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This page was generated on 2025-08-09 12:05 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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

Package 1402/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
musicatk 2.3.1  (landing page)
Joshua D. Campbell
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/musicatk
git_branch: devel
git_last_commit: 5199a17
git_last_commit_date: 2025-07-25 14:26:12 -0400 (Fri, 25 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for musicatk on nebbiolo2

To the developers/maintainers of the musicatk package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/musicatk.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: musicatk
Version: 2.3.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:musicatk.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings musicatk_2.3.1.tar.gz
StartedAt: 2025-08-09 00:43:06 -0400 (Sat, 09 Aug 2025)
EndedAt: 2025-08-09 01:00:52 -0400 (Sat, 09 Aug 2025)
EllapsedTime: 1065.2 seconds
RetCode: 0
Status:   OK  
CheckDir: musicatk.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:musicatk.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings musicatk_2.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/musicatk.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘musicatk/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘musicatk’ version ‘2.3.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 44 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  add_flank_to_variants.Rd: BSgenome-class
  build_standard_table.Rd: BSgenome-class
  create_musica_from_variants.Rd: BSgenome-class
  create_sbs192_table.Rd: BSgenome-class
  create_sbs96_table.Rd: BSgenome-class
  extract_variants.Rd: CollapsedVCF-class, ExpandedVCF-class, MAF-class
  variants.Rd: data.table-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
plot_k_comparison    208.605  6.328 214.915
compare_k_vals       182.388  9.343 191.716
build_standard_table   6.495  0.394   6.889
plot_cluster           5.017  0.133   5.159
create_umap            4.937  0.091   5.035
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/musicatk.Rcheck/00check.log’
for details.


Installation output

musicatk.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL musicatk
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘musicatk’ ...
** this is package ‘musicatk’ version ‘2.3.1’
** 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

musicatk.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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:generics':

    fit

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

    compare

> 
> test_check("musicatk")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 41 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 41 ]
> 
> proc.time()
   user  system elapsed 
 21.076   1.096  22.169 

Example timings

musicatk.Rcheck/musicatk-Ex.timings

nameusersystemelapsed
add_flank_to_variants2.7540.2583.012
add_result0.0520.0000.052
add_variant_type0.0140.0010.015
annotate_replication_strand0.1940.0150.209
annotate_transcript_strand1.9970.0762.074
annotate_variant_length0.0120.0000.012
annotate_variant_type0.0020.0000.003
auto_predict_grid1.7210.0151.736
build_custom_table0.8210.0300.852
build_standard_table6.4950.3946.889
built_tables0.0010.0000.001
cluster_exposure0.0120.0010.014
combine_count_tables2.0780.1222.200
combine_predict_grid0.4120.0060.418
compare_cosmic_v22.6300.0372.667
compare_cosmic_v31.4700.0021.472
compare_k_vals182.388 9.343191.716
compare_results1.7440.0761.820
cosmic_v2_subtype_map0.0010.0000.001
create_musica_from_counts0.0020.0020.004
create_musica_from_variants0.7160.0770.769
create_umap4.9370.0915.035
credible_intervals0.0030.0000.003
discover_signatures0.6410.0370.678
drop_annotation0.0020.0000.001
exposure_differential_analysis0.0100.0000.009
exposures0.0160.0010.016
extract_count_tables0.0040.0000.003
extract_variants3.8400.0323.821
extract_variants_from_maf0.1250.0060.101
extract_variants_from_maf_file0.1030.0010.079
extract_variants_from_matrix0.1140.0000.090
extract_variants_from_vcf0.5940.0090.603
extract_variants_from_vcf_file0.4120.0020.413
generate_result_grid0.3500.0040.355
get_modality0.0040.0010.005
get_model0.0030.0000.004
get_result_list_entry0.0050.0000.005
hyperparameter0.0010.0010.002
k_select0.6470.0060.653
metrics0.0020.0000.002
modality0.0010.0010.002
model_id0.0010.0010.001
musicatk000
name_signatures0.0290.0000.030
num_signatures0.0020.0000.001
other_parameters0.0020.0000.002
parameter0.0010.0000.002
pipe0.0030.0000.002
plot_cluster5.0170.1335.159
plot_differential_analysis0.1560.0000.156
plot_exposures0.2980.0010.298
plot_heatmap0.7410.0000.741
plot_k_comparison208.605 6.328214.915
plot_sample_counts0.5060.0100.516
plot_sample_reconstruction_error0.6950.0020.697
plot_signatures0.7420.0000.742
plot_umap4.6370.1514.800
predict_exposure1.0140.0421.056
rc0.0020.0000.002
result_list0.0020.0000.003
samp_annot0.0050.0000.006
sample_names0.0020.0000.003
select_genome000
signatures0.0170.0010.018
subset_musica_by_annotation0.0050.0000.005
subset_musica_by_counts0.0090.0000.009
subset_variant_by_type0.0050.0000.006
subset_variants_by_samples0.0040.0010.005
table_selected0.0020.0000.002
tables0.0030.0000.004
umap0.0010.0010.002
variants0.0050.0000.004