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This page was generated on 2025-03-17 11:39 -0400 (Mon, 17 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
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: 2025-03-16 13:40 -0400 (Sun, 16 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)
palomino7Windows 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
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: 2025-03-16 22:25:21 -0400 (Sun, 16 Mar 2025)
EndedAt: 2025-03-16 22:38:46 -0400 (Sun, 16 Mar 2025)
EllapsedTime: 804.8 seconds
RetCode: 0
Status:   OK  
CheckDir: musicatk.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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    200.345  2.144 203.956
compare_k_vals       180.139  1.248 182.559
build_standard_table   8.752  1.109  10.293
plot_cluster           5.415  0.179   5.616
create_umap            5.170  0.064   5.255
* 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 
 22.191   1.164  23.516 

Example timings

musicatk.Rcheck/musicatk-Ex.timings

nameusersystemelapsed
add_flank_to_variants3.4300.2753.765
add_variant_type0.0170.0050.021
annotate_replication_strand0.1380.0180.157
annotate_transcript_strand1.3620.1061.520
annotate_variant_length0.0170.0030.020
annotate_variant_type0.0030.0010.004
auto_predict_grid2.1210.0582.190
build_custom_table2.1520.0342.197
build_standard_table 8.752 1.10910.293
built_tables0.0010.0010.003
cluster_exposure0.0160.0050.022
combine_count_tables2.9140.3463.339
combine_predict_grid0.4810.0300.517
compare_cosmic_v23.3300.0593.435
compare_cosmic_v31.7830.0171.814
compare_k_vals180.139 1.248182.559
compare_results2.0150.0332.057
cosmic_v2_subtype_map0.0010.0010.002
create_musica_from_counts0.0050.0020.007
create_musica_from_variants0.9770.2091.220
create_result_model0.0020.0000.002
create_umap5.1700.0645.255
credible_intervals0.0040.0010.005
discover_signatures0.8450.1150.969
drop_annotation0.0020.0010.002
exposure_differential_analysis0.0120.0020.015
exposures0.0170.0030.020
extract_count_tables0.0050.0020.007
extract_variants4.6540.0634.742
extract_variants_from_maf0.1130.0020.115
extract_variants_from_maf_file0.0970.0010.100
extract_variants_from_matrix0.1130.0020.115
extract_variants_from_vcf0.8310.0300.863
extract_variants_from_vcf_file0.4540.0060.461
generate_result_grid0.3670.0030.371
get_modality0.0070.0040.010
get_model0.0040.0030.007
get_result_list_entry0.0050.0010.007
hyperparameter0.0020.0020.004
k_select0.7200.0150.737
metrics0.0020.0010.005
modality0.0030.0020.004
model_id0.0020.0020.004
musicatk0.0000.0010.000
name_signatures0.0360.0020.038
num_signatures0.0030.0020.004
other_parameters0.0020.0020.003
parameter0.0020.0010.003
pipe0.0020.0000.004
plot_cluster5.4150.1795.616
plot_differential_analysis0.1740.0030.179
plot_exposures0.3250.0040.331
plot_heatmap0.7670.0170.786
plot_k_comparison200.345 2.144203.956
plot_sample_counts0.5620.0080.575
plot_sample_reconstruction_error0.7940.0170.817
plot_signatures0.7870.0060.795
plot_umap4.6400.0784.738
predict_exposure1.2150.0871.310
rc0.0020.0000.002
result_list0.0040.0020.006
samp_annot0.0080.0040.012
sample_names0.0030.0010.005
select_genome0.0010.0000.000
signatures0.0200.0070.026
subset_musica_by_annotation0.0050.0030.009
subset_musica_by_counts0.0120.0030.015
subset_variant_by_type0.0070.0030.010
subset_variants_by_samples0.0060.0030.009
table_selected0.0020.0020.003
tables0.0030.0020.005
umap0.0020.0010.004
variants0.0050.0020.006