Multiple platform build/check report for BioC 3.13 - CHECK results for musicatk on tokay2

Package: musicatk

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:musicatk.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings musicatk_1.2.0.tar.gz

StartedAt: 2021-10-15 02:31:28 -0400 (Fri, 15 Oct 2021)

EndedAt: 2021-10-15 02:41:35 -0400 (Fri, 15 Oct 2021)

EllapsedTime: 607.1 seconds

RetCode: 0

Status: OK

CheckDir: musicatk.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:musicatk.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings musicatk_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/musicatk.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.2.0'
* 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 ... NOTE
plot_heatmap: no visible binding for global variable '.'
Undefined global functions or variables:
  .
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
build_standard_table 8.55   0.91    9.45
extract_variants     5.14   0.00    5.22
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
build_standard_table 9.32   0.83   10.16
extract_variants     7.36   0.00    7.36
plot_cluster         5.78   0.03    5.83
create_umap          5.03   0.03    5.08
* 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-3.13-bioc/meat/musicatk.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/musicatk_1.2.0.tar.gz && rm -rf musicatk.buildbin-libdir && mkdir musicatk.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=musicatk.buildbin-libdir musicatk_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL musicatk_1.2.0.zip && rm musicatk_1.2.0.tar.gz musicatk_1.2.0.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
 75  590k   75  442k    0     0  1061k      0 --:--:-- --:--:-- --:--:-- 1062k
100  590k  100  590k    0     0  1193k      0 --:--:-- --:--:-- --:--:-- 1192k

install for i386

* 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  
    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

install for x64

* installing *source* package 'musicatk' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'musicatk' as musicatk_1.2.0.zip
* DONE (musicatk)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'musicatk' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
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 1 | SKIP 0 | PASS 42 ]
> 
> proc.time()
   user  system elapsed 
  20.06    2.31   22.36


R version 4.1.1 (2021-08-10) -- "Kick Things"
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 1 | SKIP 0 | PASS 42 ]
> 
> proc.time()
   user  system elapsed 
  25.26    0.95   26.21

name	user	system	elapsed
add_flank_to_variants	2.81	0.68	3.48
add_variant_type	0.00	0.03	0.03
annotate_replication_strand	0.14	0.03	0.17
annotate_transcript_strand	1.91	0.05	1.95
annotate_variant_length	0.01	0.00	0.02
annotate_variant_type	0.00	0.02	0.01
auto_predict_grid	2.86	0.14	3.00
build_custom_table	0.97	0.04	1.02
build_standard_table	8.55	0.91	9.45
built_tables	0	0	0
cluster_exposure	0.01	0.02	0.21
combine_count_tables	3.07	0.31	3.37
combine_predict_grid	2.28	0.03	2.31
compare_cosmic_v2	2.54	0.01	2.57
compare_cosmic_v3	0.75	0.00	0.75
compare_results	0.99	0.00	0.98
cosmic_v2_subtype_map	0	0	0
create_musica	1.16	0.13	1.67
create_umap	3.98	0.08	4.08
discover_signatures	0.91	0.15	1.17
drop_annotation	0.01	0.00	0.02
exposure_differential_analysis	0.03	0.00	0.03
exposures	0.00	0.02	0.01
extract_count_tables	0	0	0
extract_variants	5.14	0.00	5.22
extract_variants_from_maf	0.09	0.00	0.10
extract_variants_from_maf_file	0.10	0.00	0.09
extract_variants_from_matrix	0.09	0.00	0.10
extract_variants_from_vcf	0.67	0.03	0.70
extract_variants_from_vcf_file	0.48	0.00	0.49
generate_result_grid	0.39	0.00	0.39
get_musica	0	0	0
k_select	0.85	0.03	0.87
name_signatures	0.00	0.01	0.02
pipe	0	0	0
plot_cluster	4.18	0.07	4.25
plot_differential_analysis	0.14	0.00	0.14
plot_exposures	0.16	0.00	0.16
plot_heatmap	0.63	0.06	0.68
plot_sample_counts	0.23	0.00	0.24
plot_sample_reconstruction_error	0.41	0.00	0.40
plot_signatures	0.39	0.00	0.40
plot_umap	3.58	0.09	3.72
predict_exposure	1.81	0.25	2.06
rc	0	0	0
samp_annot	0.00	0.02	0.02
sample_names	0	0	0
select_genome	0	0	0
signatures	0.00	0.01	0.01
subset_musica_by_annotation	0.02	0.00	0.02
subset_musica_by_counts	0.00	0.02	0.01
subset_variant_by_type	0	0	0
subset_variants_by_samples	0.01	0.00	0.02
table_selected	0	0	0
tables	0.02	0.00	0.02
umap	0.00	0.01	0.01
variants	0.02	0.00	0.02

name	user	system	elapsed
add_flank_to_variants	3.16	0.17	3.33
add_variant_type	0.03	0.00	0.03
annotate_replication_strand	0.14	0.00	0.14
annotate_transcript_strand	1.34	0.07	1.41
annotate_variant_length	0.02	0.00	0.02
annotate_variant_type	0.01	0.00	0.01
auto_predict_grid	3.28	0.01	3.30
build_custom_table	1.04	0.03	1.06
build_standard_table	9.32	0.83	10.16
built_tables	0	0	0
cluster_exposure	0.03	0.00	0.08
combine_count_tables	3.61	0.23	3.84
combine_predict_grid	2.80	0.02	2.81
compare_cosmic_v2	3.09	0.00	3.09
compare_cosmic_v3	1.2	0.0	1.2
compare_results	1.88	0.02	1.90
cosmic_v2_subtype_map	0	0	0
create_musica	1.30	0.14	1.43
create_umap	5.03	0.03	5.08
discover_signatures	1.06	0.15	1.28
drop_annotation	0.01	0.00	0.02
exposure_differential_analysis	0.04	0.00	0.03
exposures	0.00	0.04	0.03
extract_count_tables	0.01	0.00	0.02
extract_variants	7.36	0.00	7.36
extract_variants_from_maf	0.16	0.00	0.15
extract_variants_from_maf_file	0.14	0.00	0.14
extract_variants_from_matrix	0.14	0.00	0.14
extract_variants_from_vcf	0.84	0.01	0.86
extract_variants_from_vcf_file	0.58	0.00	0.58
generate_result_grid	0.44	0.00	0.43
get_musica	0.01	0.00	0.02
k_select	1.10	0.01	1.11
name_signatures	0.01	0.00	0.01
pipe	0	0	0
plot_cluster	5.78	0.03	5.83
plot_differential_analysis	0.22	0.00	0.22
plot_exposures	0.21	0.00	0.20
plot_heatmap	0.81	0.02	0.83
plot_sample_counts	0.40	0.00	0.41
plot_sample_reconstruction_error	0.93	0.01	0.94
plot_signatures	0.89	0.00	0.89
plot_umap	4.59	0.04	4.62
predict_exposure	1.86	0.09	1.97
rc	0	0	0
samp_annot	0.00	0.02	0.02
sample_names	0.00	0.01	0.01
select_genome	0	0	0
signatures	0.02	0.00	0.02
subset_musica_by_annotation	0	0	0
subset_musica_by_counts	0.00	0.02	0.01
subset_variant_by_type	0	0	0
subset_variants_by_samples	0	0	0
table_selected	0	0	0
tables	0.00	0.02	0.01
umap	0.00	0.01	0.02
variants	0.01	0.00	0.02

CHECK results for musicatk on tokay2

Summary

Command output

Installation output

Tests output

Example timings