Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-03-17 11:39 -0400 (Mon, 17 Mar 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4545 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R 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 1396/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
musicatk 2.1.0 (landing page) Joshua D. Campbell
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | |||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
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. |
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 |
############################################################################## ############################################################################## ### ### 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.
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)
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
musicatk.Rcheck/musicatk-Ex.timings
name | user | system | elapsed | |
add_flank_to_variants | 3.430 | 0.275 | 3.765 | |
add_variant_type | 0.017 | 0.005 | 0.021 | |
annotate_replication_strand | 0.138 | 0.018 | 0.157 | |
annotate_transcript_strand | 1.362 | 0.106 | 1.520 | |
annotate_variant_length | 0.017 | 0.003 | 0.020 | |
annotate_variant_type | 0.003 | 0.001 | 0.004 | |
auto_predict_grid | 2.121 | 0.058 | 2.190 | |
build_custom_table | 2.152 | 0.034 | 2.197 | |
build_standard_table | 8.752 | 1.109 | 10.293 | |
built_tables | 0.001 | 0.001 | 0.003 | |
cluster_exposure | 0.016 | 0.005 | 0.022 | |
combine_count_tables | 2.914 | 0.346 | 3.339 | |
combine_predict_grid | 0.481 | 0.030 | 0.517 | |
compare_cosmic_v2 | 3.330 | 0.059 | 3.435 | |
compare_cosmic_v3 | 1.783 | 0.017 | 1.814 | |
compare_k_vals | 180.139 | 1.248 | 182.559 | |
compare_results | 2.015 | 0.033 | 2.057 | |
cosmic_v2_subtype_map | 0.001 | 0.001 | 0.002 | |
create_musica_from_counts | 0.005 | 0.002 | 0.007 | |
create_musica_from_variants | 0.977 | 0.209 | 1.220 | |
create_result_model | 0.002 | 0.000 | 0.002 | |
create_umap | 5.170 | 0.064 | 5.255 | |
credible_intervals | 0.004 | 0.001 | 0.005 | |
discover_signatures | 0.845 | 0.115 | 0.969 | |
drop_annotation | 0.002 | 0.001 | 0.002 | |
exposure_differential_analysis | 0.012 | 0.002 | 0.015 | |
exposures | 0.017 | 0.003 | 0.020 | |
extract_count_tables | 0.005 | 0.002 | 0.007 | |
extract_variants | 4.654 | 0.063 | 4.742 | |
extract_variants_from_maf | 0.113 | 0.002 | 0.115 | |
extract_variants_from_maf_file | 0.097 | 0.001 | 0.100 | |
extract_variants_from_matrix | 0.113 | 0.002 | 0.115 | |
extract_variants_from_vcf | 0.831 | 0.030 | 0.863 | |
extract_variants_from_vcf_file | 0.454 | 0.006 | 0.461 | |
generate_result_grid | 0.367 | 0.003 | 0.371 | |
get_modality | 0.007 | 0.004 | 0.010 | |
get_model | 0.004 | 0.003 | 0.007 | |
get_result_list_entry | 0.005 | 0.001 | 0.007 | |
hyperparameter | 0.002 | 0.002 | 0.004 | |
k_select | 0.720 | 0.015 | 0.737 | |
metrics | 0.002 | 0.001 | 0.005 | |
modality | 0.003 | 0.002 | 0.004 | |
model_id | 0.002 | 0.002 | 0.004 | |
musicatk | 0.000 | 0.001 | 0.000 | |
name_signatures | 0.036 | 0.002 | 0.038 | |
num_signatures | 0.003 | 0.002 | 0.004 | |
other_parameters | 0.002 | 0.002 | 0.003 | |
parameter | 0.002 | 0.001 | 0.003 | |
pipe | 0.002 | 0.000 | 0.004 | |
plot_cluster | 5.415 | 0.179 | 5.616 | |
plot_differential_analysis | 0.174 | 0.003 | 0.179 | |
plot_exposures | 0.325 | 0.004 | 0.331 | |
plot_heatmap | 0.767 | 0.017 | 0.786 | |
plot_k_comparison | 200.345 | 2.144 | 203.956 | |
plot_sample_counts | 0.562 | 0.008 | 0.575 | |
plot_sample_reconstruction_error | 0.794 | 0.017 | 0.817 | |
plot_signatures | 0.787 | 0.006 | 0.795 | |
plot_umap | 4.640 | 0.078 | 4.738 | |
predict_exposure | 1.215 | 0.087 | 1.310 | |
rc | 0.002 | 0.000 | 0.002 | |
result_list | 0.004 | 0.002 | 0.006 | |
samp_annot | 0.008 | 0.004 | 0.012 | |
sample_names | 0.003 | 0.001 | 0.005 | |
select_genome | 0.001 | 0.000 | 0.000 | |
signatures | 0.020 | 0.007 | 0.026 | |
subset_musica_by_annotation | 0.005 | 0.003 | 0.009 | |
subset_musica_by_counts | 0.012 | 0.003 | 0.015 | |
subset_variant_by_type | 0.007 | 0.003 | 0.010 | |
subset_variants_by_samples | 0.006 | 0.003 | 0.009 | |
table_selected | 0.002 | 0.002 | 0.003 | |
tables | 0.003 | 0.002 | 0.005 | |
umap | 0.002 | 0.001 | 0.004 | |
variants | 0.005 | 0.002 | 0.006 | |