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"	4259
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*

##############################################################################
##############################################################################
###
### Running command:
###
###   /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
###
##############################################################################
##############################################################################


* 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 10.716  0.768  11.903
extract_variants      5.970  0.056   6.026
plot_cluster          5.754  0.088   5.871
create_umap           5.326  0.188   5.529
plot_umap             5.095  0.028   5.121
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL musicatk
###
##############################################################################
##############################################################################


* 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 
 26.048   0.992  27.018

Example timings

name	user	system	elapsed
add_flank_to_variants	3.519	0.253	3.802
add_variant_type	0.02	0.00	0.02
annotate_replication_strand	0.296	0.008	0.304
annotate_transcript_strand	2.703	0.036	2.739
annotate_variant_length	0.014	0.000	0.014
annotate_variant_type	0.002	0.000	0.003
auto_predict_grid	2.904	0.016	2.922
build_custom_table	1.339	0.016	1.354
build_standard_table	10.716	0.768	11.903
built_tables	0.002	0.000	0.002
cluster_exposure	0.014	0.004	0.018
combine_count_tables	3.108	0.188	3.296
combine_predict_grid	2.809	0.024	2.836
compare_cosmic_v2	3.465	0.020	3.485
compare_cosmic_v3	1.527	0.011	1.538
compare_results	1.982	0.000	1.982
cosmic_v2_subtype_map	0.001	0.000	0.001
create_musica	0.978	0.135	1.340
create_umap	5.326	0.188	5.529
discover_signatures	0.872	0.064	0.936
drop_annotation	0.003	0.000	0.002
exposure_differential_analysis	0.021	0.003	0.025
exposures	0.001	0.003	0.005
extract_count_tables	0.001	0.004	0.005
extract_variants	5.970	0.056	6.026
extract_variants_from_maf	0.156	0.000	0.155
extract_variants_from_maf_file	0.133	0.000	0.132
extract_variants_from_matrix	0.143	0.000	0.141
extract_variants_from_vcf	0.923	0.016	0.938
extract_variants_from_vcf_file	0.694	0.000	0.694
generate_result_grid	0.242	0.000	0.241
get_musica	0.008	0.000	0.009
k_select	1.329	0.008	1.336
musicatk	0	0	0
name_signatures	0.004	0.000	0.003
pipe	0.003	0.000	0.003
plot_cluster	5.754	0.088	5.871
plot_differential_analysis	0.254	0.000	0.255
plot_exposures	0.25	0.00	0.25
plot_heatmap	1.016	0.000	1.016
plot_sample_counts	0.484	0.000	0.484
plot_sample_reconstruction_error	0.881	0.000	0.881
plot_signatures	0.829	0.012	0.840
plot_umap	5.095	0.028	5.121
predict_exposure	1.715	0.088	1.802
rc	0.002	0.000	0.003
samp_annot	0.008	0.000	0.009
sample_names	0.003	0.000	0.003
select_genome	0	0	0
signatures	0.002	0.004	0.006
subset_musica_by_annotation	0.002	0.004	0.006
subset_musica_by_counts	0.008	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	0.003
tables	0.01	0.00	0.01
umap	0.005	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