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) (2023-01-14 r83615) -- "Unsuffered Consequences"	4266
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/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) (2023-01-14 r83615)
* 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 22.04.1 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 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 10.776  0.771  11.551
plot_cluster          5.692  0.172   5.863
extract_variants      5.766  0.024   5.791
create_umap           5.507  0.100   5.606
plot_umap             5.112  0.036   5.146
* 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/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) (2023-01-14 r83615) -- "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 31/32
  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 
 26.027   1.015  27.022

Example timings

name	user	system	elapsed
add_flank_to_variants	3.642	0.236	3.879
add_variant_type	0.02	0.00	0.02
annotate_replication_strand	0.305	0.012	0.317
annotate_transcript_strand	2.668	0.036	2.705
annotate_variant_length	0.014	0.000	0.014
annotate_variant_type	0.003	0.000	0.003
auto_predict_grid	2.924	0.024	2.951
build_custom_table	1.393	0.004	1.398
build_standard_table	10.776	0.771	11.551
built_tables	0.002	0.001	0.002
cluster_exposure	0.015	0.004	0.023
combine_count_tables	3.218	0.184	3.402
combine_predict_grid	2.82	0.02	2.84
compare_cosmic_v2	3.596	0.000	3.596
compare_cosmic_v3	1.543	0.000	1.543
compare_results	2.029	0.000	2.028
cosmic_v2_subtype_map	0.002	0.000	0.002
create_musica	1.003	0.136	1.205
create_umap	5.507	0.100	5.606
discover_signatures	0.870	0.064	0.940
drop_annotation	0.002	0.000	0.002
exposure_differential_analysis	0.024	0.000	0.024
exposures	0.005	0.000	0.005
extract_count_tables	0.001	0.004	0.005
extract_variants	5.766	0.024	5.791
extract_variants_from_maf	0.144	0.000	0.143
extract_variants_from_maf_file	0.126	0.000	0.124
extract_variants_from_matrix	0.140	0.004	0.143
extract_variants_from_vcf	0.867	0.008	0.875
extract_variants_from_vcf_file	0.653	0.004	0.656
generate_result_grid	0.230	0.004	0.233
get_musica	0.008	0.000	0.008
k_select	1.242	0.012	1.256
musicatk	0	0	0
name_signatures	0.003	0.000	0.003
pipe	0.003	0.000	0.003
plot_cluster	5.692	0.172	5.863
plot_differential_analysis	0.258	0.000	0.258
plot_exposures	0.247	0.004	0.251
plot_heatmap	1.055	0.024	1.079
plot_sample_counts	0.493	0.016	0.508
plot_sample_reconstruction_error	0.916	0.016	0.933
plot_signatures	0.844	0.004	0.847
plot_umap	5.112	0.036	5.146
predict_exposure	1.725	0.084	1.809
rc	0.002	0.000	0.002
samp_annot	0.008	0.000	0.008
sample_names	0.003	0.000	0.003
select_genome	0	0	0
signatures	0.004	0.002	0.005
subset_musica_by_annotation	0.004	0.001	0.006
subset_musica_by_counts	0.009	0.000	0.009
subset_variant_by_type	0.003	0.003	0.006
subset_variants_by_samples	0.005	0.000	0.005
table_selected	0.002	0.000	0.002
tables	0.01	0.00	0.01
umap	0.004	0.000	0.004
variants	0.009	0.000	0.010

CHECK results for musicatk on kunpeng1

Summary

Command output

Installation output

Tests output

Example timings