Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-31 17:03:06 -0400 (Fri, 31 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 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
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 | |||||||||
kjohnson3 | macOS 13.6.5 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: 1.14.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:musicatk.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings musicatk_1.14.0.tar.gz |
StartedAt: 2024-05-31 06:01:40 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 06:09:14 -0400 (Fri, 31 May 2024) |
EllapsedTime: 454.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: musicatk.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:musicatk.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings musicatk_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/musicatk.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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 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 ... 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 6.666 1.089 7.754 create_umap 5.345 0.192 5.536 plot_cluster 5.393 0.144 5.536 * 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: 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/musicatk.Rcheck/00check.log’ for details.
musicatk.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL musicatk ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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 4.4.0 (2024-04-24) -- "Puppy Cup" 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 2 | SKIP 0 | PASS 42 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 42 ] > > proc.time() user system elapsed 21.448 1.255 22.735
musicatk.Rcheck/musicatk-Ex.timings
name | user | system | elapsed | |
add_flank_to_variants | 3.099 | 0.340 | 3.439 | |
add_variant_type | 0.015 | 0.003 | 0.019 | |
annotate_replication_strand | 0.116 | 0.012 | 0.128 | |
annotate_transcript_strand | 1.254 | 0.056 | 1.310 | |
annotate_variant_length | 0.014 | 0.001 | 0.014 | |
annotate_variant_type | 0.000 | 0.002 | 0.002 | |
auto_predict_grid | 2.692 | 0.076 | 2.769 | |
build_custom_table | 0.948 | 0.036 | 0.984 | |
build_standard_table | 6.666 | 1.089 | 7.754 | |
built_tables | 0.002 | 0.000 | 0.003 | |
cluster_exposure | 0.013 | 0.004 | 0.018 | |
combine_count_tables | 2.305 | 0.284 | 2.590 | |
combine_predict_grid | 1.607 | 0.028 | 1.635 | |
compare_cosmic_v2 | 2.414 | 0.024 | 2.438 | |
compare_cosmic_v3 | 1.443 | 0.052 | 1.495 | |
compare_results | 1.640 | 0.004 | 1.645 | |
cosmic_v2_subtype_map | 0.001 | 0.000 | 0.002 | |
create_musica | 0.697 | 0.252 | 0.928 | |
create_umap | 5.345 | 0.192 | 5.536 | |
discover_signatures | 0.656 | 0.091 | 0.748 | |
drop_annotation | 0.002 | 0.000 | 0.002 | |
exposure_differential_analysis | 0.01 | 0.00 | 0.01 | |
exposures | 0.001 | 0.003 | 0.004 | |
extract_count_tables | 0.003 | 0.000 | 0.004 | |
extract_variants | 3.865 | 0.052 | 3.872 | |
extract_variants_from_maf | 0.133 | 0.000 | 0.111 | |
extract_variants_from_maf_file | 0.099 | 0.004 | 0.079 | |
extract_variants_from_matrix | 0.119 | 0.000 | 0.097 | |
extract_variants_from_vcf | 0.648 | 0.008 | 0.657 | |
extract_variants_from_vcf_file | 0.443 | 0.000 | 0.442 | |
generate_result_grid | 0.152 | 0.000 | 0.152 | |
get_musica | 0.006 | 0.004 | 0.010 | |
k_select | 0.756 | 0.000 | 0.757 | |
musicatk | 0.000 | 0.000 | 0.001 | |
name_signatures | 0.000 | 0.003 | 0.003 | |
pipe | 0.003 | 0.000 | 0.002 | |
plot_cluster | 5.393 | 0.144 | 5.536 | |
plot_differential_analysis | 0.264 | 0.012 | 0.275 | |
plot_exposures | 0.144 | 0.008 | 0.152 | |
plot_heatmap | 0.720 | 0.007 | 0.728 | |
plot_sample_counts | 0.471 | 0.000 | 0.472 | |
plot_sample_reconstruction_error | 0.697 | 0.008 | 0.705 | |
plot_signatures | 0.650 | 0.000 | 0.651 | |
plot_umap | 4.904 | 0.088 | 4.991 | |
predict_exposure | 1.000 | 0.144 | 1.144 | |
rc | 0.002 | 0.000 | 0.003 | |
samp_annot | 0.006 | 0.003 | 0.009 | |
sample_names | 0.002 | 0.000 | 0.003 | |
select_genome | 0 | 0 | 0 | |
signatures | 0.006 | 0.000 | 0.006 | |
subset_musica_by_annotation | 0.005 | 0.000 | 0.005 | |
subset_musica_by_counts | 0.005 | 0.004 | 0.009 | |
subset_variant_by_type | 0.006 | 0.000 | 0.006 | |
subset_variants_by_samples | 0.002 | 0.004 | 0.006 | |
table_selected | 0.002 | 0.000 | 0.002 | |
tables | 0.008 | 0.000 | 0.008 | |
umap | 0.003 | 0.000 | 0.004 | |
variants | 0.010 | 0.000 | 0.011 | |