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This page was generated on 2022-12-09 11:09:52 -0500 (Fri, 09 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4449
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-11-30 r83393 ucrt) -- "Unsuffered Consequences" 4194
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4237
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 merida1


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 1296/2155HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
musicatk 1.9.0  (landing page)
Aaron Chevalier
Snapshot Date: 2022-12-08 14:00:20 -0500 (Thu, 08 Dec 2022)
git_url: https://git.bioconductor.org/packages/musicatk
git_branch: master
git_last_commit: 69829e2
git_last_commit_date: 2022-11-01 11:23:15 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  NO, package depends on 'TCGAbiolinks' which is not available
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'SummarizedExperiment' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'VariantAnnotation' which is not available

Summary

Package: musicatk
Version: 1.9.0
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_1.9.0.tar.gz
StartedAt: 2022-12-09 04:01:00 -0500 (Fri, 09 Dec 2022)
EndedAt: 2022-12-09 04:16:06 -0500 (Fri, 09 Dec 2022)
EllapsedTime: 906.0 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_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/musicatk.Rcheck’
* using R Under development (unstable) (2022-11-30 r83393)
* 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 ‘1.9.0’
* 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  16.811  0.958  23.831
extract_variants       8.978  0.083  11.980
plot_cluster           6.340  0.164   9.128
create_umap            5.975  0.067   8.682
add_flank_to_variants  5.664  0.366   7.992
compare_cosmic_v2      5.806  0.025   7.666
plot_umap              5.176  0.054   7.738
combine_count_tables   4.963  0.243   6.939
combine_predict_grid   3.910  0.069   5.344
* 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-3.17-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/4.3/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) (2022-11-30 r83393) -- "Unsuffered Consequences"
Copyright (C) 2022 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 23/24
  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 
 38.510   1.516  53.907 

Example timings

musicatk.Rcheck/musicatk-Ex.timings

nameusersystemelapsed
add_flank_to_variants5.6640.3667.992
add_variant_type0.0280.0030.041
annotate_replication_strand0.2510.0140.339
annotate_transcript_strand2.2880.0493.085
annotate_variant_length0.0830.0050.113
annotate_variant_type0.0040.0020.012
auto_predict_grid3.5640.0764.918
build_custom_table1.9670.0252.746
build_standard_table16.811 0.95823.831
built_tables0.0040.0020.009
cluster_exposure0.0260.0050.039
combine_count_tables4.9630.2436.939
combine_predict_grid3.9100.0695.344
compare_cosmic_v25.8060.0257.666
compare_cosmic_v32.5450.0113.441
compare_results3.3060.0114.329
cosmic_v2_subtype_map0.0020.0010.003
create_musica1.6900.1732.499
create_umap5.9750.0678.682
discover_signatures1.4440.1012.086
drop_annotation0.0040.0020.006
exposure_differential_analysis0.0330.0030.046
exposures0.0070.0040.015
extract_count_tables0.0080.0020.015
extract_variants 8.978 0.08311.980
extract_variants_from_maf0.2290.0030.308
extract_variants_from_maf_file0.1970.0020.258
extract_variants_from_matrix0.2270.0060.312
extract_variants_from_vcf1.4420.0261.955
extract_variants_from_vcf_file0.9750.0061.283
generate_result_grid0.3040.0040.408
get_musica0.0120.0030.021
k_select2.0360.0392.692
musicatk000
name_signatures0.0050.0020.010
pipe0.0040.0010.004
plot_cluster6.3400.1649.128
plot_differential_analysis0.4150.0030.545
plot_exposures0.4360.0050.591
plot_heatmap1.7250.0162.303
plot_sample_counts0.8480.0071.117
plot_sample_reconstruction_error1.4080.0071.852
plot_signatures1.3530.0071.815
plot_umap5.1760.0547.738
predict_exposure2.3370.1253.232
rc0.0040.0000.005
samp_annot0.0120.0040.023
sample_names0.0050.0020.009
select_genome0.0010.0000.001
signatures0.0080.0060.018
subset_musica_by_annotation0.0080.0030.017
subset_musica_by_counts0.0140.0030.024
subset_variant_by_type0.0090.0020.014
subset_variants_by_samples0.0080.0030.011
table_selected0.0030.0020.010
tables0.0150.0050.025
umap0.0060.0040.013
variants0.0140.0050.025