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This page was generated on 2024-07-24 11:42 -0400 (Wed, 24 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4688
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4284
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4455
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4404
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 1359/2248HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
musicatk 1.15.1  (landing page)
Joshua D. Campbell
Snapshot Date: 2024-07-23 14:00 -0400 (Tue, 23 Jul 2024)
git_url: https://git.bioconductor.org/packages/musicatk
git_branch: devel
git_last_commit: f17a334
git_last_commit_date: 2024-07-17 11:01:12 -0400 (Wed, 17 Jul 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for musicatk on kjohnson3

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: 1.15.1
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_1.15.1.tar.gz
StartedAt: 2024-07-23 23:27:59 -0400 (Tue, 23 Jul 2024)
EndedAt: 2024-07-23 23:30:26 -0400 (Tue, 23 Jul 2024)
EllapsedTime: 146.9 seconds
RetCode: 0
Status:   OK  
CheckDir: musicatk.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/musicatk.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-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 Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘musicatk/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘musicatk’ version ‘1.15.1’
* 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 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
* 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-arm64/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 version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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 2 | SKIP 0 | PASS 42 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 42 ]
> 
> proc.time()
   user  system elapsed 
  8.134   0.289   8.427 

Example timings

musicatk.Rcheck/musicatk-Ex.timings

nameusersystemelapsed
add_flank_to_variants1.2550.0731.328
add_variant_type0.0080.0010.009
annotate_replication_strand0.0510.0050.056
annotate_transcript_strand0.4410.0150.456
annotate_variant_length0.0050.0020.006
annotate_variant_type0.0010.0010.002
auto_predict_grid1.2170.0391.262
build_custom_table0.3210.0120.334
build_standard_table2.1300.3312.470
built_tables0.0010.0000.001
cluster_exposure0.0060.0020.008
combine_count_tables0.7480.0960.845
combine_predict_grid0.6680.0190.688
compare_cosmic_v20.8100.0100.819
compare_cosmic_v30.4480.0020.449
compare_results0.5430.0020.546
cosmic_v2_subtype_map0.0000.0000.001
create_musica0.2540.0700.327
create_umap2.2710.0232.309
discover_signatures0.2170.0370.256
drop_annotation0.0010.0010.002
exposure_differential_analysis0.0040.0010.005
exposures0.0010.0010.003
extract_count_tables0.0010.0010.002
extract_variants1.2040.0201.226
extract_variants_from_maf0.0360.0020.037
extract_variants_from_maf_file0.0280.0010.030
extract_variants_from_matrix0.0330.0020.035
extract_variants_from_vcf0.1950.0070.202
extract_variants_from_vcf_file0.1200.0020.121
generate_result_grid0.0740.0010.075
get_musica0.0020.0010.003
k_select0.2250.0040.229
musicatk000
name_signatures0.0010.0010.002
pipe0.0010.0000.001
plot_cluster2.2870.0422.334
plot_differential_analysis0.0900.0030.093
plot_exposures0.0570.0020.060
plot_heatmap0.2390.0060.247
plot_sample_counts0.1550.0020.158
plot_sample_reconstruction_error0.2180.0020.220
plot_signatures0.2120.0020.214
plot_umap2.1870.0152.204
predict_exposure0.3440.0430.388
rc0.0010.0000.001
samp_annot0.0030.0010.004
sample_names0.0010.0010.001
select_genome000
signatures0.0010.0020.003
subset_musica_by_annotation0.0020.0010.003
subset_musica_by_counts0.0030.0010.004
subset_variant_by_type0.0020.0010.003
subset_variants_by_samples0.0010.0010.002
table_selected0.0010.0010.002
tables0.0020.0010.003
umap0.0020.0010.002
variants0.0030.0020.005