
make_catalogue_strata_df	0.001	0.000	0.001
make_comparison_matrix	0.117	0.009	0.131
make_strata_df	0.001	0.000	0.000
make_subgroups_df	0.037	0.006	0.043
melt_exposures	0.001	0.000	0.001
merge_exposures	0	0	0
normalizeMotifs_otherRownames	0.000	0.000	0.001
normalize_df_per_dim	0.011	0.001	0.012
plotExchangeSpectra	0	0	0
plot_SMC	0	0	0
plot_exposures	1.475	0.018	1.515
plot_strata	0	0	0
repeat_df	0.003	0.000	0.003
run_SMC	4.916	0.151	5.148
run_annotate_vcf_pl	0	0	0
run_comparison_catalogues	0.000	0.000	0.001
run_comparison_general	0	0	0
run_kmer_frequency_correction	0.001	0.001	0.001
run_kmer_frequency_normalization	0.001	0.000	0.000
run_plot_strata_general	0.001	0.000	0.000
shapiro_if_possible	0.001	0.000	0.002
split_exposures_by_subgroups	0	0	0
stat_plot_subgroups	0.000	0.000	0.001
stat_test_SMC	0.001	0.000	0.000
stat_test_subgroups	0.001	0.000	0.001
stderrmean	0.000	0.000	0.001
sum_over_list_of_df	0.003	0.001	0.003
test_exposureAffected	0	0	0
test_gene_list_in_exposures	0.001	0.000	0.001
transform_rownames_R_to_MATLAB	0.001	0.000	0.000
translate_to_hg19	0.004	0.001	0.005
trellis_rainfall_plot	2.571	0.022	2.631