Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-30 11:35:45 -0400 (Thu, 30 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4518 |
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 1.14.0 (landing page) Joshua D. Campbell
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.14.0 |
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_1.14.0.tar.gz |
StartedAt: 2024-05-29 22:24:23 -0400 (Wed, 29 May 2024) |
EndedAt: 2024-05-29 22:31:40 -0400 (Wed, 29 May 2024) |
EllapsedTime: 437.3 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_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/musicatk.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘musicatk/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘musicatk’ version ‘1.14.0’ * 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 ... NOTE checkRd: (-1) plot_umap.Rd:53: Lost braces 53 | code{color_by = "annotation"}. This not recommended if the annotation is | ^ checkRd: (-1) plot_umap.Rd:58: Lost braces 58 | code{color_by = "annotation"} and \code{add_annotation_labels = TRUE}. | ^ checkRd: (-1) plot_umap.Rd:62: Lost braces 62 | to improve readability. Only used if code{color_by = "annotation"} and | ^ * 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 8.775 0.987 9.900 plot_cluster 5.577 0.219 5.840 create_umap 5.148 0.110 5.306 extract_variants 5.056 0.102 5.212 * 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-3.19-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/4.4-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 4.4.0 (2024-04-24) -- "Puppy Cup" 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 23.807 1.386 25.482
musicatk.Rcheck/musicatk-Ex.timings
name | user | system | elapsed | |
add_flank_to_variants | 3.555 | 0.299 | 3.905 | |
add_variant_type | 0.022 | 0.006 | 0.029 | |
annotate_replication_strand | 0.177 | 0.020 | 0.203 | |
annotate_transcript_strand | 1.484 | 0.056 | 1.558 | |
annotate_variant_length | 0.014 | 0.003 | 0.017 | |
annotate_variant_type | 0.002 | 0.002 | 0.005 | |
auto_predict_grid | 2.980 | 0.101 | 3.105 | |
build_custom_table | 1.079 | 0.032 | 1.118 | |
build_standard_table | 8.775 | 0.987 | 9.900 | |
built_tables | 0.002 | 0.003 | 0.005 | |
cluster_exposure | 0.019 | 0.004 | 0.024 | |
combine_count_tables | 2.852 | 0.317 | 3.251 | |
combine_predict_grid | 1.949 | 0.049 | 2.020 | |
compare_cosmic_v2 | 3.072 | 0.061 | 3.165 | |
compare_cosmic_v3 | 1.781 | 0.024 | 1.824 | |
compare_results | 2.056 | 0.028 | 2.107 | |
cosmic_v2_subtype_map | 0.001 | 0.001 | 0.002 | |
create_musica | 0.967 | 0.181 | 1.169 | |
create_umap | 5.148 | 0.110 | 5.306 | |
discover_signatures | 0.866 | 0.139 | 1.029 | |
drop_annotation | 0.002 | 0.002 | 0.003 | |
exposure_differential_analysis | 0.011 | 0.003 | 0.014 | |
exposures | 0.004 | 0.004 | 0.009 | |
extract_count_tables | 0.004 | 0.002 | 0.006 | |
extract_variants | 5.056 | 0.102 | 5.212 | |
extract_variants_from_maf | 0.119 | 0.005 | 0.125 | |
extract_variants_from_maf_file | 0.112 | 0.002 | 0.115 | |
extract_variants_from_matrix | 0.113 | 0.004 | 0.118 | |
extract_variants_from_vcf | 0.801 | 0.032 | 0.840 | |
extract_variants_from_vcf_file | 0.577 | 0.010 | 0.591 | |
generate_result_grid | 0.180 | 0.005 | 0.187 | |
get_musica | 0.010 | 0.003 | 0.013 | |
k_select | 0.967 | 0.023 | 1.001 | |
musicatk | 0.000 | 0.000 | 0.001 | |
name_signatures | 0.003 | 0.002 | 0.005 | |
pipe | 0.002 | 0.001 | 0.004 | |
plot_cluster | 5.577 | 0.219 | 5.840 | |
plot_differential_analysis | 0.390 | 0.012 | 0.405 | |
plot_exposures | 0.195 | 0.005 | 0.203 | |
plot_heatmap | 0.940 | 0.023 | 0.975 | |
plot_sample_counts | 0.583 | 0.008 | 0.595 | |
plot_sample_reconstruction_error | 0.816 | 0.010 | 0.832 | |
plot_signatures | 0.845 | 0.009 | 0.860 | |
plot_umap | 4.813 | 0.076 | 4.927 | |
predict_exposure | 1.333 | 0.148 | 1.497 | |
rc | 0.003 | 0.000 | 0.002 | |
samp_annot | 0.010 | 0.003 | 0.013 | |
sample_names | 0.004 | 0.002 | 0.006 | |
select_genome | 0 | 0 | 0 | |
signatures | 0.005 | 0.005 | 0.011 | |
subset_musica_by_annotation | 0.006 | 0.003 | 0.010 | |
subset_musica_by_counts | 0.012 | 0.003 | 0.016 | |
subset_variant_by_type | 0.008 | 0.002 | 0.010 | |
subset_variants_by_samples | 0.008 | 0.003 | 0.011 | |
table_selected | 0.002 | 0.002 | 0.004 | |
tables | 0.009 | 0.004 | 0.013 | |
umap | 0.004 | 0.003 | 0.007 | |
variants | 0.013 | 0.005 | 0.019 | |