Multiple platform build/check report for BioC 3.6 - CHECK report for YAPSA on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings YAPSA_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/YAPSA.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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 ‘1.4.0’
* 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
* 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

Installation output

* 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)

Tests output


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, cbind, colMeans, colSums, colnames, 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 
 12.680   0.284  13.400

Example timings

name	user	system	elapsed
LCD	0.100	0.000	0.101
LCD_complex_cutoff	0.004	0.000	0.000
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	0.692	0.004	0.698
annotate_intermut_dist_cohort	0.068	0.000	0.069
annotation_exposures_barplot	0	0	0
annotation_heatmap_exposures	0	0	0
attribute_nucleotide_exchanges	0.004	0.000	0.003
build_gene_list_for_pathway	0.000	0.000	0.001
compare_SMCs	0.004	0.000	0.001
compare_exposures	0	0	0
compare_sets	0.02	0.00	0.02
compare_to_catalogues	0	0	0
complex_heatmap_exposures	2.172	0.020	2.194
compute_comparison_stat_df	0	0	0
cosineDist	0	0	0
create_mutation_catalogue_from_VR	3.704	0.056	3.765
create_mutation_catalogue_from_df	0.808	0.072	0.883
cut_breaks_as_intervals	0.664	0.004	0.669
exampleYAPSA	0.072	0.000	0.072
exposures_barplot	1.196	0.000	1.194
extract_names_from_gene_list	0	0	0
find_affected_PIDs	0	0	0
get_extreme_PIDs	0.024	0.000	0.024
hclust_exposures	0.004	0.000	0.007
makeVRangesFromDataFrame	0.072	0.008	0.079
make_catalogue_strata_df	0.000	0.000	0.001
make_comparison_matrix	0.104	0.000	0.108
make_strata_df	0	0	0
make_subgroups_df	0.036	0.004	0.039
melt_exposures	0	0	0
merge_exposures	0	0	0
normalizeMotifs_otherRownames	0	0	0
normalize_df_per_dim	0.008	0.000	0.010
plotExchangeSpectra	0	0	0
plot_SMC	0	0	0
plot_exposures	1.512	0.000	1.517
plot_strata	0	0	0
repeat_df	0.004	0.000	0.002
run_SMC	4.600	0.064	4.669
run_annotate_vcf_pl	0.004	0.000	0.000
run_comparison_catalogues	0	0	0
run_comparison_general	0	0	0
run_kmer_frequency_correction	0	0	0
run_kmer_frequency_normalization	0	0	0
run_plot_strata_general	0	0	0
shapiro_if_possible	0.000	0.000	0.001
split_exposures_by_subgroups	0.004	0.000	0.000
stat_plot_subgroups	0	0	0
stat_test_SMC	0	0	0
stat_test_subgroups	0	0	0
stderrmean	0.004	0.000	0.000
sum_over_list_of_df	0.000	0.000	0.002
test_exposureAffected	0	0	0
test_gene_list_in_exposures	0	0	0
transform_rownames_R_to_MATLAB	0	0	0
translate_to_hg19	0.004	0.000	0.004
trellis_rainfall_plot	2.964	0.000	2.981

CHECK report for YAPSA on malbec1

Summary

Command output

Installation output

Tests output

Example timings