Back to Multiple platform build/check report for BioC 3.17
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2022-12-09 11:06:11 -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 nebbiolo1


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: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:musicatk.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings musicatk_1.9.0.tar.gz
StartedAt: 2022-12-08 21:53:58 -0500 (Thu, 08 Dec 2022)
EndedAt: 2022-12-08 22:01:29 -0500 (Thu, 08 Dec 2022)
EllapsedTime: 451.7 seconds
RetCode: 0
Status:   OK  
CheckDir: musicatk.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:musicatk.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings musicatk_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/musicatk.Rcheck’
* using R Under development (unstable) (2022-11-30 r83393)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 7.187  1.164   8.351
plot_cluster         6.225  0.372   6.596
create_umap          5.841  0.584   6.425
plot_umap            5.666  0.256   5.921
* 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 ...
  ‘musicatk.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/musicatk.Rcheck/00check.log’
for details.



Installation output

musicatk.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL musicatk
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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-pc-linux-gnu (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 71/72
  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 
 22.028   1.182  23.237 

Example timings

musicatk.Rcheck/musicatk-Ex.timings

nameusersystemelapsed
add_flank_to_variants3.3480.3273.675
add_variant_type0.0110.0040.016
annotate_replication_strand0.1220.0030.126
annotate_transcript_strand1.2030.0471.252
annotate_variant_length0.0080.0040.012
annotate_variant_type0.0000.0020.003
auto_predict_grid1.5840.0171.601
build_custom_table2.0730.0952.168
build_standard_table7.1871.1648.351
built_tables0.0020.0010.002
cluster_exposure0.0140.0030.018
combine_count_tables2.3810.3172.697
combine_predict_grid1.8130.0071.820
compare_cosmic_v22.4470.0402.487
compare_cosmic_v31.0810.0001.081
compare_results1.4220.0001.422
cosmic_v2_subtype_map0.0010.0000.001
create_musica0.8320.2961.104
create_umap5.8410.5846.425
discover_signatures0.7120.1720.884
drop_annotation0.0010.0010.002
exposure_differential_analysis0.0160.0060.022
exposures0.0040.0000.005
extract_count_tables0.0050.0000.005
extract_variants4.3230.3164.579
extract_variants_from_maf0.1370.0000.104
extract_variants_from_maf_file0.1280.0000.092
extract_variants_from_matrix0.1320.0040.112
extract_variants_from_vcf0.7280.0520.779
extract_variants_from_vcf_file0.4850.0250.508
generate_result_grid0.1620.0030.166
get_musica0.0080.0010.008
k_select0.9540.0430.997
musicatk0.0010.0000.000
name_signatures0.0030.0000.003
pipe0.0030.0000.003
plot_cluster6.2250.3726.596
plot_differential_analysis0.1950.0120.207
plot_exposures0.1970.0200.217
plot_heatmap0.7130.0520.765
plot_sample_counts0.3670.0000.367
plot_sample_reconstruction_error0.5830.0160.599
plot_signatures0.5500.0240.574
plot_umap5.6660.2565.921
predict_exposure1.0770.2151.293
rc0.0000.0030.003
samp_annot0.0080.0000.009
sample_names0.0030.0000.004
select_genome000
signatures0.0060.0000.007
subset_musica_by_annotation0.0050.0010.006
subset_musica_by_counts0.0060.0030.008
subset_variant_by_type0.0060.0010.005
subset_variants_by_samples0.0010.0030.005
table_selected0.0020.0010.002
tables0.0000.0080.008
umap0.0010.0020.003
variants0.0090.0000.008