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This page was generated on 2025-08-14 11:41 -0400 (Thu, 14 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4566
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 1411/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
musicatk 2.2.1  (landing page)
Joshua D. Campbell
Snapshot Date: 2025-08-11 13:40 -0400 (Mon, 11 Aug 2025)
git_url: https://git.bioconductor.org/packages/musicatk
git_branch: RELEASE_3_21
git_last_commit: d92d323
git_last_commit_date: 2025-07-15 20:34:01 -0400 (Tue, 15 Jul 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for musicatk on nebbiolo1

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: 2.2.1
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:musicatk.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings musicatk_2.2.1.tar.gz
StartedAt: 2025-08-14 00:42:49 -0400 (Thu, 14 Aug 2025)
EndedAt: 2025-08-14 01:00:20 -0400 (Thu, 14 Aug 2025)
EllapsedTime: 1050.7 seconds
RetCode: 0
Status:   OK  
CheckDir: musicatk.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:musicatk.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings musicatk_2.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘musicatk/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘musicatk’ version ‘2.2.1’
* 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    191.919  9.772 201.708
compare_k_vals       180.631 10.975 191.598
build_standard_table   6.586  1.219   7.806
plot_cluster           5.288  0.364   5.665
create_umap            4.958  0.481   5.449
* 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-3.21-bioc/meat/musicatk.Rcheck/00check.log’
for details.


Installation output

musicatk.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL musicatk
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘musicatk’ ...
** this is package ‘musicatk’ version ‘2.2.1’
** 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 
 21.359   1.081  22.434 

Example timings

musicatk.Rcheck/musicatk-Ex.timings

nameusersystemelapsed
add_flank_to_variants2.7920.3543.145
add_result0.0520.0000.053
add_variant_type0.0150.0010.015
annotate_replication_strand0.1060.0120.118
annotate_transcript_strand1.9980.0752.073
annotate_variant_length0.0100.0010.013
annotate_variant_type0.0000.0010.002
auto_predict_grid1.7170.0131.731
build_custom_table0.7840.0190.804
build_standard_table6.5861.2197.806
built_tables0.0010.0010.002
cluster_exposure0.0120.0010.015
combine_count_tables2.0580.3232.382
combine_predict_grid0.4170.0010.419
compare_cosmic_v22.5840.0302.613
compare_cosmic_v31.5030.0011.508
compare_k_vals180.631 10.975191.598
compare_results1.7170.1001.817
cosmic_v2_subtype_map0.0010.0000.002
create_musica_from_counts0.0030.0010.005
create_musica_from_variants0.7510.3301.060
create_umap4.9580.4815.449
credible_intervals0.0030.0000.003
discover_signatures0.6930.1370.830
drop_annotation0.0020.0000.002
exposure_differential_analysis0.0110.0000.010
exposures0.0170.0030.019
extract_count_tables0.0040.0000.004
extract_variants4.0880.1204.211
extract_variants_from_maf0.1180.0030.098
extract_variants_from_maf_file0.1140.0080.091
extract_variants_from_matrix0.1240.0140.105
extract_variants_from_vcf0.6570.0310.689
extract_variants_from_vcf_file0.4400.0040.444
generate_result_grid0.3520.0010.353
get_modality0.0060.0020.007
get_model0.0040.0030.006
get_result_list_entry0.0060.0000.005
hyperparameter0.0010.0010.002
k_select0.6740.0120.687
metrics0.0030.0000.003
modality0.0020.0010.002
model_id0.0010.0020.002
musicatk000
name_signatures0.0300.0040.034
num_signatures0.0030.0000.002
other_parameters0.0020.0010.002
parameter0.0020.0000.002
pipe0.0010.0010.003
plot_cluster5.2880.3645.665
plot_differential_analysis0.1630.0120.176
plot_exposures0.3000.0040.304
plot_heatmap0.7020.0460.748
plot_k_comparison191.919 9.772201.708
plot_sample_counts0.4930.0350.528
plot_sample_reconstruction_error0.6700.0180.687
plot_signatures0.7140.0200.734
plot_umap4.2930.2194.524
predict_exposure1.0190.1401.159
rc0.0020.0010.003
result_list0.0010.0020.004
samp_annot0.0050.0020.007
sample_names0.0030.0000.003
select_genome0.0000.0000.001
signatures0.0170.0040.021
subset_musica_by_annotation0.0050.0010.006
subset_musica_by_counts0.0070.0030.011
subset_variant_by_type0.0040.0020.007
subset_variants_by_samples0.0060.0000.005
table_selected0.0020.0000.002
tables0.0020.0020.004
umap0.0020.0000.002
variants0.0040.0010.006