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This page was generated on 2025-03-19 11:44 -0400 (Wed, 19 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4742
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
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 1396/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
musicatk 2.1.0  (landing page)
Joshua D. Campbell
Snapshot Date: 2025-03-18 13:40 -0400 (Tue, 18 Mar 2025)
git_url: https://git.bioconductor.org/packages/musicatk
git_branch: devel
git_last_commit: 45539aa
git_last_commit_date: 2024-10-29 10:52:22 -0400 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
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
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for musicatk on lconway

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: 2.1.0
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_2.1.0.tar.gz
StartedAt: 2025-03-18 22:26:24 -0400 (Tue, 18 Mar 2025)
EndedAt: 2025-03-18 22:39:59 -0400 (Tue, 18 Mar 2025)
EllapsedTime: 815.0 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_2.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/musicatk.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘musicatk/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘musicatk’ version ‘2.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 45 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    203.705  2.084 207.221
compare_k_vals       184.512  1.263 186.956
build_standard_table   8.650  1.082  10.076
plot_cluster           5.511  0.174   5.705
create_umap            5.299  0.061   5.373
plot_umap              4.931  0.081   5.038
* 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-x86_64/Resources/library’
* installing *source* package ‘musicatk’ ...
** this is package ‘musicatk’ version ‘2.1.0’
** 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 Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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 1 | SKIP 0 | PASS 41 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 41 ]
> 
> proc.time()
   user  system elapsed 
 22.746   1.173  24.085 

Example timings

musicatk.Rcheck/musicatk-Ex.timings

nameusersystemelapsed
add_flank_to_variants3.2980.2593.613
add_variant_type0.0160.0040.021
annotate_replication_strand0.1270.0140.142
annotate_transcript_strand1.4050.0941.554
annotate_variant_length0.0140.0040.019
annotate_variant_type0.0020.0020.004
auto_predict_grid1.9870.0622.062
build_custom_table2.1610.0372.211
build_standard_table 8.650 1.08210.076
built_tables0.0010.0010.004
cluster_exposure0.0170.0050.023
combine_count_tables2.7710.2953.115
combine_predict_grid0.5080.0250.538
compare_cosmic_v22.9870.0463.046
compare_cosmic_v31.6350.0121.654
compare_k_vals184.512 1.263186.956
compare_results1.8930.0301.934
cosmic_v2_subtype_map0.0000.0010.001
create_musica_from_counts0.0040.0010.005
create_musica_from_variants0.9470.2081.276
create_result_model0.0010.0000.002
create_umap5.2990.0615.373
credible_intervals0.0030.0010.004
discover_signatures0.8190.1130.939
drop_annotation0.0010.0010.002
exposure_differential_analysis0.0090.0020.012
exposures0.0180.0030.021
extract_count_tables0.0050.0020.008
extract_variants4.5340.0534.602
extract_variants_from_maf0.1210.0040.125
extract_variants_from_maf_file0.1000.0010.101
extract_variants_from_matrix0.1150.0040.120
extract_variants_from_vcf0.8270.0260.856
extract_variants_from_vcf_file0.5180.0060.525
generate_result_grid0.4160.0030.420
get_modality0.0070.0040.012
get_model0.0050.0040.009
get_result_list_entry0.0070.0020.009
hyperparameter0.0030.0010.004
k_select0.7620.0160.781
metrics0.0030.0020.005
modality0.0030.0020.004
model_id0.0020.0010.004
musicatk0.0000.0000.001
name_signatures0.0320.0010.034
num_signatures0.0020.0020.004
other_parameters0.0020.0010.003
parameter0.0020.0010.004
pipe0.0030.0010.003
plot_cluster5.5110.1745.705
plot_differential_analysis0.1940.0040.199
plot_exposures0.3510.0050.357
plot_heatmap0.8410.0170.864
plot_k_comparison203.705 2.084207.221
plot_sample_counts0.5720.0100.585
plot_sample_reconstruction_error0.8090.0180.831
plot_signatures0.8010.0060.811
plot_umap4.9310.0815.038
predict_exposure1.1670.0901.268
rc0.0030.0010.003
result_list0.0030.0020.005
samp_annot0.0060.0030.010
sample_names0.0030.0010.004
select_genome000
signatures0.0210.0070.027
subset_musica_by_annotation0.0060.0030.009
subset_musica_by_counts0.0090.0030.012
subset_variant_by_type0.0070.0030.009
subset_variants_by_samples0.0080.0040.010
table_selected0.0020.0020.003
tables0.0040.0020.006
umap0.0020.0010.003
variants0.0060.0030.008