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This page was generated on 2022-01-17 11:06:07 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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? here 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 1249/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
musicatk 1.5.0  (landing page)
Aaron Chevalier
Snapshot Date: 2022-01-16 13:55:18 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/musicatk
git_branch: master
git_last_commit: ab8dbf0
git_last_commit_date: 2021-10-26 13:04:15 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
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  UNNEEDED, same version is already published

Summary

Package: musicatk
Version: 1.5.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:musicatk.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings musicatk_1.5.0.tar.gz
StartedAt: 2022-01-16 20:08:21 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 20:13:53 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 332.4 seconds
RetCode: 0
Status:   OK  
CheckDir: musicatk.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:musicatk.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings musicatk_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/musicatk.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (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 ‘1.5.0’
* 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 7.612  1.723   9.336
create_umap          5.388  0.628   6.015
plot_cluster         5.436  0.104   5.560
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/musicatk.Rcheck/00check.log’
for details.



Installation output

musicatk.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL musicatk
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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) (2022-01-05 r81451) -- "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: pkgmaker
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 1 | SKIP 0 | PASS 42 ]
> 
> proc.time()
   user  system elapsed 
 20.535   0.886  21.424 

Example timings

musicatk.Rcheck/musicatk-Ex.timings

nameusersystemelapsed
add_flank_to_variants2.9930.3163.309
add_variant_type0.0150.0000.016
annotate_replication_strand0.1130.0110.124
annotate_transcript_strand2.6100.0652.675
annotate_variant_length0.0090.0030.012
annotate_variant_type0.0030.0010.003
auto_predict_grid1.5990.0391.639
build_custom_table1.0110.0451.055
build_standard_table7.6121.7239.336
built_tables0.0030.0000.003
cluster_exposure0.0150.0150.031
combine_count_tables2.2460.4572.701
combine_predict_grid1.6620.0721.734
compare_cosmic_v21.9650.0231.989
compare_cosmic_v30.8530.0280.881
compare_results1.1650.1631.330
cosmic_v2_subtype_map0.0010.0010.001
create_musica0.7420.2961.008
create_umap5.3880.6286.015
discover_signatures0.6660.1410.806
drop_annotation0.0020.0000.002
exposure_differential_analysis0.0160.0030.021
exposures0.0050.0010.005
extract_count_tables0.0040.0000.005
extract_variants4.1020.0164.068
extract_variants_from_maf0.1350.0000.110
extract_variants_from_maf_file0.1130.0030.087
extract_variants_from_matrix0.1290.0010.103
extract_variants_from_vcf0.6530.0000.653
extract_variants_from_vcf_file0.4030.0000.403
generate_result_grid0.1490.0000.149
get_musica0.0080.0000.008
k_select0.7690.0080.777
musicatk000
name_signatures0.0030.0000.003
pipe0.0020.0000.003
plot_cluster5.4360.1045.560
plot_differential_analysis0.1420.0000.142
plot_exposures0.1520.0000.153
plot_heatmap0.6830.0040.687
plot_sample_counts0.2720.0000.272
plot_sample_reconstruction_error0.5270.0000.527
plot_signatures0.4350.0000.435
plot_umap4.6420.0414.700
predict_exposure0.9480.1841.135
rc0.0020.0000.003
samp_annot0.0060.0020.008
sample_names0.0010.0010.003
select_genome0.0000.0000.001
signatures0.0040.0020.007
subset_musica_by_annotation0.0010.0060.006
subset_musica_by_counts0.0070.0000.008
subset_variant_by_type0.0050.0000.005
subset_variants_by_samples0.0040.0000.005
table_selected0.0000.0020.002
tables0.0060.0010.008
umap0.0000.0030.003
variants0.0010.0080.008