Package: YAPSA

Version: 1.9.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:YAPSA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings YAPSA_1.9.1.tar.gz

StartedAt: 2019-04-09 04:25:48 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:31:37 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 349.5 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 --install=check:YAPSA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings YAPSA_1.9.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/YAPSA.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.9.1’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
run_SMC 5.507  0.241    5.75
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL YAPSA
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘YAPSA’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (YAPSA)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(YAPSA)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: ggplot2
Loading required package: grid
> 
> test_check("YAPSA")
YAPSA:::shapiro_if_possible::error: Non-numeric inputYAPSA:::makeVRangesFromDataFrame::warning:strand  information missing, set to "+".
YAPSA:::makeVRangesFromDataFrame::in_PID.field found.  Retrieving PID information.
YAPSA:::makeVRangesFromDataFrame::in_subgroup.field found.  Retrieving subgroup information.
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 63 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 14.612   0.708  15.299 

name	user	system	elapsed
LCD	0.010	0.001	0.012
LCD_complex_cutoff	0.000	0.000	0.001
add_annotation	0.000	0.000	0.001
add_as_fist_to_list	0.000	0.000	0.001
aggregate_exposures_by_category	0.000	0.000	0.001
annotate_intermut_dist_PID	0.184	0.009	0.194
annotate_intermut_dist_cohort	0.028	0.002	0.031
annotation_exposures_barplot	0.000	0.001	0.000
annotation_heatmap_exposures	0	0	0
attribute_nucleotide_exchanges	0.004	0.000	0.004
build_gene_list_for_pathway	0	0	0
compare_SMCs	0	0	0
compare_exposures	0	0	0
compare_sets	0.005	0.001	0.005
compare_to_catalogues	0.000	0.000	0.001
complex_heatmap_exposures	0.890	0.045	0.935
compute_comparison_stat_df	0	0	0
cosineDist	0	0	0
create_mutation_catalogue_from_VR	1.978	0.117	2.095
create_mutation_catalogue_from_df	0.935	0.070	1.006
cut_breaks_as_intervals	0.195	0.004	0.202
exampleYAPSA	0.079	0.010	0.089
exposures_barplot	2.739	0.147	2.887
extract_names_from_gene_list	0	0	0
find_affected_PIDs	0.000	0.000	0.001
get_extreme_PIDs	0.030	0.002	0.032
hclust_exposures	0.007	0.001	0.008
makeVRangesFromDataFrame	0.099	0.004	0.104
make_catalogue_strata_df	0.000	0.000	0.001
make_comparison_matrix	0.104	0.006	0.113
make_strata_df	0	0	0
make_subgroups_df	0.041	0.006	0.048
melt_exposures	0	0	0
merge_exposures	0	0	0
normalizeMotifs_otherRownames	0.001	0.001	0.000
normalize_df_per_dim	0.011	0.001	0.012
plotExchangeSpectra	0	0	0
plot_SMC	0.001	0.000	0.000
plot_exposures	0.679	0.014	0.694
plot_strata	0	0	0
repeat_df	0.002	0.001	0.003
run_SMC	5.507	0.241	5.750
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	0.000	0.001	0.000
run_plot_strata_general	0.001	0.000	0.001
shapiro_if_possible	0.001	0.000	0.002
split_exposures_by_subgroups	0	0	0
stat_plot_subgroups	0.001	0.000	0.000
stat_test_SMC	0	0	0
stat_test_subgroups	0	0	0
stderrmean	0.000	0.000	0.001
sum_over_list_of_df	0.002	0.000	0.003
test_exposureAffected	0.000	0.000	0.001
test_gene_list_in_exposures	0.000	0.000	0.001
transform_rownames_R_to_MATLAB	0.000	0.000	0.001
translate_to_hg19	0.004	0.001	0.006
trellis_rainfall_plot	2.260	0.055	2.319