Build/check report for BioC 3.17 - CHECK results for musicatk on kunpeng1

Hostname	OS	Arch (*)	R version	Installed pkgs
kunpeng1	Linux (Ubuntu 22.04.1 LTS)	aarch64	R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"	6083
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/bbs-3.17-bioc/R/bin/R CMD check --install=check:musicatk.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings musicatk_1.9.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/musicatk.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘musicatk/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘musicatk’ version ‘1.9.0’
* 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 R 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 ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
build_standard_table 9.048  0.751  10.238
plot_cluster         5.637  0.172   5.824
create_umap          5.431  0.124   5.554
extract_variants     5.510  0.039   5.552
plot_umap            4.995  0.028   5.020
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘musicatk.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/musicatk.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL musicatk
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/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) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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: 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 5 | SKIP 0 | PASS 42 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 42 ]
> 
> proc.time()
   user  system elapsed 
 25.542   1.569  27.087

Example timings

name	user	system	elapsed
add_flank_to_variants	3.382	0.284	3.705
add_variant_type	0.014	0.005	0.019
annotate_replication_strand	0.285	0.012	0.297
annotate_transcript_strand	2.539	0.128	2.666
annotate_variant_length	0.009	0.004	0.014
annotate_variant_type	0.003	0.000	0.003
auto_predict_grid	2.837	0.020	2.859
build_custom_table	2.349	0.044	2.394
build_standard_table	9.048	0.751	10.238
built_tables	0.003	0.000	0.003
cluster_exposure	0.010	0.008	0.018
combine_count_tables	3.066	0.132	3.199
combine_predict_grid	2.788	0.028	2.816
compare_cosmic_v2	3.202	0.027	3.230
compare_cosmic_v3	1.415	0.008	1.424
compare_results	1.860	0.059	1.919
cosmic_v2_subtype_map	0.001	0.000	0.002
create_musica	0.954	0.160	1.374
create_umap	5.431	0.124	5.554
discover_signatures	0.866	0.036	0.902
drop_annotation	0.002	0.000	0.002
exposure_differential_analysis	0.022	0.000	0.022
exposures	0.000	0.005	0.005
extract_count_tables	0.003	0.002	0.005
extract_variants	5.510	0.039	5.552
extract_variants_from_maf	0.136	0.004	0.138
extract_variants_from_maf_file	0.123	0.000	0.121
extract_variants_from_matrix	0.141	0.000	0.140
extract_variants_from_vcf	0.873	0.012	0.884
extract_variants_from_vcf_file	0.633	0.000	0.633
generate_result_grid	0.228	0.004	0.232
get_musica	0.008	0.000	0.008
k_select	1.191	0.012	1.203
musicatk	0.001	0.000	0.000
name_signatures	0.004	0.000	0.003
pipe	0.003	0.000	0.003
plot_cluster	5.637	0.172	5.824
plot_differential_analysis	0.239	0.000	0.239
plot_exposures	0.242	0.000	0.242
plot_heatmap	0.960	0.004	0.965
plot_sample_counts	0.460	0.004	0.465
plot_sample_reconstruction_error	0.803	0.032	0.835
plot_signatures	0.765	0.004	0.769
plot_umap	4.995	0.028	5.020
predict_exposure	1.663	0.092	1.755
rc	0.003	0.000	0.002
samp_annot	0.008	0.000	0.009
sample_names	0.000	0.003	0.004
select_genome	0	0	0
signatures	0.004	0.002	0.006
subset_musica_by_annotation	0.005	0.001	0.007
subset_musica_by_counts	0.009	0.000	0.009
subset_variant_by_type	0.005	0.000	0.005
subset_variants_by_samples	0.005	0.000	0.005
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	0.000	0.009

CHECK results for musicatk on kunpeng1

Summary

Command output

Installation output

Tests output

Example timings