Aaron Chevalier
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/musicatk |
| git_branch: master |
| git_last_commit: ab8dbf0 |
| git_last_commit_date: 2021-10-26 13:04:15 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:08 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1261/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| musicatk 1.5.0 (landing page) Aaron Chevalier
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: musicatk |
| Version: 1.5.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:musicatk.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings musicatk_1.5.0.tar.gz |
| StartedAt: 2022-03-17 19:41:58 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:46:57 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 298.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: musicatk.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:musicatk.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings musicatk_1.5.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/musicatk.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'musicatk/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'musicatk' version '1.5.0'
* 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 5.6 1.12 6.72
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/musicatk.Rcheck/00check.log'
for details.
musicatk.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL musicatk
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-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
converting help for package 'musicatk'
finding HTML links ... done
add_flank_to_variants html
finding level-2 HTML links ... done
add_variant_type html
annotate_replication_strand html
annotate_transcript_strand html
annotate_variant_length html
annotate_variant_type html
auto_predict_grid html
auto_subset_sigs html
build_custom_table html
build_standard_table html
built_tables html
cluster_exposure html
combine_count_tables html
combine_predict_grid html
compare_cosmic_v2 html
compare_cosmic_v3 html
compare_results html
cosmic_v2_sigs html
cosmic_v2_subtype_map html
cosmic_v3_dbs_sigs html
cosmic_v3_indel_sigs html
cosmic_v3_sbs_sigs html
cosmic_v3_sbs_sigs_exome html
count_table-class html
create_dbs78_table html
create_musica html
create_sbs192_table html
create_sbs96_table html
create_umap html
dbs_musica html
discover_signatures html
dot-jsd html
drop_annotation html
exposure_differential_analysis html
exposures html
extract_count_tables html
extract_variants html
extract_variants_from_maf html
extract_variants_from_maf_file html
extract_variants_from_matrix html
extract_variants_from_vcf html
extract_variants_from_vcf_file html
generate_result_grid html
get_musica html
indel_musica html
k_select html
musica-class html
musica html
musica_annot html
musica_result-class html
musica_result_grid-class html
musica_sbs96 html
musica_sbs96_tiny html
musicatk html
name_signatures html
pipe html
plot_cluster html
plot_differential_analysis html
plot_exposures html
plot_heatmap html
plot_sample_counts html
plot_sample_reconstruction_error html
plot_signatures html
plot_umap html
predict_exposure html
rc html
rep_range html
res html
res_annot html
samp_annot html
sample_names html
select_genome html
signatures html
subset_musica_by_annotation html
subset_musica_by_counts html
subset_variant_by_type html
subset_variants_by_samples html
table_96 html
table_selected html
tables html
umap html
variants html
** 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)
Making 'packages.html' ... done
musicatk.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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: pkgmaker
Loading required package: registry
Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: windows] | Cores 79/80
Attaching package: 'NMF'
The following object is masked from 'package:testthat':
compare
>
> test_check("musicatk")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 42 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 42 ]
>
> proc.time()
user system elapsed
17.20 1.26 18.89
musicatk.Rcheck/musicatk-Ex.timings
| name | user | system | elapsed | |
| add_flank_to_variants | 2.11 | 0.31 | 2.42 | |
| add_variant_type | 0 | 0 | 0 | |
| annotate_replication_strand | 0.08 | 0.03 | 0.11 | |
| annotate_transcript_strand | 0.90 | 0.06 | 0.97 | |
| annotate_variant_length | 0.00 | 0.02 | 0.02 | |
| annotate_variant_type | 0 | 0 | 0 | |
| auto_predict_grid | 2.35 | 0.03 | 2.37 | |
| build_custom_table | 0.68 | 0.03 | 0.72 | |
| build_standard_table | 5.60 | 1.12 | 6.72 | |
| built_tables | 0 | 0 | 0 | |
| cluster_exposure | 0.01 | 0.02 | 0.03 | |
| combine_count_tables | 1.81 | 0.41 | 2.22 | |
| combine_predict_grid | 1.93 | 0.01 | 1.94 | |
| compare_cosmic_v2 | 1.51 | 0.00 | 1.51 | |
| compare_cosmic_v3 | 0.72 | 0.00 | 0.72 | |
| compare_results | 0.89 | 0.00 | 0.89 | |
| cosmic_v2_subtype_map | 0 | 0 | 0 | |
| create_musica | 0.55 | 0.17 | 0.72 | |
| create_umap | 3.55 | 0.05 | 3.61 | |
| discover_signatures | 0.48 | 0.08 | 0.56 | |
| drop_annotation | 0.02 | 0.00 | 0.02 | |
| exposure_differential_analysis | 0.01 | 0.00 | 0.02 | |
| exposures | 0 | 0 | 0 | |
| extract_count_tables | 0.02 | 0.00 | 0.01 | |
| extract_variants | 2.92 | 0.03 | 2.95 | |
| extract_variants_from_maf | 0.08 | 0.00 | 0.08 | |
| extract_variants_from_maf_file | 0.06 | 0.00 | 0.06 | |
| extract_variants_from_matrix | 0.09 | 0.00 | 0.10 | |
| extract_variants_from_vcf | 0.44 | 0.03 | 0.47 | |
| extract_variants_from_vcf_file | 0.31 | 0.00 | 0.32 | |
| generate_result_grid | 0.26 | 0.00 | 0.26 | |
| get_musica | 0.02 | 0.00 | 0.02 | |
| k_select | 0.62 | 0.00 | 0.62 | |
| musicatk | 0 | 0 | 0 | |
| name_signatures | 0.02 | 0.00 | 0.02 | |
| pipe | 0 | 0 | 0 | |
| plot_cluster | 3.42 | 0.14 | 3.59 | |
| plot_differential_analysis | 0.11 | 0.00 | 0.11 | |
| plot_exposures | 0.13 | 0.00 | 0.13 | |
| plot_heatmap | 0.56 | 0.08 | 0.64 | |
| plot_sample_counts | 0.2 | 0.0 | 0.2 | |
| plot_sample_reconstruction_error | 0.38 | 0.00 | 0.37 | |
| plot_signatures | 0.36 | 0.00 | 0.36 | |
| plot_umap | 3.47 | 0.03 | 3.52 | |
| predict_exposure | 0.90 | 0.13 | 1.03 | |
| rc | 0 | 0 | 0 | |
| samp_annot | 0.02 | 0.00 | 0.02 | |
| sample_names | 0 | 0 | 0 | |
| select_genome | 0 | 0 | 0 | |
| signatures | 0 | 0 | 0 | |
| subset_musica_by_annotation | 0 | 0 | 0 | |
| subset_musica_by_counts | 0.01 | 0.00 | 0.01 | |
| subset_variant_by_type | 0 | 0 | 0 | |
| subset_variants_by_samples | 0.00 | 0.01 | 0.02 | |
| table_selected | 0 | 0 | 0 | |
| tables | 0.00 | 0.02 | 0.01 | |
| umap | 0.00 | 0.01 | 0.02 | |
| variants | 0.02 | 0.00 | 0.02 | |