Back to Multiple platform build/check report for BioC 3.16:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2023-04-12 11:06:17 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for musicatk on lconway


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? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1312/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
musicatk 1.8.0  (landing page)
Aaron Chevalier
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/musicatk
git_branch: RELEASE_3_16
git_last_commit: a7a8454
git_last_commit_date: 2022-11-01 11:23:15 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: musicatk
Version: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2023-04-10 21:28:16 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 21:33:54 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 338.1 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/musicatk.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘musicatk/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘musicatk’ version ‘1.8.0’
* 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 ... 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 6.938  0.733   7.716
* 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
  ‘/Users/biocbuild/bbs-3.16-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/4.2/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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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: 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 
 19.582   0.925  20.554 

Example timings

musicatk.Rcheck/musicatk-Ex.timings

nameusersystemelapsed
add_flank_to_variants2.6610.2002.877
add_variant_type0.0160.0040.020
annotate_replication_strand0.2200.0130.235
annotate_transcript_strand2.0280.0442.081
annotate_variant_length0.0120.0030.014
annotate_variant_type0.0030.0010.004
auto_predict_grid1.5520.0701.630
build_custom_table1.9480.0271.988
build_standard_table6.9380.7337.716
built_tables0.0020.0020.004
cluster_exposure0.0170.0040.023
combine_count_tables2.3970.2132.629
combine_predict_grid1.7520.0511.806
compare_cosmic_v22.0680.0162.090
compare_cosmic_v30.8720.0070.881
compare_results2.1760.0182.199
cosmic_v2_subtype_map0.0010.0000.002
create_musica0.7740.1370.918
create_umap4.4600.0604.526
discover_signatures0.6820.1050.804
drop_annotation0.0020.0020.004
exposure_differential_analysis0.0140.0020.016
exposures0.0020.0020.005
extract_count_tables0.0030.0010.004
extract_variants3.8700.0453.922
extract_variants_from_maf0.0830.0030.086
extract_variants_from_maf_file0.0770.0000.078
extract_variants_from_matrix0.0970.0030.100
extract_variants_from_vcf0.6850.0180.705
extract_variants_from_vcf_file0.4550.0040.461
generate_result_grid0.1640.0030.167
get_musica0.0060.0020.008
k_select0.7690.0230.795
musicatk000
name_signatures0.0030.0010.003
pipe0.0020.0000.003
plot_cluster4.5410.1504.716
plot_differential_analysis0.1480.0020.150
plot_exposures0.1910.0080.199
plot_heatmap0.5870.0150.603
plot_sample_counts0.3400.0050.344
plot_sample_reconstruction_error0.4600.0040.464
plot_signatures0.5680.0050.575
plot_umap4.2390.0424.290
predict_exposure1.0400.1041.150
rc0.0020.0000.002
samp_annot0.0060.0020.009
sample_names0.0020.0010.003
select_genome000
signatures0.0040.0030.006
subset_musica_by_annotation0.0050.0020.007
subset_musica_by_counts0.0060.0020.008
subset_variant_by_type0.0040.0020.006
subset_variants_by_samples0.0190.0090.028
table_selected0.0010.0010.003
tables0.0060.0020.008
umap0.0030.0020.005
variants0.0050.0030.008