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This page was generated on 2024-03-01 11:39:16 -0500 (Fri, 01 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 1362/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
musicatk 1.13.0  (landing page)
Aaron Chevalier
Snapshot Date: 2024-02-28 14:00:14 -0500 (Wed, 28 Feb 2024)
git_url: https://git.bioconductor.org/packages/musicatk
git_branch: devel
git_last_commit: 9bedf9c
git_last_commit_date: 2023-10-24 11:27:12 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for musicatk on merida1


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.

raw results


Summary

Package: musicatk
Version: 1.13.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:musicatk.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings musicatk_1.13.0.tar.gz
StartedAt: 2024-02-29 07:37:29 -0500 (Thu, 29 Feb 2024)
EndedAt: 2024-02-29 07:52:04 -0500 (Thu, 29 Feb 2024)
EllapsedTime: 875.5 seconds
RetCode: 0
Status:   OK  
CheckDir: musicatk.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:musicatk.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings musicatk_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/musicatk.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘musicatk/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘musicatk’ version ‘1.13.0’
* 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 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 ... 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
build_standard_table  16.435  1.519  21.972
extract_variants       9.625  0.130  11.836
plot_cluster           6.426  0.339   8.083
create_umap            6.480  0.126   7.823
compare_cosmic_v2      6.494  0.067   7.521
add_flank_to_variants  5.697  0.639   7.740
combine_count_tables   5.182  0.390   6.686
plot_umap              5.269  0.115   6.492
auto_predict_grid      4.732  0.148   5.813
compare_results        4.313  0.031   5.001
* 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: OK


Installation output

musicatk.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL musicatk
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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)

Tests output

musicatk.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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: synchronicity] | 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 5 | SKIP 0 | PASS 42 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 42 ]
> 
> proc.time()
   user  system elapsed 
 39.135   2.271  49.491 

Example timings

musicatk.Rcheck/musicatk-Ex.timings

nameusersystemelapsed
add_flank_to_variants5.6970.6397.740
add_variant_type0.0320.0100.048
annotate_replication_strand0.2760.0260.393
annotate_transcript_strand2.3750.1493.077
annotate_variant_length0.0250.0060.039
annotate_variant_type0.0040.0030.010
auto_predict_grid4.7320.1485.813
build_custom_table1.9190.0352.281
build_standard_table16.435 1.51921.972
built_tables0.0040.0040.008
cluster_exposure0.0490.0070.073
combine_count_tables5.1820.3906.686
combine_predict_grid3.7040.0714.350
compare_cosmic_v26.4940.0677.521
compare_cosmic_v33.7590.0324.383
compare_results4.3130.0315.001
cosmic_v2_subtype_map0.0030.0010.003
create_musica1.6990.3112.503
create_umap6.4800.1267.823
discover_signatures1.5360.1762.104
drop_annotation0.0040.0040.009
exposure_differential_analysis0.0200.0060.036
exposures0.0070.0070.021
extract_count_tables0.0080.0040.014
extract_variants 9.625 0.13011.836
extract_variants_from_maf0.2320.0060.272
extract_variants_from_maf_file0.2350.0060.288
extract_variants_from_matrix0.2440.0080.308
extract_variants_from_vcf1.4700.0441.813
extract_variants_from_vcf_file1.0970.0161.337
generate_result_grid0.3000.0080.363
get_musica0.0160.0080.033
k_select1.8590.0362.286
musicatk0.0000.0010.001
name_signatures0.0050.0040.010
pipe0.0030.0020.006
plot_cluster6.4260.3398.083
plot_differential_analysis0.7020.0130.880
plot_exposures0.3860.0150.479
plot_heatmap1.8880.1992.460
plot_sample_counts1.2820.0251.510
plot_sample_reconstruction_error1.9170.0402.280
plot_signatures1.8180.0232.216
plot_umap5.2690.1156.492
predict_exposure2.4370.2283.252
rc0.0040.0010.006
samp_annot0.0150.0080.027
sample_names0.0050.0040.009
select_genome0.0000.0010.001
signatures0.0090.0120.025
subset_musica_by_annotation0.0090.0050.018
subset_musica_by_counts0.0170.0060.026
subset_variant_by_type0.0120.0050.023
subset_variants_by_samples0.0100.0060.019
table_selected0.0030.0040.006
tables0.0160.0070.026
umap0.0070.0070.015
variants0.0200.0100.036