Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-25 17:40 -0400 (Tue, 25 Jun 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" | 4760 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:musicatk.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings musicatk_1.14.0.tar.gz |
StartedAt: 2024-06-24 07:33:03 -0400 (Mon, 24 Jun 2024) |
EndedAt: 2024-06-24 07:44:44 -0400 (Mon, 24 Jun 2024) |
EllapsedTime: 701.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: musicatk.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:musicatk.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings musicatk_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/musicatk.Rcheck' * using R version 4.4.0 (2024-04-24 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * 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 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 9.13 1.83 11.10 plot_cluster 5.28 0.66 7.55 create_umap 5.46 0.12 5.86 plot_umap 4.92 0.11 5.05 * 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 'F:/biocbuild/bbs-3.19-bioc/meat/musicatk.Rcheck/00check.log' for details.
musicatk.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL musicatk ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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: windows] | Cores 2/2 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 22.48 13.75 35.32
musicatk.Rcheck/musicatk-Ex.timings
name | user | system | elapsed | |
add_flank_to_variants | 3.61 | 0.33 | 4.05 | |
add_variant_type | 0.03 | 0.01 | 0.05 | |
annotate_replication_strand | 0.17 | 0.02 | 0.19 | |
annotate_transcript_strand | 1.33 | 0.08 | 1.41 | |
annotate_variant_length | 0.00 | 0.01 | 0.01 | |
annotate_variant_type | 0.00 | 0.02 | 0.02 | |
auto_predict_grid | 3.39 | 0.17 | 3.65 | |
build_custom_table | 1.08 | 0.12 | 1.19 | |
build_standard_table | 9.13 | 1.83 | 11.10 | |
built_tables | 0 | 0 | 0 | |
cluster_exposure | 0.03 | 0.00 | 0.12 | |
combine_count_tables | 2.72 | 0.54 | 3.28 | |
combine_predict_grid | 2.39 | 0.16 | 2.61 | |
compare_cosmic_v2 | 3.31 | 0.19 | 3.52 | |
compare_cosmic_v3 | 1.86 | 0.01 | 1.87 | |
compare_results | 1.89 | 0.03 | 1.92 | |
cosmic_v2_subtype_map | 0 | 0 | 0 | |
create_musica | 1.22 | 0.40 | 2.80 | |
create_umap | 5.46 | 0.12 | 5.86 | |
discover_signatures | 0.79 | 0.27 | 1.45 | |
drop_annotation | 0 | 0 | 0 | |
exposure_differential_analysis | 0.00 | 0.01 | 0.03 | |
exposures | 0.00 | 0.02 | 0.02 | |
extract_count_tables | 0.00 | 0.01 | 0.01 | |
extract_variants | 4.71 | 0.11 | 4.86 | |
extract_variants_from_maf | 0.17 | 0.00 | 0.17 | |
extract_variants_from_maf_file | 0.12 | 0.02 | 0.16 | |
extract_variants_from_matrix | 0.14 | 0.01 | 0.16 | |
extract_variants_from_vcf | 0.77 | 1.96 | 2.82 | |
extract_variants_from_vcf_file | 0.53 | 0.01 | 0.57 | |
generate_result_grid | 0.30 | 0.02 | 0.31 | |
get_musica | 0.00 | 0.01 | 0.01 | |
k_select | 0.78 | 0.00 | 0.82 | |
musicatk | 0 | 0 | 0 | |
name_signatures | 0.00 | 0.02 | 0.01 | |
pipe | 0 | 0 | 0 | |
plot_cluster | 5.28 | 0.66 | 7.55 | |
plot_differential_analysis | 0.39 | 0.00 | 0.39 | |
plot_exposures | 0.24 | 0.04 | 0.28 | |
plot_heatmap | 1.17 | 0.94 | 1.13 | |
plot_sample_counts | 0.77 | 0.29 | 0.63 | |
plot_sample_reconstruction_error | 0.89 | 0.02 | 0.92 | |
plot_signatures | 0.88 | 0.03 | 0.91 | |
plot_umap | 4.92 | 0.11 | 5.05 | |
predict_exposure | 1.16 | 0.22 | 1.39 | |
rc | 0 | 0 | 0 | |
samp_annot | 0.03 | 0.00 | 0.03 | |
sample_names | 0 | 0 | 0 | |
select_genome | 0 | 0 | 0 | |
signatures | 0.01 | 0.01 | 0.03 | |
subset_musica_by_annotation | 0.00 | 0.00 | 0.02 | |
subset_musica_by_counts | 0.02 | 0.02 | 0.03 | |
subset_variant_by_type | 0 | 0 | 0 | |
subset_variants_by_samples | 0.02 | 0.00 | 0.01 | |
table_selected | 0.00 | 0.01 | 0.02 | |
tables | 0.01 | 0.00 | 0.01 | |
umap | 0.00 | 0.02 | 0.02 | |
variants | 0.02 | 0.02 | 0.03 | |