Multiple platform build/check report for BioC 3.12 - CHECK report for musicatk on tokay1

Package: musicatk

Version: 1.0.0

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:musicatk.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings musicatk_1.0.0.tar.gz

StartedAt: 2021-05-06 04:57:28 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 05:08:02 -0400 (Thu, 06 May 2021)

EllapsedTime: 634.0 seconds

RetCode: 0

Status: OK

CheckDir: musicatk.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:musicatk.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings musicatk_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/musicatk.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.0.0'
* 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
* 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 ... 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 R/sysdata.rda ... 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
build_standard_table 11.42   1.31   12.75
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
build_standard_table 12.97   1.36   14.33
extract_variants      5.56   0.11    5.68
plot_umap             5.25   0.05    5.29
create_umap           4.97   0.08    5.04
* 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: OK

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/musicatk_1.0.0.tar.gz && rm -rf musicatk.buildbin-libdir && mkdir musicatk.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=musicatk.buildbin-libdir musicatk_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL musicatk_1.0.0.zip && rm musicatk_1.0.0.tar.gz musicatk_1.0.0.zip
###
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  % 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  679k  100  679k    0     0  11.1M      0 --:--:-- --:--:-- --:--:-- 11.4M

install for i386

* installing *source* package 'musicatk' ...
** using staged installation
** R
** data
** 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  
    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_dbs_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  
    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  
    indel_musica                            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  
    name_signatures                         html  
    pipe                                    html  
    plot_exposures                          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_name                              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

install for x64

* installing *source* package 'musicatk' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'musicatk' as musicatk_1.0.0.zip
* DONE (musicatk)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'musicatk' successfully unpacked and MD5 sums checked


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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.

> 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 39/40

Attaching package: 'NMF'

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

    compare

> 
> test_check("musicatk")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
> 
> proc.time()
   user  system elapsed 
  20.42    1.92   24.04


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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 39/40

Attaching package: 'NMF'

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

    compare

> 
> test_check("musicatk")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
> 
> proc.time()
   user  system elapsed 
  22.87    0.57   25.82

name	user	system	elapsed
add_flank_to_variants	3.56	0.55	4.11
add_variant_type	0.03	0.00	0.03
annotate_replication_strand	0.55	0.14	0.68
annotate_transcript_strand	1.25	0.18	1.44
annotate_variant_length	0.03	0.00	0.03
annotate_variant_type	0.02	0.02	0.03
auto_predict_grid	2.53	0.03	2.56
build_custom_table	2.03	0.02	2.05
build_standard_table	11.42	1.31	12.75
combine_count_tables	2.79	0.22	3.00
combine_predict_grid	2.57	0.01	2.59
compare_cosmic_v2	2.46	0.05	2.50
compare_cosmic_v3	1.37	0.03	1.41
compare_results	1.66	0.03	1.69
cosmic_v2_subtype_map	0	0	0
create_musica	0.83	0.13	1.17
create_umap	3.92	0.04	3.97
discover_signatures	0.76	0.11	1.81
drop_annotation	0.03	0.00	0.03
exposures	0.04	0.05	0.08
extract_count_tables	0.03	0.02	0.04
extract_variants	4.51	0.01	4.54
extract_variants_from_maf	0.14	0.03	0.17
extract_variants_from_maf_file	0.16	0.00	0.15
extract_variants_from_matrix	0.17	0.00	0.18
extract_variants_from_vcf	1.05	0.02	1.06
extract_variants_from_vcf_file	0.53	0.00	0.53
generate_result_grid	0.42	0.00	0.42
musica	0.03	0.00	0.03
name_signatures	0.00	0.03	0.03
pipe	0	0	0
plot_exposures	0.17	0.00	0.17
plot_sample_counts	0.45	0.02	0.47
plot_sample_reconstruction_error	0.8	0.0	0.8
plot_signatures	0.80	0.01	0.81
plot_umap	3.93	0.02	4.28
predict_exposure	1.40	0.36	1.75
rc	0	0	0
samp_annot	0.03	0.03	0.06
sample_names	0.01	0.00	0.02
select_genome	0	0	0
signatures	0.03	0.04	0.08
subset_musica_by_annotation	0.03	0.02	0.04
subset_musica_by_counts	0.04	0.00	0.04
subset_variant_by_type	0.03	0.02	0.04
subset_variants_by_samples	0.00	0.03	0.03
table_name	0.00	0.03	0.03
tables	0.06	0.00	0.07
umap	0.03	0.04	0.08
variants	0.05	0.04	0.07

name	user	system	elapsed
add_flank_to_variants	3.03	0.27	3.30
add_variant_type	0.03	0.01	0.05
annotate_replication_strand	1.86	0.20	2.06
annotate_transcript_strand	1.56	0.07	1.63
annotate_variant_length	0.02	0.01	0.03
annotate_variant_type	0.00	0.02	0.02
auto_predict_grid	3.23	0.01	3.25
build_custom_table	1.53	0.05	1.57
build_standard_table	12.97	1.36	14.33
combine_count_tables	3.01	0.30	3.31
combine_predict_grid	2.36	0.01	2.37
compare_cosmic_v2	2.52	0.03	2.55
compare_cosmic_v3	0.96	0.02	0.98
compare_results	1.32	0.00	1.32
cosmic_v2_subtype_map	0	0	0
create_musica	0.68	0.37	1.06
create_umap	4.97	0.08	5.04
discover_signatures	1.02	0.13	1.18
drop_annotation	0.03	0.00	0.03
exposures	0.00	0.06	0.06
extract_count_tables	0.02	0.03	0.05
extract_variants	5.56	0.11	5.68
extract_variants_from_maf	0.12	0.00	0.13
extract_variants_from_maf_file	0.11	0.00	0.11
extract_variants_from_matrix	0.14	0.00	0.14
extract_variants_from_vcf	0.69	0.02	0.70
extract_variants_from_vcf_file	0.47	0.00	0.47
generate_result_grid	0.37	0.01	0.39
musica	0.02	0.02	0.03
name_signatures	0.00	0.01	0.02
pipe	0.02	0.00	0.01
plot_exposures	0.29	0.00	0.30
plot_sample_counts	0.41	0.03	0.44
plot_sample_reconstruction_error	0.73	0.04	0.76
plot_signatures	0.55	0.01	0.57
plot_umap	5.25	0.05	5.29
predict_exposure	1.87	0.12	2.00
rc	0	0	0
samp_annot	0.05	0.03	0.08
sample_names	0.03	0.00	0.03
select_genome	0	0	0
signatures	0.03	0.04	0.07
subset_musica_by_annotation	0.04	0.01	0.04
subset_musica_by_counts	0.01	0.02	0.03
subset_variant_by_type	0.02	0.03	0.05
subset_variants_by_samples	0.03	0.00	0.03
table_name	0.00	0.03	0.03
tables	0.03	0.03	0.07
umap	0.01	0.03	0.04
variants	0.05	0.00	0.05

CHECK report for musicatk on tokay1

Summary

Command output

Installation output

Tests output

Example timings