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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1381/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
musicatk 2.0.0  (landing page)
Joshua D. Campbell
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/musicatk
git_branch: RELEASE_3_20
git_last_commit: c0c8b45
git_last_commit_date: 2024-10-29 10:52:22 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 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
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


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: 2.0.0
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_2.0.0.tar.gz
StartedAt: 2024-12-21 02:55:45 -0500 (Sat, 21 Dec 2024)
EndedAt: 2024-12-21 03:09:49 -0500 (Sat, 21 Dec 2024)
EllapsedTime: 843.9 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_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/musicatk.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘musicatk/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘musicatk’ version ‘2.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ... OK
* 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    224.637  1.247 226.153
compare_k_vals       196.384  1.373 198.203
build_standard_table   8.163  1.021   9.315
plot_cluster           6.079  0.125   6.268
create_umap            6.099  0.067   6.179
plot_umap              5.797  0.060   5.863
* 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: OK


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/4.4-arm64/Resources/library’
* installing *source* package ‘musicatk’ ...
** 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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: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 
 23.929   0.920  24.863 

Example timings

musicatk.Rcheck/musicatk-Ex.timings

nameusersystemelapsed
add_flank_to_variants2.1180.2342.355
add_variant_type0.1690.0060.176
annotate_replication_strand0.1480.0090.158
annotate_transcript_strand2.5500.0392.589
annotate_variant_length0.0160.0040.020
annotate_variant_type0.0030.0020.005
auto_predict_grid1.5000.0321.575
build_custom_table0.6110.0160.658
build_standard_table8.1631.0219.315
built_tables0.0020.0030.005
cluster_exposure0.0180.0050.024
combine_count_tables2.4450.2992.772
combine_predict_grid0.4690.0330.502
compare_cosmic_v22.6400.0482.688
compare_cosmic_v31.4570.0091.467
compare_k_vals196.384 1.373198.203
compare_results1.7200.0311.753
cosmic_v2_subtype_map0.0010.0010.002
create_musica_from_counts0.0050.0020.007
create_musica_from_variants1.0440.2701.203
create_result_model0.0020.0000.003
create_umap6.0990.0676.179
credible_intervals0.0040.0020.006
discover_signatures0.7690.1150.888
drop_annotation0.0030.0030.005
exposure_differential_analysis0.0130.0030.015
exposures0.0200.0050.024
extract_count_tables0.0050.0030.007
extract_variants4.0620.0823.903
extract_variants_from_maf0.1410.0110.093
extract_variants_from_maf_file0.1030.0100.059
extract_variants_from_matrix0.1670.0130.094
extract_variants_from_vcf0.8190.0400.718
extract_variants_from_vcf_file0.4710.0050.476
generate_result_grid0.4170.0040.421
get_modality0.0070.0040.011
get_model0.0050.0040.009
get_result_list_entry0.0060.0030.009
hyperparameter0.0030.0020.005
k_select0.6780.0140.694
metrics0.0030.0020.005
modality0.0020.0020.005
model_id0.0020.0020.005
musicatk000
name_signatures0.0320.0020.035
num_signatures0.0030.0030.005
other_parameters0.0020.0020.005
parameter0.0020.0020.004
pipe0.0030.0000.003
plot_cluster6.0790.1256.268
plot_differential_analysis0.1610.0040.167
plot_exposures0.3350.0130.348
plot_heatmap0.7430.0190.762
plot_k_comparison224.637 1.247226.153
plot_sample_counts0.5420.0200.562
plot_sample_reconstruction_error0.6460.0060.654
plot_signatures0.7100.0060.716
plot_umap5.7970.0605.863
predict_exposure1.2200.1241.343
rc0.0020.0000.002
result_list0.0040.0030.006
samp_annot0.0080.0050.013
sample_names0.0040.0030.006
select_genome000
signatures0.0200.0070.027
subset_musica_by_annotation0.0070.0040.011
subset_musica_by_counts0.0110.0040.015
subset_variant_by_type0.0070.0030.010
subset_variants_by_samples0.0060.0030.009
table_selected0.0020.0020.004
tables0.0040.0020.007
umap0.0020.0020.004
variants0.0050.0030.009