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This page was generated on 2022-01-17 11:11:36 -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 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? 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: /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_1.5.0.tar.gz
StartedAt: 2022-01-17 03:19:56 -0500 (Mon, 17 Jan 2022)
EndedAt: 2022-01-17 03:29:31 -0500 (Mon, 17 Jan 2022)
EllapsedTime: 575.5 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/musicatk.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘1.5.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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  13.856  0.922  14.796
extract_variants       8.405  0.102   9.072
plot_cluster           6.004  0.151   6.448
create_umap            6.033  0.081   6.353
add_flank_to_variants  4.741  0.291   5.045
compare_cosmic_v2      4.992  0.017   5.175
plot_umap              4.815  0.052   5.025
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-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 Under development (unstable) (2022-01-05 r81451) -- "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: pkgmaker
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 1 | SKIP 0 | PASS 42 ]
> 
> proc.time()
   user  system elapsed 
 31.918   1.306  33.231 

Example timings

musicatk.Rcheck/musicatk-Ex.timings

nameusersystemelapsed
add_flank_to_variants4.7410.2915.045
add_variant_type0.0230.0030.026
annotate_replication_strand0.2250.0140.239
annotate_transcript_strand3.2000.0493.253
annotate_variant_length0.0190.0020.021
annotate_variant_type0.0040.0020.006
auto_predict_grid3.3430.0823.429
build_custom_table1.6960.0201.717
build_standard_table13.856 0.92214.796
built_tables0.0030.0020.005
cluster_exposure0.0240.0040.030
combine_count_tables4.3680.2284.602
combine_predict_grid3.4560.0473.515
compare_cosmic_v24.9920.0175.175
compare_cosmic_v32.1590.0082.228
compare_results2.8540.0132.953
cosmic_v2_subtype_map0.0020.0000.002
create_musica1.4410.1681.725
create_umap6.0330.0816.353
discover_signatures1.3180.1081.463
drop_annotation0.0040.0020.006
exposure_differential_analysis0.0350.0040.041
exposures0.0060.0040.011
extract_count_tables0.0070.0020.009
extract_variants8.4050.1029.072
extract_variants_from_maf0.2300.0030.258
extract_variants_from_maf_file0.1950.0030.215
extract_variants_from_matrix0.2250.0030.249
extract_variants_from_vcf1.3230.0231.424
extract_variants_from_vcf_file0.9460.0061.012
generate_result_grid0.3070.0030.346
get_musica0.0120.0030.017
k_select1.7230.0261.947
musicatk000
name_signatures0.0050.0020.006
pipe0.0040.0010.006
plot_cluster6.0040.1516.448
plot_differential_analysis0.3250.0030.333
plot_exposures0.3550.0050.367
plot_heatmap1.6130.0241.653
plot_sample_counts0.6850.0050.694
plot_sample_reconstruction_error1.2050.0061.218
plot_signatures1.1380.0061.200
plot_umap4.8150.0525.025
predict_exposure3.1950.1043.305
rc0.0030.0000.004
samp_annot0.0120.0050.016
sample_names0.0060.0030.008
select_genome0.0000.0000.001
signatures0.0070.0050.012
subset_musica_by_annotation0.0080.0030.010
subset_musica_by_counts0.0110.0020.014
subset_variant_by_type0.0080.0020.010
subset_variants_by_samples0.0060.0020.009
table_selected0.0040.0020.005
tables0.0130.0050.018
umap0.0060.0030.009
variants0.0120.0040.017