Multiple platform build/check report for BioC 3.14 - CHECK results for musicatk on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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*

Package: musicatk

Version: 1.4.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:musicatk.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings musicatk_1.4.0.tar.gz

StartedAt: 2022-04-12 23:30:22 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 23:39:41 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 559.8 seconds

RetCode: 0

Status: OK

CheckDir: musicatk.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:musicatk.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings musicatk_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/musicatk.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.4.0'
* 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
build_standard_table 8.89   0.83    9.72
extract_variants     5.80   0.57    6.64
plot_cluster         4.36   0.28   11.47
create_musica        1.11   0.18    9.17
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
build_standard_table 9.32   1.04   10.34
plot_cluster         5.36   0.22    8.48
extract_variants     5.36   0.03    5.39
create_umap          4.33   0.11   10.00
auto_predict_grid    2.72   0.01    5.46
* 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/musicatk.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/musicatk_1.4.0.tar.gz && rm -rf musicatk.buildbin-libdir && mkdir musicatk.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=musicatk.buildbin-libdir musicatk_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL musicatk_1.4.0.zip && rm musicatk_1.4.0.tar.gz musicatk_1.4.0.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
  5 15.1M    5  879k    0     0  1241k      0  0:00:12 --:--:--  0:00:12 1241k
 20 15.1M   20 3144k    0     0  1829k      0  0:00:08  0:00:01  0:00:07 1829k
 40 15.1M   40 6298k    0     0  2319k      0  0:00:06  0:00:02  0:00:04 2319k
 66 15.1M   66 10.0M    0     0  2798k      0  0:00:05  0:00:03  0:00:02 2798k
 96 15.1M   96 14.6M    0     0  3201k      0  0:00:04  0:00:04 --:--:-- 3201k
100 15.1M  100 15.1M    0     0  3256k      0  0:00:04  0:00:04 --:--:-- 3608k

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  
    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

install for x64

* installing *source* package 'musicatk' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'musicatk' as musicatk_1.4.0.zip
* DONE (musicatk)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'musicatk' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 42 ]
> 
> proc.time()
   user  system elapsed 
  20.28    2.03   22.29


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 42 ]
> 
> proc.time()
   user  system elapsed 
  23.92    0.89   24.79

name	user	system	elapsed
add_flank_to_variants	2.58	0.53	3.11
add_variant_type	0.01	0.00	0.02
annotate_replication_strand	0.14	0.00	0.14
annotate_transcript_strand	1.97	0.07	2.03
annotate_variant_length	0.01	0.00	0.02
annotate_variant_type	0.00	0.01	0.02
auto_predict_grid	2.99	0.19	3.32
build_custom_table	1.04	0.01	1.07
build_standard_table	8.89	0.83	9.72
built_tables	0	0	0
cluster_exposure	0.00	0.02	0.40
combine_count_tables	3.14	0.23	3.38
combine_predict_grid	3.24	0.05	3.28
compare_cosmic_v2	2.00	0.01	2.01
compare_cosmic_v3	0.89	0.00	0.89
compare_results	1.11	0.00	1.11
cosmic_v2_subtype_map	0.01	0.00	0.02
create_musica	1.11	0.18	9.17
create_umap	4.16	0.07	4.26
discover_signatures	0.87	0.11	2.63
drop_annotation	0	0	0
exposure_differential_analysis	0.03	0.02	0.04
exposures	0.02	0.02	0.04
extract_count_tables	0.01	0.00	0.01
extract_variants	5.80	0.57	6.64
extract_variants_from_maf	0.17	0.02	0.19
extract_variants_from_maf_file	0.16	0.00	0.16
extract_variants_from_matrix	0.11	0.06	0.17
extract_variants_from_vcf	0.67	0.16	0.83
extract_variants_from_vcf_file	0.55	0.02	0.56
generate_result_grid	0.34	0.00	0.34
get_musica	0.02	0.00	0.02
k_select	0.67	0.04	0.70
musicatk	0	0	0
name_signatures	0	0	0
pipe	0	0	0
plot_cluster	4.36	0.28	11.47
plot_differential_analysis	0.25	0.00	0.25
plot_exposures	0.22	0.00	0.21
plot_heatmap	0.80	0.08	0.88
plot_sample_counts	0.33	0.00	0.33
plot_sample_reconstruction_error	0.53	0.00	0.53
plot_signatures	0.40	0.00	0.41
plot_umap	3.57	0.09	3.67
predict_exposure	1.50	0.45	1.95
rc	0	0	0
samp_annot	0.03	0.00	0.03
sample_names	0	0	0
select_genome	0	0	0
signatures	0.01	0.02	0.03
subset_musica_by_annotation	0.02	0.00	0.02
subset_musica_by_counts	0.01	0.00	0.01
subset_variant_by_type	0	0	0
subset_variants_by_samples	0.00	0.01	0.02
table_selected	0.00	0.02	0.02
tables	0.00	0.01	0.01
umap	0.02	0.00	0.02
variants	0.02	0.00	0.01

name	user	system	elapsed
add_flank_to_variants	2.75	0.14	2.91
add_variant_type	0.01	0.00	0.02
annotate_replication_strand	0.11	0.00	0.11
annotate_transcript_strand	1.68	0.06	1.73
annotate_variant_length	0.01	0.00	0.02
annotate_variant_type	0	0	0
auto_predict_grid	2.72	0.01	5.46
build_custom_table	0.84	0.00	0.85
build_standard_table	9.32	1.04	10.34
built_tables	0	0	0
cluster_exposure	0.01	0.00	0.02
combine_count_tables	2.31	0.21	2.53
combine_predict_grid	2.10	0.05	2.17
compare_cosmic_v2	1.94	0.00	1.93
compare_cosmic_v3	0.82	0.00	0.83
compare_results	1.13	0.00	1.13
cosmic_v2_subtype_map	0	0	0
create_musica	0.75	0.06	0.81
create_umap	4.33	0.11	10.00
discover_signatures	0.86	0.10	2.66
drop_annotation	0.01	0.00	0.01
exposure_differential_analysis	0.03	0.00	0.03
exposures	0.03	0.00	0.03
extract_count_tables	0	0	0
extract_variants	5.36	0.03	5.39
extract_variants_from_maf	0.13	0.00	0.12
extract_variants_from_maf_file	0.09	0.00	0.10
extract_variants_from_matrix	0.10	0.00	0.09
extract_variants_from_vcf	0.67	0.00	0.67
extract_variants_from_vcf_file	0.57	0.00	0.56
generate_result_grid	0.34	0.00	0.36
get_musica	0	0	0
k_select	0.78	0.00	0.78
musicatk	0	0	0
name_signatures	0.00	0.02	0.02
pipe	0	0	0
plot_cluster	5.36	0.22	8.48
plot_differential_analysis	0.24	0.01	0.25
plot_exposures	0.20	0.02	0.22
plot_heatmap	0.84	0.00	0.84
plot_sample_counts	0.3	0.0	0.3
plot_sample_reconstruction_error	0.50	0.01	0.51
plot_signatures	0.42	0.02	0.44
plot_umap	4.39	0.09	4.49
predict_exposure	1.56	0.05	1.60
rc	0	0	0
samp_annot	0	0	0
sample_names	0	0	0
select_genome	0	0	0
signatures	0.00	0.01	0.01
subset_musica_by_annotation	0	0	0
subset_musica_by_counts	0.01	0.00	0.02
subset_variant_by_type	0.02	0.00	0.01
subset_variants_by_samples	0	0	0
table_selected	0.00	0.02	0.02
tables	0.01	0.00	0.01
umap	0	0	0
variants	0.00	0.01	0.02

CHECK results for musicatk on tokay2

Summary

Command output

Installation output

Tests output

Example timings