Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-01-11 11:40 -0500 (Sat, 11 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4760
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4479
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4443
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4398
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4391
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 1377/2277HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
musicatk 2.1.0  (landing page)
Joshua D. Campbell
Snapshot Date: 2025-01-10 13:40 -0500 (Fri, 10 Jan 2025)
git_url: https://git.bioconductor.org/packages/musicatk
git_branch: devel
git_last_commit: 45539aa
git_last_commit_date: 2024-10-29 10:52:22 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows 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  NO, package depends on 'VariantAnnotation' which is only available as a source package that needs compilation
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'VariantAnnotation' which is only available as a source package that needs compilation
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for musicatk on nebbiolo1

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: 2.1.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:musicatk.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings musicatk_2.1.0.tar.gz
StartedAt: 2025-01-11 00:22:39 -0500 (Sat, 11 Jan 2025)
EndedAt: 2025-01-11 00:40:52 -0500 (Sat, 11 Jan 2025)
EllapsedTime: 1093.7 seconds
RetCode: 0
Status:   OK  
CheckDir: musicatk.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:musicatk.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings musicatk_2.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/musicatk.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘musicatk/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘musicatk’ version ‘2.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 45 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 loading without being on the library search path ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  add_flank_to_variants.Rd: BSgenome-class
  build_standard_table.Rd: BSgenome-class
  create_musica_from_variants.Rd: BSgenome-class
  create_sbs192_table.Rd: BSgenome-class
  create_sbs96_table.Rd: BSgenome-class
  extract_variants.Rd: CollapsedVCF-class, ExpandedVCF-class, MAF-class
  variants.Rd: data.table-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
plot_k_comparison    209.873 11.299 221.158
compare_k_vals       186.390 12.169 198.578
build_standard_table   6.704  1.295   8.000
plot_cluster           5.423  0.115   5.549
create_umap            5.084  0.190   5.283
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/musicatk.Rcheck/00check.log’
for details.


Installation output

musicatk.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL musicatk
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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: bigmemory] | Cores 2/2
  To enable shared memory capabilities, try: install.extras('
NMF
')

Attaching package: 'NMF'

The following object is masked from 'package:generics':

    fit

The following object is masked from 'package:testthat':

    compare

> 
> test_check("musicatk")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 41 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 41 ]
> 
> proc.time()
   user  system elapsed 
 18.620   1.055  19.672 

Example timings

musicatk.Rcheck/musicatk-Ex.timings

nameusersystemelapsed
add_flank_to_variants2.9260.3683.295
add_variant_type0.0130.0020.015
annotate_replication_strand0.1070.0110.118
annotate_transcript_strand1.1020.0421.144
annotate_variant_length0.0100.0030.012
annotate_variant_type0.0020.0010.002
auto_predict_grid2.7350.0072.742
build_custom_table0.8400.0360.876
build_standard_table6.7041.2958.000
built_tables0.0010.0010.002
cluster_exposure0.0120.0030.015
combine_count_tables2.0920.3322.426
combine_predict_grid0.4340.0210.455
compare_cosmic_v22.5330.0502.583
compare_cosmic_v31.4760.0341.510
compare_k_vals186.390 12.169198.578
compare_results1.6320.0601.691
cosmic_v2_subtype_map0.0010.0000.001
create_musica_from_counts0.0030.0010.004
create_musica_from_variants0.7500.2831.009
create_result_model0.0020.0000.002
create_umap5.0840.1905.283
credible_intervals0.0020.0010.003
discover_signatures0.6700.1880.858
drop_annotation0.0010.0010.002
exposure_differential_analysis0.0080.0020.011
exposures0.0160.0030.019
extract_count_tables0.0030.0010.004
extract_variants3.9610.1894.094
extract_variants_from_maf0.1270.0050.100
extract_variants_from_maf_file0.1270.0010.097
extract_variants_from_matrix0.1260.0000.095
extract_variants_from_vcf0.5850.0150.600
extract_variants_from_vcf_file0.4020.0020.404
generate_result_grid0.3300.0030.333
get_modality0.0050.0030.008
get_model0.0020.0040.006
get_result_list_entry0.0040.0010.005
hyperparameter0.0010.0010.002
k_select0.7320.0120.744
metrics0.0010.0020.002
modality0.0000.0020.002
model_id0.0020.0000.002
musicatk0.0010.0000.000
name_signatures0.0290.0010.030
num_signatures0.0020.0010.002
other_parameters0.0030.0000.002
parameter0.0010.0010.002
pipe0.0020.0000.002
plot_cluster5.4230.1155.549
plot_differential_analysis0.1570.0000.157
plot_exposures0.2920.0010.293
plot_heatmap0.6970.0020.700
plot_k_comparison209.873 11.299221.158
plot_sample_counts0.5000.0060.506
plot_sample_reconstruction_error0.6850.0250.711
plot_signatures0.7050.0000.706
plot_umap4.6570.1024.768
predict_exposure1.0050.1481.153
rc0.0020.0000.003
result_list0.0030.0000.003
samp_annot0.0060.0010.006
sample_names0.0020.0010.003
select_genome000
signatures0.0170.0020.019
subset_musica_by_annotation0.0050.0000.006
subset_musica_by_counts0.0070.0030.010
subset_variant_by_type0.0060.0000.006
subset_variants_by_samples0.0060.0000.006
table_selected0.0020.0000.002
tables0.0020.0020.004
umap0.0010.0010.002
variants0.0050.0000.005