Multiple platform build/check report for BioC 3.19 - CHECK results for musicatk on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"	4708
palomino3	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"	4446
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"	4471
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"	4426
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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###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:musicatk.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings musicatk_1.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/musicatk.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘musicatk/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘musicatk’ version ‘1.13.0’
* 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 loading without being on the library search path ... 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 9.781  0.507  10.307
plot_cluster         6.034  0.204   6.245
create_umap          5.824  0.163   5.996
extract_variants     5.710  0.076   5.802
plot_umap            5.392  0.052   5.450
* 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
  ‘/home/biocbuild/bbs-3.19-bioc/meat/musicatk.Rcheck/00check.log’
for details.

Installation output

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###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL musicatk
###
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* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-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 Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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: bigmemory] | 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 5 | SKIP 0 | PASS 42 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 42 ]
> 
> proc.time()
   user  system elapsed 
 26.211   1.283  27.525

Example timings

name	user	system	elapsed
add_flank_to_variants	3.917	0.264	4.188
add_variant_type	0.021	0.000	0.021
annotate_replication_strand	0.160	0.008	0.168
annotate_transcript_strand	1.602	0.024	1.628
annotate_variant_length	0.016	0.000	0.016
annotate_variant_type	0.003	0.000	0.003
auto_predict_grid	4.067	0.115	4.189
build_custom_table	1.252	0.032	1.286
build_standard_table	9.781	0.507	10.307
built_tables	0.002	0.000	0.002
cluster_exposure	0.016	0.000	0.017
combine_count_tables	3.183	0.144	3.333
combine_predict_grid	2.712	0.016	2.733
compare_cosmic_v2	4.010	0.020	4.039
compare_cosmic_v3	2.250	0.028	2.283
compare_results	2.652	0.052	2.709
cosmic_v2_subtype_map	0.002	0.000	0.002
create_musica	1.025	0.120	1.182
create_umap	5.824	0.163	5.996
discover_signatures	0.897	0.072	0.970
drop_annotation	0.002	0.000	0.002
exposure_differential_analysis	0.012	0.000	0.012
exposures	0.004	0.000	0.004
extract_count_tables	0.004	0.000	0.004
extract_variants	5.710	0.076	5.802
extract_variants_from_maf	0.172	0.000	0.171
extract_variants_from_maf_file	0.131	0.000	0.129
extract_variants_from_matrix	0.150	0.008	0.157
extract_variants_from_vcf	0.905	0.012	0.919
extract_variants_from_vcf_file	0.626	0.020	0.647
generate_result_grid	0.238	0.000	0.238
get_musica	0.009	0.000	0.009
k_select	1.139	0.008	1.149
musicatk	0.000	0.000	0.001
name_signatures	0.000	0.003	0.003
pipe	0.003	0.000	0.003
plot_cluster	6.034	0.204	6.245
plot_differential_analysis	0.421	0.008	0.429
plot_exposures	0.231	0.000	0.231
plot_heatmap	1.027	0.012	1.040
plot_sample_counts	0.743	0.000	0.744
plot_sample_reconstruction_error	1.086	0.016	1.104
plot_signatures	1.059	0.004	1.065
plot_umap	5.392	0.052	5.450
predict_exposure	1.769	0.044	1.817
rc	0.003	0.000	0.002
samp_annot	0.01	0.00	0.01
sample_names	0.003	0.000	0.003
select_genome	0	0	0
signatures	0.003	0.002	0.004
subset_musica_by_annotation	0.004	0.002	0.007
subset_musica_by_counts	0.01	0.00	0.01
subset_variant_by_type	0.007	0.000	0.007
subset_variants_by_samples	0.007	0.000	0.006
table_selected	0.002	0.000	0.002
tables	0.009	0.000	0.009
umap	0.004	0.000	0.004
variants	0.009	0.004	0.013

CHECK results for musicatk on kunpeng2

Summary

Command output

Installation output

Tests output

Example timings