Package: YAPSA

Version: 1.8.0

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_1.8.0.tar.gz

StartedAt: 2019-04-16 03:25:13 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 03:30:40 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 327.1 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_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/YAPSA.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.8.0’
* 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 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 5.111  0.306   5.417
* 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/3.5/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 version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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, lengths, 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 
 14.103   0.716  14.800 

name	user	system	elapsed
LCD	0.008	0.000	0.009
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	0.299	0.002	0.301
annotate_intermut_dist_cohort	0.028	0.001	0.028
annotation_exposures_barplot	0.001	0.000	0.001
annotation_heatmap_exposures	0.000	0.000	0.001
attribute_nucleotide_exchanges	0.003	0.000	0.004
build_gene_list_for_pathway	0.000	0.001	0.000
compare_SMCs	0	0	0
compare_exposures	0	0	0
compare_sets	0.006	0.000	0.006
compare_to_catalogues	0	0	0
complex_heatmap_exposures	1.832	0.036	1.868
compute_comparison_stat_df	0.000	0.000	0.001
cosineDist	0.001	0.000	0.000
create_mutation_catalogue_from_VR	1.852	0.141	1.992
create_mutation_catalogue_from_df	0.889	0.090	0.980
cut_breaks_as_intervals	0.185	0.009	0.195
exampleYAPSA	0.097	0.013	0.110
exposures_barplot	1.455	0.066	1.521
extract_names_from_gene_list	0.001	0.000	0.001
find_affected_PIDs	0.000	0.000	0.001
get_extreme_PIDs	0.038	0.007	0.044
hclust_exposures	0.010	0.003	0.012
makeVRangesFromDataFrame	0.154	0.008	0.162
make_catalogue_strata_df	0	0	0
make_comparison_matrix	0.104	0.009	0.114
make_strata_df	0	0	0
make_subgroups_df	0.040	0.006	0.047
melt_exposures	0	0	0
merge_exposures	0	0	0
normalizeMotifs_otherRownames	0	0	0
normalize_df_per_dim	0.011	0.000	0.012
plotExchangeSpectra	0	0	0
plot_SMC	0	0	0
plot_exposures	0.699	0.008	0.707
plot_strata	0	0	0
repeat_df	0.002	0.000	0.003
run_SMC	5.111	0.306	5.417
run_annotate_vcf_pl	0.001	0.000	0.000
run_comparison_catalogues	0	0	0
run_comparison_general	0	0	0
run_kmer_frequency_correction	0.000	0.000	0.001
run_kmer_frequency_normalization	0	0	0
run_plot_strata_general	0	0	0
shapiro_if_possible	0.001	0.001	0.001
split_exposures_by_subgroups	0	0	0
stat_plot_subgroups	0	0	0
stat_test_SMC	0	0	0
stat_test_subgroups	0.001	0.000	0.000
stderrmean	0.001	0.000	0.001
sum_over_list_of_df	0.003	0.000	0.003
test_exposureAffected	0	0	0
test_gene_list_in_exposures	0.000	0.001	0.001
transform_rownames_R_to_MATLAB	0.000	0.000	0.001
translate_to_hg19	0.005	0.000	0.005
trellis_rainfall_plot	2.980	0.020	3.002