Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-17 13:07:14 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for YAPSA on tokay2


To the developers/maintainers of the YAPSA package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/YAPSA.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2078/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
YAPSA 1.20.1  (landing page)
Daniel Huebschmann
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/YAPSA
git_branch: RELEASE_3_14
git_last_commit: 6c3f437
git_last_commit_date: 2021-11-29 09:31:15 -0500 (Mon, 29 Nov 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: YAPSA
Version: 1.20.1
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:YAPSA.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings YAPSA_1.20.1.tar.gz
StartedAt: 2022-01-17 05:44:53 -0500 (Mon, 17 Jan 2022)
EndedAt: 2022-01-17 05:56:45 -0500 (Mon, 17 Jan 2022)
EllapsedTime: 711.8 seconds
RetCode: 0
Status:   OK  
CheckDir: YAPSA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:YAPSA.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings YAPSA_1.20.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/YAPSA.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.20.1'
* package encoding: UTF-8
* 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 ... 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
* 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
* 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 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 ... NOTE
read_list: no visible global function definition for 'detectCores'
read_list: no visible global function definition for 'makeCluster'
read_list: no visible global function definition for 'mclapply'
read_list: no visible global function definition for 'stopCluster'
Undefined global functions or variables:
  detectCores makeCluster mclapply stopCluster
* 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
Examples with CPU (user + system) or elapsed time > 5s
                                         user system elapsed
confidence_indel_only_calulation        22.80   0.08   22.88
create_indel_mutation_catalogue_from_df 16.89   0.70   17.59
build_gene_list_for_pathway              7.60   0.56   23.96
run_SMC                                  5.47   0.45    5.92
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                         user system elapsed
confidence_indel_only_calulation        24.22   0.00   24.22
create_indel_mutation_catalogue_from_df 16.78   0.51   17.30
build_gene_list_for_pathway              8.44   0.02   24.70
run_SMC                                  5.78   0.36    6.18
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/YAPSA.Rcheck/00check.log'
for details.



Installation output

YAPSA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/YAPSA_1.20.1.tar.gz && rm -rf YAPSA.buildbin-libdir && mkdir YAPSA.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=YAPSA.buildbin-libdir YAPSA_1.20.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL YAPSA_1.20.1.zip && rm YAPSA_1.20.1.tar.gz YAPSA_1.20.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1293k  100 1293k    0     0  5377k      0 --:--:-- --:--:-- --:--:-- 5389k

install for i386

* installing *source* package 'YAPSA' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
** help
*** installing help indices
  converting help for package 'YAPSA'
    finding HTML links ... done
    GenomeOfNl_raw                          html  
    LCD                                     html  
    LCD_SMC                                 html  
    LCD_complex_cutoff                      html  
    MutCat_indel_df                         html  
    SMC                                     html  
    SMC_perPID                              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_exposures_list_barplot       html  
    annotation_heatmap_exposures            html  
    attribute_nucleotide_exchanges          html  
    attribute_sequence_contex_indel         html  
    attribution_of_indels                   html  
    build_gene_list_for_pathway             html  
    classify_indels                         html  
    compare_SMCs                            html  
    compare_exposures                       html  
    compare_expousre_sets                   html  
    compare_sets                            html  
    compare_to_catalogues                   html  
    complex_heatmap_exposures               html  
    computeLogLik                           html  
    compute_comparison_stat_df              html  
    confIntExp                              html  
    confidence_indel_calulation             html  
    confidence_indel_only_calulation        html  
    correct_rounded                         html  
    cosineDist                              html  
    cosineMatchDist                         html  
    create_indel_mut_cat_from_df            html  
    create_indel_mutation_catalogue_from_df
                                            html  
    create_mutation_catalogue_from_VR       html  
    create_mutation_catalogue_from_df       html  
    finding level-2 HTML links ... done

    cut_breaks_as_intervals                 html  
    cutoffs                                 html  
    cutoffs_pcawg                           html  
    deriveSigInd_df                         html  
    disambiguateVector                      html  
    enrichSigs                              html  
    exampleINDEL_YAPSA                      html  
    exampleYAPSA                            html  
    exchange_colour_vector                  html  
    exome_mutCatRaw_df                      html  
    exposures_barplot                       html  
    extract_names_from_gene_list            html  
    find_affected_PIDs                      html  
    getSequenceContext                      html  
    get_extreme_PIDs                        html  
    hclust_exposures                        html  
    logLikelihood                           html  
    lymphomaNature2013_mutCat_df            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  
    normalize_df_per_dim                    html  
    plotExchangeSpectra                     html  
    plotExchangeSpectra_indel               html  
    plotExposuresConfidence                 html  
    plotExposuresConfidence_indel           html  
    plot_SMC                                html  
    plot_exposures                          html  
    plot_strata                             html  
    read_entry                              html  
    relateSigs                              html  
    repeat_df                               html  
    round_precision                         html  
    run_SMC                                 html  
    run_annotate_vcf_pl                     html  
    run_comparison_catalogues               html  
    run_comparison_general                  html  
    run_kmer_frequency_correction           html  
    run_kmer_frequency_normalization        html  
    run_plot_strata_general                 html  
    shapiro_if_possible                     html  
    sigs                                    html  
    sigs_pcawg                              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  
    temp_trellis_rainfall_plot              html  
    testSigs                                html  
    test_exposureAffected                   html  
    test_gene_list_in_exposures             html  
    transform_rownames_R_to_MATLAB          html  
    translate_to_hg19                       html  
    trellis_rainfall_plot                   html  
    trellis_rainfall_plot_old               html  
    variateExp                              html  
    variateExpSingle                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
** testing if installed package can be loaded from final location
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'YAPSA' ...
** testing if installed package can be loaded
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
* MD5 sums
packaged installation of 'YAPSA' as YAPSA_1.20.1.zip
* DONE (YAPSA)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'YAPSA' successfully unpacked and MD5 sums checked

Tests output

YAPSA.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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.

> Sys.setenv(R_TESTS=" ")
> library(testthat)
> library(YAPSA)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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, 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, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
Loading required package: ggplot2
Loading required package: grid
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
> 
> 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.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 62 ]
> 
> proc.time()
   user  system elapsed 
  17.51    1.90   19.42 

YAPSA.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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.

> Sys.setenv(R_TESTS=" ")
> library(testthat)
> library(YAPSA)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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, 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, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
Loading required package: ggplot2
Loading required package: grid
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
> 
> 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.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 62 ]
> 
> proc.time()
   user  system elapsed 
  18.42    0.76   19.21 

Example timings

YAPSA.Rcheck/examples_i386/YAPSA-Ex.timings

nameusersystemelapsed
GenomeOfNl_raw0.010.000.01
LCD0.160.000.16
LCD_complex_cutoff000
MutCat_indel_df0.020.000.01
SMC000
SMC_perPID000
add_annotation000
add_as_fist_to_list000
aggregate_exposures_by_category000
annotate_intermut_dist_PID0.020.000.02
annotate_intermut_dist_cohort0.010.000.01
annotation_exposures_barplot000
annotation_exposures_list_barplot000
annotation_heatmap_exposures000
attribute_nucleotide_exchanges000
attribute_sequence_contex_indel0.610.090.70
attribution_of_indels1.370.391.77
build_gene_list_for_pathway 7.60 0.5623.96
classify_indels000
compare_SMCs000
compare_exposures000
compare_expousre_sets0.010.000.01
compare_sets000
compare_to_catalogues000
complex_heatmap_exposures1.220.081.30
computeLogLik000
compute_comparison_stat_df000
confIntExp1.840.372.22
confidence_indel_calulation0.000.020.01
confidence_indel_only_calulation22.80 0.0822.88
correct_rounded000
cosineDist000
cosineMatchDist000
create_indel_mut_cat_from_df1.510.001.52
create_indel_mutation_catalogue_from_df16.89 0.7017.59
create_mutation_catalogue_from_VR1.630.221.85
create_mutation_catalogue_from_df1.150.141.29
cut_breaks_as_intervals0.140.000.14
deriveSigInd_df000
disambiguateVector000
enrichSigs000
exampleYAPSA0.130.000.13
exome_mutCatRaw_df0.010.000.02
exposures_barplot2.830.082.90
extract_names_from_gene_list000
find_affected_PIDs000
getSequenceContext0.160.000.15
get_extreme_PIDs0.030.000.03
hclust_exposures0.020.000.02
logLikelihood1.200.161.36
lymphomaNature2013_mutCat_df0.010.000.02
makeVRangesFromDataFrame0.220.010.23
make_catalogue_strata_df000
make_comparison_matrix0.100.000.09
make_strata_df000
make_subgroups_df0.050.000.05
melt_exposures000
merge_exposures000
normalizeMotifs_otherRownames000
normalize_df_per_dim0.020.000.01
plotExchangeSpectra000
plotExchangeSpectra_indel1.090.021.11
plotExposuresConfidence000
plotExposuresConfidence_indel000
plot_SMC000
plot_exposures0.470.000.47
plot_strata000
read_entry000
relateSigs000
repeat_df0.010.000.02
round_precision000
run_SMC5.470.455.92
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
temp_trellis_rainfall_plot1.850.011.88
testSigs000
test_exposureAffected000
test_gene_list_in_exposures000
transform_rownames_R_to_MATLAB000
translate_to_hg19000
trellis_rainfall_plot1.970.021.99
trellis_rainfall_plot_old1.810.031.84
variateExp2.820.132.94
variateExpSingle1.130.181.32

YAPSA.Rcheck/examples_x64/YAPSA-Ex.timings

nameusersystemelapsed
GenomeOfNl_raw0.000.020.02
LCD0.010.000.01
LCD_complex_cutoff000
MutCat_indel_df0.000.010.02
SMC000
SMC_perPID000
add_annotation000
add_as_fist_to_list000
aggregate_exposures_by_category000
annotate_intermut_dist_PID0.020.000.02
annotate_intermut_dist_cohort0.010.000.01
annotation_exposures_barplot000
annotation_exposures_list_barplot000
annotation_heatmap_exposures000
attribute_nucleotide_exchanges000
attribute_sequence_contex_indel0.550.030.58
attribution_of_indels0.450.110.56
build_gene_list_for_pathway 8.44 0.0224.70
classify_indels000
compare_SMCs000
compare_exposures000
compare_expousre_sets0.010.000.02
compare_sets000
compare_to_catalogues000
complex_heatmap_exposures1.330.051.37
computeLogLik000
compute_comparison_stat_df000
confIntExp1.750.171.92
confidence_indel_calulation0.020.000.02
confidence_indel_only_calulation24.22 0.0024.22
correct_rounded000
cosineDist000
cosineMatchDist000
create_indel_mut_cat_from_df0.810.000.81
create_indel_mutation_catalogue_from_df16.78 0.5117.30
create_mutation_catalogue_from_VR1.840.111.96
create_mutation_catalogue_from_df1.250.191.43
cut_breaks_as_intervals0.140.000.14
deriveSigInd_df000
disambiguateVector000
enrichSigs000
exampleYAPSA0.050.050.10
exome_mutCatRaw_df0.000.010.01
exposures_barplot3.200.023.22
extract_names_from_gene_list000
find_affected_PIDs000
getSequenceContext0.170.010.19
get_extreme_PIDs0.030.000.03
hclust_exposures0.020.000.02
logLikelihood1.250.141.39
lymphomaNature2013_mutCat_df0.000.020.01
makeVRangesFromDataFrame0.200.000.21
make_catalogue_strata_df000
make_comparison_matrix0.110.000.11
make_strata_df000
make_subgroups_df0.050.000.04
melt_exposures000
merge_exposures000
normalizeMotifs_otherRownames000
normalize_df_per_dim0.010.000.02
plotExchangeSpectra000
plotExchangeSpectra_indel1.240.021.25
plotExposuresConfidence000
plotExposuresConfidence_indel000
plot_SMC000
plot_exposures0.480.000.49
plot_strata000
read_entry000
relateSigs000
repeat_df000
round_precision000
run_SMC5.780.366.18
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
temp_trellis_rainfall_plot1.920.051.96
testSigs000
test_exposureAffected000
test_gene_list_in_exposures000
transform_rownames_R_to_MATLAB000
translate_to_hg19000
trellis_rainfall_plot2.020.002.02
trellis_rainfall_plot_old1.970.032.00
variateExp3.090.163.25
variateExpSingle1.300.191.48