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This page was generated on 2022-01-17 11:07:53 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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 musicatk on riesling1


To the developers/maintainers of the musicatk package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/musicatk.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 1249/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
musicatk 1.5.0  (landing page)
Aaron Chevalier
Snapshot Date: 2022-01-16 13:55:18 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/musicatk
git_branch: master
git_last_commit: ab8dbf0
git_last_commit_date: 2021-10-26 13:04:15 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'SummarizedExperiment' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: musicatk
Version: 1.5.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:musicatk.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings musicatk_1.5.0.tar.gz
StartedAt: 2022-01-16 19:35:29 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 19:40:24 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 295.3 seconds
RetCode: 0
Status:   OK  
CheckDir: musicatk.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:musicatk.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings musicatk_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/musicatk.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'musicatk/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'musicatk' version '1.5.0'
* 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 'musicatk' 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 ... NOTE
Namespaces in Imports field not imported from:
  'TCGAbiolinks' 'shinyBS' 'shinyalert' 'shinybusy' 'shinydashboard'
  'shinyjqui' 'shinyjs' 'sortable'
  All declared Imports should be used.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
build_standard_table 5.28   0.92     6.2
* 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: 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/musicatk.Rcheck/00check.log'
for details.



Installation output

musicatk.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL musicatk
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'musicatk' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'musicatk'
    finding HTML links ... done
    add_flank_to_variants                   html  
    finding level-2 HTML links ... done

    add_variant_type                        html  
    annotate_replication_strand             html  
    annotate_transcript_strand              html  
    annotate_variant_length                 html  
    annotate_variant_type                   html  
    auto_predict_grid                       html  
    auto_subset_sigs                        html  
    build_custom_table                      html  
    build_standard_table                    html  
    built_tables                            html  
    cluster_exposure                        html  
    combine_count_tables                    html  
    combine_predict_grid                    html  
    compare_cosmic_v2                       html  
    compare_cosmic_v3                       html  
    compare_results                         html  
    cosmic_v2_sigs                          html  
    cosmic_v2_subtype_map                   html  
    cosmic_v3_dbs_sigs                      html  
    cosmic_v3_indel_sigs                    html  
    cosmic_v3_sbs_sigs                      html  
    cosmic_v3_sbs_sigs_exome                html  
    count_table-class                       html  
    create_dbs78_table                      html  
    create_musica                           html  
    create_sbs192_table                     html  
    create_sbs96_table                      html  
    create_umap                             html  
    dbs_musica                              html  
    discover_signatures                     html  
    dot-jsd                                 html  
    drop_annotation                         html  
    exposure_differential_analysis          html  
    exposures                               html  
    extract_count_tables                    html  
    extract_variants                        html  
    extract_variants_from_maf               html  
    extract_variants_from_maf_file          html  
    extract_variants_from_matrix            html  
    extract_variants_from_vcf               html  
    extract_variants_from_vcf_file          html  
    generate_result_grid                    html  
    get_musica                              html  
    indel_musica                            html  
    k_select                                html  
    musica-class                            html  
    musica                                  html  
    musica_annot                            html  
    musica_result-class                     html  
    musica_result_grid-class                html  
    musica_sbs96                            html  
    musica_sbs96_tiny                       html  
    musicatk                                html  
    name_signatures                         html  
    pipe                                    html  
    plot_cluster                            html  
    plot_differential_analysis              html  
    plot_exposures                          html  
    plot_heatmap                            html  
    plot_sample_counts                      html  
    plot_sample_reconstruction_error        html  
    plot_signatures                         html  
    plot_umap                               html  
    predict_exposure                        html  
    rc                                      html  
    rep_range                               html  
    res                                     html  
    res_annot                               html  
    samp_annot                              html  
    sample_names                            html  
    select_genome                           html  
    signatures                              html  
    subset_musica_by_annotation             html  
    subset_musica_by_counts                 html  
    subset_variant_by_type                  html  
    subset_variants_by_samples              html  
    table_96                                html  
    table_selected                          html  
    tables                                  html  
    umap                                    html  
    variants                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (musicatk)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'ReportingTools' is missing or broken
 done

Tests output

musicatk.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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.

> library("testthat")
> library("musicatk")
Loading required package: NMF
Loading required package: pkgmaker
Loading required package: registry
Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: windows] | Cores 79/80

Attaching package: 'NMF'

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

    compare

> 
> test_check("musicatk")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 42 ]
> 
> proc.time()
   user  system elapsed 
  15.39    1.00   16.42 

Example timings

musicatk.Rcheck/musicatk-Ex.timings

nameusersystemelapsed
add_flank_to_variants2.610.403.00
add_variant_type0.000.010.02
annotate_replication_strand0.120.000.13
annotate_transcript_strand1.060.021.08
annotate_variant_length0.020.000.01
annotate_variant_type000
auto_predict_grid2.520.092.61
build_custom_table0.730.030.77
build_standard_table5.280.926.20
built_tables0.000.020.01
cluster_exposure0.020.000.02
combine_count_tables1.780.282.06
combine_predict_grid1.640.051.69
compare_cosmic_v21.550.001.54
compare_cosmic_v30.670.000.67
compare_results101
cosmic_v2_subtype_map000
create_musica0.570.150.72
create_umap3.460.053.52
discover_signatures0.440.130.56
drop_annotation000
exposure_differential_analysis0.020.000.02
exposures0.000.010.01
extract_count_tables000
extract_variants2.920.032.96
extract_variants_from_maf0.080.000.07
extract_variants_from_maf_file0.060.000.06
extract_variants_from_matrix0.090.010.11
extract_variants_from_vcf0.460.030.49
extract_variants_from_vcf_file0.310.000.31
generate_result_grid0.270.000.26
get_musica0.010.000.02
k_select0.580.040.61
musicatk000
name_signatures000
pipe000
plot_cluster3.970.144.12
plot_differential_analysis0.120.000.13
plot_exposures0.140.000.14
plot_heatmap0.600.000.59
plot_sample_counts0.220.000.22
plot_sample_reconstruction_error0.390.000.39
plot_signatures0.360.000.36
plot_umap3.730.043.80
predict_exposure0.940.131.06
rc000
samp_annot0.000.010.02
sample_names000
select_genome000
signatures0.000.020.01
subset_musica_by_annotation000
subset_musica_by_counts0.010.000.02
subset_variant_by_type000
subset_variants_by_samples0.020.000.01
table_selected000
tables0.000.020.02
umap000
variants0.000.010.02