Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:40 -0500 (Mon, 02 Jan 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
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 |
To the developers/maintainers of the musicatk package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1297/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
musicatk 1.9.0 (landing page) Aaron Chevalier
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
Package: musicatk |
Version: 1.9.0 |
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:musicatk.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings musicatk_1.9.0.tar.gz |
StartedAt: 2022-12-29 01:44:59 -0500 (Thu, 29 Dec 2022) |
EndedAt: 2022-12-29 01:50:00 -0500 (Thu, 29 Dec 2022) |
EllapsedTime: 301.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: musicatk.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:musicatk.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings musicatk_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/musicatk.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * running under: Windows Server 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 '1.9.0' * 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 R 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 ... NOTE Namespaces in Imports field not imported from: 'TCGAbiolinks' 'shinyBS' 'shinyalert' 'shinybusy' 'shinydashboard' 'shinyjqui' 'shinyjs' 'sortable' All declared Imports should be used. * 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 7.33 1.34 8.67 plot_cluster 3.94 0.19 5.01 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... 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-3.17-bioc-rtools43/meat/musicatk.Rcheck/00check.log' for details.
musicatk.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL musicatk ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) 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 31/32 Attaching package: 'NMF' The following object is masked from 'package:testthat': compare > > test_check("musicatk") [ FAIL 0 | WARN 5 | SKIP 0 | PASS 42 ] [ FAIL 0 | WARN 5 | SKIP 0 | PASS 42 ] > > proc.time() user system elapsed 15.93 1.01 16.90
musicatk.Rcheck/musicatk-Ex.timings
name | user | system | elapsed | |
add_flank_to_variants | 1.72 | 0.20 | 1.92 | |
add_variant_type | 0.01 | 0.01 | 0.03 | |
annotate_replication_strand | 0.80 | 0.02 | 0.81 | |
annotate_transcript_strand | 0.92 | 0.05 | 0.97 | |
annotate_variant_length | 0.02 | 0.00 | 0.02 | |
annotate_variant_type | 0.01 | 0.00 | 0.01 | |
auto_predict_grid | 1.91 | 0.01 | 1.94 | |
build_custom_table | 0.75 | 0.02 | 0.77 | |
build_standard_table | 7.33 | 1.34 | 8.67 | |
built_tables | 0 | 0 | 0 | |
cluster_exposure | 0.00 | 0.03 | 0.03 | |
combine_count_tables | 2.18 | 0.33 | 2.52 | |
combine_predict_grid | 2 | 0 | 2 | |
compare_cosmic_v2 | 1.86 | 0.00 | 1.85 | |
compare_cosmic_v3 | 0.79 | 0.03 | 0.82 | |
compare_results | 1.06 | 0.00 | 1.06 | |
cosmic_v2_subtype_map | 0 | 0 | 0 | |
create_musica | 0.84 | 0.24 | 1.14 | |
create_umap | 3.77 | 0.08 | 3.89 | |
discover_signatures | 0.58 | 0.12 | 0.70 | |
drop_annotation | 0 | 0 | 0 | |
exposure_differential_analysis | 0.01 | 0.00 | 0.02 | |
exposures | 0 | 0 | 0 | |
extract_count_tables | 0.00 | 0.01 | 0.01 | |
extract_variants | 3.52 | 0.06 | 3.58 | |
extract_variants_from_maf | 0.09 | 0.00 | 0.09 | |
extract_variants_from_maf_file | 0.11 | 0.00 | 0.11 | |
extract_variants_from_matrix | 0.16 | 0.00 | 0.16 | |
extract_variants_from_vcf | 0.54 | 0.04 | 0.58 | |
extract_variants_from_vcf_file | 0.47 | 0.01 | 0.48 | |
generate_result_grid | 0.33 | 0.00 | 0.32 | |
get_musica | 0.02 | 0.00 | 0.02 | |
k_select | 0.65 | 0.04 | 0.70 | |
musicatk | 0 | 0 | 0 | |
name_signatures | 0.00 | 0.02 | 0.02 | |
pipe | 0 | 0 | 0 | |
plot_cluster | 3.94 | 0.19 | 5.01 | |
plot_differential_analysis | 0.16 | 0.00 | 0.16 | |
plot_exposures | 0.14 | 0.00 | 0.16 | |
plot_heatmap | 0.56 | 0.01 | 0.58 | |
plot_sample_counts | 0.27 | 0.00 | 0.26 | |
plot_sample_reconstruction_error | 0.47 | 0.00 | 0.47 | |
plot_signatures | 0.42 | 0.00 | 0.42 | |
plot_umap | 3.39 | 0.06 | 3.47 | |
predict_exposure | 1.03 | 0.11 | 1.14 | |
rc | 0 | 0 | 0 | |
samp_annot | 0.03 | 0.00 | 0.03 | |
sample_names | 0 | 0 | 0 | |
select_genome | 0 | 0 | 0 | |
signatures | 0.02 | 0.00 | 0.02 | |
subset_musica_by_annotation | 0.00 | 0.02 | 0.01 | |
subset_musica_by_counts | 0.01 | 0.00 | 0.02 | |
subset_variant_by_type | 0 | 0 | 0 | |
subset_variants_by_samples | 0.02 | 0.00 | 0.01 | |
table_selected | 0 | 0 | 0 | |
tables | 0.00 | 0.02 | 0.02 | |
umap | 0.00 | 0.01 | 0.02 | |
variants | 0.00 | 0.02 | 0.01 | |