Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-24 09:06 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 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 1392/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
musicatk 1.14.1 (landing page) Joshua D. Campbell
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 1.14.1 |
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_1.14.1.tar.gz |
StartedAt: 2024-07-22 09:08:22 -0400 (Mon, 22 Jul 2024) |
EndedAt: 2024-07-22 09:23:48 -0400 (Mon, 22 Jul 2024) |
EllapsedTime: 925.9 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_1.14.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/musicatk.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-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 Monterey 12.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘musicatk/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘musicatk’ version ‘1.14.1’ * 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 build_standard_table 18.063 1.531 25.228 extract_variants 10.515 0.107 13.234 compare_cosmic_v2 7.064 0.080 9.229 plot_cluster 6.786 0.307 8.891 create_umap 6.651 0.121 8.452 add_flank_to_variants 5.895 0.495 8.107 combine_count_tables 5.670 0.416 7.817 plot_umap 5.498 0.081 6.952 auto_predict_grid 4.891 0.156 6.342 compare_results 4.767 0.042 6.099 compare_cosmic_v3 4.056 0.031 5.142 combine_predict_grid 3.814 0.073 5.058 * 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
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-x86_64/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)
musicatk.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 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:testthat': compare > > test_check("musicatk") [ FAIL 0 | WARN 2 | SKIP 0 | PASS 42 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 42 ] > > proc.time() user system elapsed 39.437 2.080 51.836
musicatk.Rcheck/musicatk-Ex.timings
name | user | system | elapsed | |
add_flank_to_variants | 5.895 | 0.495 | 8.107 | |
add_variant_type | 0.032 | 0.010 | 0.059 | |
annotate_replication_strand | 0.266 | 0.038 | 0.417 | |
annotate_transcript_strand | 2.396 | 0.160 | 3.372 | |
annotate_variant_length | 0.027 | 0.007 | 0.045 | |
annotate_variant_type | 0.004 | 0.003 | 0.009 | |
auto_predict_grid | 4.891 | 0.156 | 6.342 | |
build_custom_table | 1.950 | 0.030 | 2.473 | |
build_standard_table | 18.063 | 1.531 | 25.228 | |
built_tables | 0.004 | 0.004 | 0.010 | |
cluster_exposure | 0.028 | 0.006 | 0.047 | |
combine_count_tables | 5.670 | 0.416 | 7.817 | |
combine_predict_grid | 3.814 | 0.073 | 5.058 | |
compare_cosmic_v2 | 7.064 | 0.080 | 9.229 | |
compare_cosmic_v3 | 4.056 | 0.031 | 5.142 | |
compare_results | 4.767 | 0.042 | 6.099 | |
cosmic_v2_subtype_map | 0.003 | 0.001 | 0.008 | |
create_musica | 1.905 | 0.332 | 2.965 | |
create_umap | 6.651 | 0.121 | 8.452 | |
discover_signatures | 1.703 | 0.183 | 2.399 | |
drop_annotation | 0.004 | 0.003 | 0.008 | |
exposure_differential_analysis | 0.021 | 0.004 | 0.039 | |
exposures | 0.007 | 0.005 | 0.013 | |
extract_count_tables | 0.009 | 0.004 | 0.020 | |
extract_variants | 10.515 | 0.107 | 13.234 | |
extract_variants_from_maf | 0.247 | 0.007 | 0.314 | |
extract_variants_from_maf_file | 0.221 | 0.005 | 0.289 | |
extract_variants_from_matrix | 0.252 | 0.007 | 0.312 | |
extract_variants_from_vcf | 1.620 | 0.041 | 2.077 | |
extract_variants_from_vcf_file | 1.122 | 0.010 | 1.413 | |
generate_result_grid | 0.300 | 0.006 | 0.374 | |
get_musica | 0.017 | 0.007 | 0.031 | |
k_select | 1.997 | 0.030 | 2.542 | |
musicatk | 0.001 | 0.001 | 0.001 | |
name_signatures | 0.004 | 0.003 | 0.012 | |
pipe | 0.003 | 0.002 | 0.017 | |
plot_cluster | 6.786 | 0.307 | 8.891 | |
plot_differential_analysis | 0.770 | 0.011 | 0.974 | |
plot_exposures | 0.439 | 0.011 | 0.568 | |
plot_heatmap | 1.927 | 0.031 | 2.451 | |
plot_sample_counts | 1.396 | 0.012 | 1.749 | |
plot_sample_reconstruction_error | 1.977 | 0.016 | 2.476 | |
plot_signatures | 1.993 | 0.016 | 2.526 | |
plot_umap | 5.498 | 0.081 | 6.952 | |
predict_exposure | 2.591 | 0.236 | 3.559 | |
rc | 0.005 | 0.001 | 0.009 | |
samp_annot | 0.017 | 0.008 | 0.028 | |
sample_names | 0.005 | 0.003 | 0.009 | |
select_genome | 0.001 | 0.001 | 0.001 | |
signatures | 0.008 | 0.010 | 0.024 | |
subset_musica_by_annotation | 0.010 | 0.004 | 0.015 | |
subset_musica_by_counts | 0.017 | 0.005 | 0.028 | |
subset_variant_by_type | 0.013 | 0.004 | 0.020 | |
subset_variants_by_samples | 0.013 | 0.005 | 0.026 | |
table_selected | 0.004 | 0.003 | 0.006 | |
tables | 0.017 | 0.007 | 0.029 | |
umap | 0.007 | 0.005 | 0.015 | |
variants | 0.023 | 0.009 | 0.039 | |