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This page was generated on 2024-06-11 14:42 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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 1392/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
musicatk 1.14.0  (landing page)
Joshua D. Campbell
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/musicatk
git_branch: RELEASE_3_19
git_last_commit: a447ad6
git_last_commit_date: 2024-04-30 11:28:39 -0400 (Tue, 30 Apr 2024)
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
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 lconway

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: 1.14.0
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_1.14.0.tar.gz
StartedAt: 2024-06-09 21:49:52 -0400 (Sun, 09 Jun 2024)
EndedAt: 2024-06-09 21:56:36 -0400 (Sun, 09 Jun 2024)
EllapsedTime: 404.5 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_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/musicatk.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 ‘1.14.0’
* 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 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 ... 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 8.801  0.904   9.786
plot_cluster         5.252  0.165   5.429
create_umap          5.085  0.074   5.168
* 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
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/musicatk.Rcheck/00check.log’
for details.


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 version 4.4.0 (2024-04-24) -- "Puppy Cup"
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 2 | SKIP 0 | PASS 42 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 42 ]
> 
> proc.time()
   user  system elapsed 
 22.172   1.192  23.499 

Example timings

musicatk.Rcheck/musicatk-Ex.timings

nameusersystemelapsed
add_flank_to_variants3.3390.2233.571
add_variant_type0.0190.0050.024
annotate_replication_strand0.1680.0160.186
annotate_transcript_strand1.1150.0371.152
annotate_variant_length0.0110.0020.013
annotate_variant_type0.0020.0010.003
auto_predict_grid2.8530.0962.959
build_custom_table0.9260.0230.950
build_standard_table8.8010.9049.786
built_tables0.0010.0010.003
cluster_exposure0.0130.0030.017
combine_count_tables2.7750.2563.046
combine_predict_grid1.9270.0331.965
compare_cosmic_v22.8830.0332.922
compare_cosmic_v31.7600.0081.776
compare_results2.0270.0082.040
cosmic_v2_subtype_map0.0010.0010.001
create_musica0.9850.1891.211
create_umap5.0850.0745.168
discover_signatures0.8590.1120.974
drop_annotation0.0020.0020.004
exposure_differential_analysis0.0110.0030.013
exposures0.0040.0030.007
extract_count_tables0.0040.0020.006
extract_variants4.6580.0544.724
extract_variants_from_maf0.1190.0020.121
extract_variants_from_maf_file0.1290.0030.132
extract_variants_from_matrix0.1020.0010.104
extract_variants_from_vcf0.8620.0260.890
extract_variants_from_vcf_file0.4320.0040.437
generate_result_grid0.1670.0020.168
get_musica0.0090.0030.012
k_select0.7650.0130.780
musicatk000
name_signatures0.0020.0010.003
pipe0.0020.0000.003
plot_cluster5.2520.1655.429
plot_differential_analysis0.3530.0090.363
plot_exposures0.1680.0030.173
plot_heatmap0.8910.0180.912
plot_sample_counts0.5510.0030.555
plot_sample_reconstruction_error0.8400.0090.850
plot_signatures0.7890.0050.796
plot_umap4.6120.0364.655
predict_exposure1.1760.1521.332
rc0.0030.0000.003
samp_annot0.0090.0040.013
sample_names0.0030.0020.005
select_genome000
signatures0.0050.0060.011
subset_musica_by_annotation0.0050.0030.007
subset_musica_by_counts0.0110.0030.014
subset_variant_by_type0.0070.0020.010
subset_variants_by_samples0.0060.0020.009
table_selected0.0020.0020.003
tables0.0090.0040.012
umap0.0040.0030.006
variants0.0090.0040.012