Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1381/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
musicatk 2.0.0 (landing page) Joshua D. Campbell
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 2.0.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:musicatk.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings musicatk_2.0.0.tar.gz |
StartedAt: 2024-11-20 06:29:46 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 06:45:50 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 964.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: musicatk.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:musicatk.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings musicatk_2.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/musicatk.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * 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 loading without being on the library search path ... 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 176.606 0.131 179.700 compare_k_vals 162.327 0.213 168.253 plot_cluster 4.910 0.061 5.931 build_standard_table 4.480 0.480 5.086 plot_umap 4.843 0.025 5.135 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
musicatk.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL musicatk ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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: bigmemory] | 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 16.565 0.908 18.138
musicatk.Rcheck/musicatk-Ex.timings
name | user | system | elapsed | |
add_flank_to_variants | 2.370 | 0.243 | 2.719 | |
add_variant_type | 0.011 | 0.004 | 0.015 | |
annotate_replication_strand | 0.094 | 0.017 | 0.110 | |
annotate_transcript_strand | 1.677 | 0.030 | 1.739 | |
annotate_variant_length | 0.008 | 0.001 | 0.009 | |
annotate_variant_type | 0.001 | 0.001 | 0.002 | |
auto_predict_grid | 1.174 | 0.006 | 1.207 | |
build_custom_table | 0.554 | 0.014 | 0.567 | |
build_standard_table | 4.480 | 0.480 | 5.086 | |
built_tables | 0.001 | 0.001 | 0.001 | |
cluster_exposure | 0.010 | 0.002 | 0.012 | |
combine_count_tables | 1.425 | 0.123 | 1.574 | |
combine_predict_grid | 0.368 | 0.005 | 0.387 | |
compare_cosmic_v2 | 1.881 | 0.009 | 1.903 | |
compare_cosmic_v3 | 1.049 | 0.003 | 1.056 | |
compare_k_vals | 162.327 | 0.213 | 168.253 | |
compare_results | 1.220 | 0.002 | 1.259 | |
cosmic_v2_subtype_map | 0.000 | 0.000 | 0.001 | |
create_musica_from_counts | 0.004 | 0.000 | 0.003 | |
create_musica_from_variants | 0.562 | 0.069 | 1.280 | |
create_result_model | 0.001 | 0.000 | 0.002 | |
create_umap | 4.776 | 0.032 | 4.866 | |
credible_intervals | 0.002 | 0.001 | 0.003 | |
discover_signatures | 0.454 | 0.033 | 0.505 | |
drop_annotation | 0.001 | 0.001 | 0.002 | |
exposure_differential_analysis | 0.008 | 0.000 | 0.008 | |
exposures | 0.011 | 0.001 | 0.012 | |
extract_count_tables | 0.002 | 0.001 | 0.003 | |
extract_variants | 2.864 | 0.002 | 3.031 | |
extract_variants_from_maf | 0.10 | 0.00 | 0.08 | |
extract_variants_from_maf_file | 0.094 | 0.000 | 0.109 | |
extract_variants_from_matrix | 0.109 | 0.000 | 0.160 | |
extract_variants_from_vcf | 0.394 | 0.008 | 0.405 | |
extract_variants_from_vcf_file | 0.302 | 0.000 | 0.303 | |
generate_result_grid | 0.224 | 0.001 | 0.226 | |
get_modality | 0.004 | 0.001 | 0.005 | |
get_model | 0.002 | 0.001 | 0.004 | |
get_result_list_entry | 0.004 | 0.000 | 0.004 | |
hyperparameter | 0.001 | 0.000 | 0.002 | |
k_select | 0.483 | 0.003 | 0.485 | |
metrics | 0.002 | 0.000 | 0.002 | |
modality | 0.002 | 0.000 | 0.002 | |
model_id | 0.001 | 0.001 | 0.002 | |
musicatk | 0 | 0 | 0 | |
name_signatures | 0.022 | 0.000 | 0.021 | |
num_signatures | 0.001 | 0.001 | 0.002 | |
other_parameters | 0.001 | 0.001 | 0.002 | |
parameter | 0.002 | 0.000 | 0.002 | |
pipe | 0.002 | 0.000 | 0.002 | |
plot_cluster | 4.910 | 0.061 | 5.931 | |
plot_differential_analysis | 0.118 | 0.001 | 0.120 | |
plot_exposures | 0.223 | 0.001 | 0.224 | |
plot_heatmap | 0.540 | 0.002 | 0.542 | |
plot_k_comparison | 176.606 | 0.131 | 179.700 | |
plot_sample_counts | 0.373 | 0.001 | 0.376 | |
plot_sample_reconstruction_error | 0.532 | 0.001 | 0.539 | |
plot_signatures | 0.517 | 0.002 | 0.583 | |
plot_umap | 4.843 | 0.025 | 5.135 | |
predict_exposure | 0.745 | 0.025 | 0.901 | |
rc | 0.002 | 0.000 | 0.002 | |
result_list | 0.002 | 0.000 | 0.003 | |
samp_annot | 0.004 | 0.001 | 0.005 | |
sample_names | 0.001 | 0.001 | 0.003 | |
select_genome | 0 | 0 | 0 | |
signatures | 0.011 | 0.002 | 0.013 | |
subset_musica_by_annotation | 0.002 | 0.002 | 0.004 | |
subset_musica_by_counts | 0.006 | 0.000 | 0.006 | |
subset_variant_by_type | 0.004 | 0.000 | 0.004 | |
subset_variants_by_samples | 0.002 | 0.002 | 0.004 | |
table_selected | 0.001 | 0.001 | 0.002 | |
tables | 0.002 | 0.001 | 0.003 | |
umap | 0.001 | 0.001 | 0.002 | |
variants | 0.003 | 0.001 | 0.004 | |