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CHECK report for YAPSA on tokay1

This page was generated on 2018-04-12 13:28:37 -0400 (Thu, 12 Apr 2018).

Package 1467/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
YAPSA 1.4.0
Daniel Huebschmann
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/YAPSA
Branch: RELEASE_3_6
Last Commit: 6f24150
Last Changed Date: 2017-10-30 12:41:21 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: YAPSA
Version: 1.4.0
Command: rm -rf YAPSA.buildbin-libdir YAPSA.Rcheck && mkdir YAPSA.buildbin-libdir YAPSA.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=YAPSA.buildbin-libdir YAPSA_1.4.0.tar.gz >YAPSA.Rcheck\00install.out 2>&1 && cp YAPSA.Rcheck\00install.out YAPSA-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=YAPSA.buildbin-libdir --install="check:YAPSA-install.out" --force-multiarch --no-vignettes --timings YAPSA_1.4.0.tar.gz
StartedAt: 2018-04-12 03:52:58 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 04:01:21 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 502.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: YAPSA.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf YAPSA.buildbin-libdir YAPSA.Rcheck && mkdir YAPSA.buildbin-libdir YAPSA.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=YAPSA.buildbin-libdir YAPSA_1.4.0.tar.gz >YAPSA.Rcheck\00install.out 2>&1 && cp YAPSA.Rcheck\00install.out YAPSA-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=YAPSA.buildbin-libdir --install="check:YAPSA-install.out" --force-multiarch --no-vignettes --timings YAPSA_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/YAPSA.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'YAPSA' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_VR.Rd:49: missing file link 'mutationContext'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_VR.Rd:51: missing file link 'motifMatrix'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_VR.Rd:18: missing file link 'mutationContext'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_VR.Rd:22: missing file link 'mutationContext'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_VR.Rd:86: missing file link 'mutationContext'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_VR.Rd:88: missing file link 'motifMatrix'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_df.Rd:39: missing file link 'mutationContext'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_df.Rd:43: missing file link 'mutationContext'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/normalizeMotifs_otherRownames.Rd:20: missing file link 'normalizeMotifs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/normalizeMotifs_otherRownames.Rd:22: missing file link 'SomaticSignatures'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/normalizeMotifs_otherRownames.Rd:10: missing file link 'normalizeMotifs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/normalizeMotifs_otherRownames.Rd:15: missing file link 'normalizeMotifs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_correction.Rd:40: missing file link 'normalizeMotifs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_correction.Rd:51: missing file link 'normalizeMotifs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_correction.Rd:52: missing file link 'kmerFrequency'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_correction.Rd:62: missing file link 'normalizeMotifs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_normalization.Rd:29: missing file link 'normalizeMotifs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_normalization.Rd:40: missing file link 'normalizeMotifs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_normalization.Rd:41: missing file link 'kmerFrequency'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_normalization.Rd:51: missing file link 'normalizeMotifs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/translate_to_hg19.Rd:31: missing file link 'BSgenome.Hsapiens.UCSC.hg19'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/YAPSA.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
run_SMC 6.16   0.19    6.35
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/YAPSA.Rcheck/00check.log'
for details.



Installation output

YAPSA.Rcheck/00install.out


install for i386

* installing *source* package 'YAPSA' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'YAPSA'
    finding HTML links ... done
    LCD                                     html  
    LCD_complex_cutoff                      html  
    YAPSA                                   html  
    add_annotation                          html  
    add_as_fist_to_list                     html  
    aggregate_exposures_by_category         html  
    annotate_intermut_dist_PID              html  
    annotate_intermut_dist_cohort           html  
    annotation_exposures_barplot            html  
    annotation_heatmap_exposures            html  
    attribute_nucleotide_exchanges          html  
    build_gene_list_for_pathway             html  
    compare_SMCs                            html  
    compare_exposures                       html  
    compare_sets                            html  
    compare_to_catalogues                   html  
    complex_heatmap_exposures               html  
    compute_comparison_stat_df              html  
    cosineDist                              html  
    create_mutation_catalogue_from_VR       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_VR.Rd:49: missing file link 'mutationContext'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_VR.Rd:51: missing file link 'motifMatrix'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_VR.Rd:18: missing file link 'mutationContext'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_VR.Rd:22: missing file link 'mutationContext'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_VR.Rd:86: missing file link 'mutationContext'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_VR.Rd:88: missing file link 'motifMatrix'
    create_mutation_catalogue_from_df       html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_df.Rd:39: missing file link 'mutationContext'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_df.Rd:43: missing file link 'mutationContext'
    cut_breaks_as_intervals                 html  
    cutoffs                                 html  
    exampleYAPSA                            html  
    exchange_colour_vector                  html  
    exposures_barplot                       html  
    extract_names_from_gene_list            html  
    find_affected_PIDs                      html  
    get_extreme_PIDs                        html  
    hclust_exposures                        html  
    makeVRangesFromDataFrame                html  
    make_catalogue_strata_df                html  
    make_comparison_matrix                  html  
    make_strata_df                          html  
    make_subgroups_df                       html  
    melt_exposures                          html  
    merge_exposures                         html  
    normalizeMotifs_otherRownames           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/normalizeMotifs_otherRownames.Rd:20: missing file link 'normalizeMotifs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/normalizeMotifs_otherRownames.Rd:22: missing file link 'SomaticSignatures'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/normalizeMotifs_otherRownames.Rd:10: missing file link 'normalizeMotifs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/normalizeMotifs_otherRownames.Rd:15: missing file link 'normalizeMotifs'
    normalize_df_per_dim                    html  
    plotExchangeSpectra                     html  
    plot_SMC                                html  
    plot_exposures                          html  
    plot_strata                             html  
    repeat_df                               html  
    run_SMC                                 html  
    run_annotate_vcf_pl                     html  
    run_comparison_catalogues               html  
    run_comparison_general                  html  
    run_kmer_frequency_correction           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_correction.Rd:40: missing file link 'normalizeMotifs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_correction.Rd:51: missing file link 'normalizeMotifs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_correction.Rd:52: missing file link 'kmerFrequency'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_correction.Rd:62: missing file link 'normalizeMotifs'
    run_kmer_frequency_normalization        html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_normalization.Rd:29: missing file link 'normalizeMotifs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_normalization.Rd:40: missing file link 'normalizeMotifs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_normalization.Rd:41: missing file link 'kmerFrequency'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_normalization.Rd:51: missing file link 'normalizeMotifs'
    run_plot_strata_general                 html  
    shapiro_if_possible                     html  
    sigs                                    html  
    split_exposures_by_subgroups            html  
    stat_plot_subgroups                     html  
    stat_test_SMC                           html  
    stat_test_subgroups                     html  
    stderrmean                              html  
    sum_over_list_of_df                     html  
    targetCapture_cor_factors               html  
    test_exposureAffected                   html  
    test_gene_list_in_exposures             html  
    transform_rownames_R_to_MATLAB          html  
    translate_to_hg19                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/translate_to_hg19.Rd:31: missing file link 'BSgenome.Hsapiens.UCSC.hg19'
    trellis_rainfall_plot                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'YAPSA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'YAPSA' as YAPSA_1.4.0.zip
* DONE (YAPSA)
In R CMD INSTALL
In R CMD INSTALL

Tests output

YAPSA.Rcheck/tests_i386/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
  13.45    0.56   14.12 

YAPSA.Rcheck/tests_x64/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  14.78    0.53   15.40 

Example timings

YAPSA.Rcheck/examples_i386/YAPSA-Ex.timings

nameusersystemelapsed
LCD0.100.000.11
LCD_complex_cutoff000
add_annotation000
add_as_fist_to_list000
aggregate_exposures_by_category000
annotate_intermut_dist_PID0.270.000.27
annotate_intermut_dist_cohort0.060.000.06
annotation_exposures_barplot000
annotation_heatmap_exposures000
attribute_nucleotide_exchanges0.010.000.02
build_gene_list_for_pathway000
compare_SMCs000
compare_exposures000
compare_sets0.020.000.01
compare_to_catalogues000
complex_heatmap_exposures2.590.072.66
compute_comparison_stat_df000
cosineDist000
create_mutation_catalogue_from_VR3.350.123.47
create_mutation_catalogue_from_df0.830.050.87
cut_breaks_as_intervals0.70.00.7
exampleYAPSA0.090.010.11
exposures_barplot1.220.001.22
extract_names_from_gene_list000
find_affected_PIDs000
get_extreme_PIDs0.020.020.03
hclust_exposures0.010.000.02
makeVRangesFromDataFrame0.080.000.08
make_catalogue_strata_df000
make_comparison_matrix0.130.020.14
make_strata_df000
make_subgroups_df0.030.010.05
melt_exposures000
merge_exposures000
normalizeMotifs_otherRownames000
normalize_df_per_dim0.010.000.01
plotExchangeSpectra000
plot_SMC000
plot_exposures1.420.001.42
plot_strata000
repeat_df000
run_SMC4.770.194.95
run_annotate_vcf_pl000
run_comparison_catalogues000
run_comparison_general000
run_kmer_frequency_correction000
run_kmer_frequency_normalization000
run_plot_strata_general000
shapiro_if_possible000
split_exposures_by_subgroups000
stat_plot_subgroups000
stat_test_SMC000
stat_test_subgroups000
stderrmean000
sum_over_list_of_df000
test_exposureAffected000
test_gene_list_in_exposures000
transform_rownames_R_to_MATLAB000
translate_to_hg19000
trellis_rainfall_plot2.470.012.53

YAPSA.Rcheck/examples_x64/YAPSA-Ex.timings

nameusersystemelapsed
LCD0.140.000.14
LCD_complex_cutoff000
add_annotation000
add_as_fist_to_list000
aggregate_exposures_by_category000
annotate_intermut_dist_PID0.350.000.34
annotate_intermut_dist_cohort0.090.000.10
annotation_exposures_barplot000
annotation_heatmap_exposures000
attribute_nucleotide_exchanges000
build_gene_list_for_pathway0.020.000.01
compare_SMCs000
compare_exposures000
compare_sets0.590.000.60
compare_to_catalogues000
complex_heatmap_exposures2.660.002.65
compute_comparison_stat_df000
cosineDist000
create_mutation_catalogue_from_VR3.480.063.55
create_mutation_catalogue_from_df0.920.050.97
cut_breaks_as_intervals0.860.000.86
exampleYAPSA0.110.000.11
exposures_barplot1.480.021.50
extract_names_from_gene_list000
find_affected_PIDs000
get_extreme_PIDs0.030.010.05
hclust_exposures000
makeVRangesFromDataFrame0.110.000.11
make_catalogue_strata_df000
make_comparison_matrix0.130.020.14
make_strata_df000
make_subgroups_df0.050.000.05
melt_exposures000
merge_exposures0.010.000.01
normalizeMotifs_otherRownames000
normalize_df_per_dim000
plotExchangeSpectra000
plot_SMC000
plot_exposures1.750.001.75
plot_strata000
repeat_df000
run_SMC6.160.196.35
run_annotate_vcf_pl000
run_comparison_catalogues000
run_comparison_general000
run_kmer_frequency_correction000
run_kmer_frequency_normalization000
run_plot_strata_general000
shapiro_if_possible000
split_exposures_by_subgroups000
stat_plot_subgroups000
stat_test_SMC000
stat_test_subgroups000
stderrmean000
sum_over_list_of_df000
test_exposureAffected000
test_gene_list_in_exposures000
transform_rownames_R_to_MATLAB000
translate_to_hg190.010.000.01
trellis_rainfall_plot2.890.002.89