Multiple platform build/check report for BioC 3.19 - CHECK results for musicatk on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4753
lconway	macOS 12.7.1 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4518
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*

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:musicatk.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings musicatk_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/musicatk.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘musicatk/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘musicatk’ version ‘1.14.0’
* 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 for sufficient/correct file permissions ... 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 code 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 ... 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 ... NOTE
checkRd: (-1) plot_umap.Rd:53: Lost braces
    53 | code{color_by = "annotation"}. This not recommended if the annotation is
       |     ^
checkRd: (-1) plot_umap.Rd:58: Lost braces
    58 | code{color_by = "annotation"} and \code{add_annotation_labels = TRUE}.
       |     ^
checkRd: (-1) plot_umap.Rd:62: Lost braces
    62 | to improve readability. Only used if code{color_by = "annotation"} and
       |                                          ^
* 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 8.775  0.987   9.900
plot_cluster         5.577  0.219   5.840
create_umap          5.148  0.110   5.306
extract_variants     5.056  0.102   5.212
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/musicatk.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL musicatk
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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
** 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)

Tests output


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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: registry
Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: synchronicity] | Cores 2/2
  To enable shared memory capabilities, try: install.extras('
NMF
')

Attaching package: 'NMF'

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

    compare

> 
> test_check("musicatk")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 42 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 42 ]
> 
> proc.time()
   user  system elapsed 
 23.807   1.386  25.482

Example timings

name	user	system	elapsed
add_flank_to_variants	3.555	0.299	3.905
add_variant_type	0.022	0.006	0.029
annotate_replication_strand	0.177	0.020	0.203
annotate_transcript_strand	1.484	0.056	1.558
annotate_variant_length	0.014	0.003	0.017
annotate_variant_type	0.002	0.002	0.005
auto_predict_grid	2.980	0.101	3.105
build_custom_table	1.079	0.032	1.118
build_standard_table	8.775	0.987	9.900
built_tables	0.002	0.003	0.005
cluster_exposure	0.019	0.004	0.024
combine_count_tables	2.852	0.317	3.251
combine_predict_grid	1.949	0.049	2.020
compare_cosmic_v2	3.072	0.061	3.165
compare_cosmic_v3	1.781	0.024	1.824
compare_results	2.056	0.028	2.107
cosmic_v2_subtype_map	0.001	0.001	0.002
create_musica	0.967	0.181	1.169
create_umap	5.148	0.110	5.306
discover_signatures	0.866	0.139	1.029
drop_annotation	0.002	0.002	0.003
exposure_differential_analysis	0.011	0.003	0.014
exposures	0.004	0.004	0.009
extract_count_tables	0.004	0.002	0.006
extract_variants	5.056	0.102	5.212
extract_variants_from_maf	0.119	0.005	0.125
extract_variants_from_maf_file	0.112	0.002	0.115
extract_variants_from_matrix	0.113	0.004	0.118
extract_variants_from_vcf	0.801	0.032	0.840
extract_variants_from_vcf_file	0.577	0.010	0.591
generate_result_grid	0.180	0.005	0.187
get_musica	0.010	0.003	0.013
k_select	0.967	0.023	1.001
musicatk	0.000	0.000	0.001
name_signatures	0.003	0.002	0.005
pipe	0.002	0.001	0.004
plot_cluster	5.577	0.219	5.840
plot_differential_analysis	0.390	0.012	0.405
plot_exposures	0.195	0.005	0.203
plot_heatmap	0.940	0.023	0.975
plot_sample_counts	0.583	0.008	0.595
plot_sample_reconstruction_error	0.816	0.010	0.832
plot_signatures	0.845	0.009	0.860
plot_umap	4.813	0.076	4.927
predict_exposure	1.333	0.148	1.497
rc	0.003	0.000	0.002
samp_annot	0.010	0.003	0.013
sample_names	0.004	0.002	0.006
select_genome	0	0	0
signatures	0.005	0.005	0.011
subset_musica_by_annotation	0.006	0.003	0.010
subset_musica_by_counts	0.012	0.003	0.016
subset_variant_by_type	0.008	0.002	0.010
subset_variants_by_samples	0.008	0.003	0.011
table_selected	0.002	0.002	0.004
tables	0.009	0.004	0.013
umap	0.004	0.003	0.007
variants	0.013	0.005	0.019

CHECK results for musicatk on lconway

Summary

Command output

Installation output

Tests output

Example timings