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This page was generated on 2025-08-14 11:46 -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 kjohnson1

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:musicatk.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings musicatk_2.2.1.tar.gz
StartedAt: 2025-08-13 03:59:49 -0400 (Wed, 13 Aug 2025)
EndedAt: 2025-08-13 04:14:26 -0400 (Wed, 13 Aug 2025)
EllapsedTime: 876.9 seconds
RetCode: 0
Status:   OK  
CheckDir: musicatk.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:musicatk.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings musicatk_2.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/musicatk.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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    230.795  1.878 233.307
compare_k_vals       207.380  2.509 210.882
build_standard_table   7.591  1.112   8.904
plot_cluster           6.469  0.146   6.663
create_umap            6.226  0.094   6.346
plot_umap              6.108  0.063   6.191
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/musicatk.Rcheck/00check.log’
for details.


Installation output

musicatk.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL musicatk
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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: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 
 24.650   1.113  25.897 

Example timings

musicatk.Rcheck/musicatk-Ex.timings

nameusersystemelapsed
add_flank_to_variants3.4810.3193.819
add_result0.0610.0010.062
add_variant_type0.0200.0030.024
annotate_replication_strand0.1430.0130.156
annotate_transcript_strand2.6060.0872.692
annotate_variant_length0.0150.0040.019
annotate_variant_type0.0020.0030.005
auto_predict_grid2.1080.0812.190
build_custom_table0.9940.0291.024
build_standard_table7.5911.1128.904
built_tables0.0030.0020.005
cluster_exposure0.0190.0050.024
combine_count_tables1.9060.2222.151
combine_predict_grid0.5160.0180.535
compare_cosmic_v22.7090.0372.754
compare_cosmic_v31.5520.0181.571
compare_k_vals207.380 2.509210.882
compare_results1.7710.0721.843
cosmic_v2_subtype_map0.0010.0000.001
create_musica_from_counts0.0050.0020.007
create_musica_from_variants0.8670.2661.295
create_umap6.2260.0946.346
credible_intervals0.0040.0020.006
discover_signatures0.7900.1551.076
drop_annotation0.0020.0030.004
exposure_differential_analysis0.0120.0040.017
exposures0.0190.0050.024
extract_count_tables0.0040.0030.008
extract_variants4.1040.0894.199
extract_variants_from_maf0.1110.0050.116
extract_variants_from_maf_file0.0950.0030.098
extract_variants_from_matrix0.1280.0070.135
extract_variants_from_vcf0.6940.0180.713
extract_variants_from_vcf_file0.4490.0060.455
generate_result_grid0.4040.0030.408
get_modality0.0070.0050.011
get_model0.0040.0040.010
get_result_list_entry0.0060.0020.008
hyperparameter0.0020.0020.005
k_select0.6690.0190.691
metrics0.0030.0030.005
modality0.0030.0020.004
model_id0.0020.0030.004
musicatk000
name_signatures0.0320.0030.034
num_signatures0.0020.0030.005
other_parameters0.0020.0020.005
parameter0.0020.0030.004
pipe0.0030.0010.004
plot_cluster6.4690.1466.663
plot_differential_analysis0.1800.0050.194
plot_exposures0.3240.0160.340
plot_heatmap0.8140.0340.866
plot_k_comparison230.795 1.878233.307
plot_sample_counts0.5460.0170.564
plot_sample_reconstruction_error0.7590.0200.779
plot_signatures0.7520.0080.762
plot_umap6.1080.0636.191
predict_exposure1.2120.1201.336
rc0.0020.0010.002
result_list0.0030.0030.006
samp_annot0.0070.0050.013
sample_names0.0030.0030.005
select_genome000
signatures0.0190.0080.026
subset_musica_by_annotation0.0050.0030.009
subset_musica_by_counts0.0100.0040.014
subset_variant_by_type0.0060.0030.009
subset_variants_by_samples0.0060.0030.010
table_selected0.0030.0020.005
tables0.0040.0020.006
umap0.0020.0020.005
variants0.0050.0030.008