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CHECK report for musicatk on merida1

This page was generated on 2021-05-06 12:35:54 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the musicatk package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1188/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
musicatk 1.0.0  (landing page)
Aaron Chevalier
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/musicatk
Branch: RELEASE_3_12
Last Commit: 22a0020
Last Changed Date: 2020-10-27 12:03:18 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: musicatk
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:musicatk.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings musicatk_1.0.0.tar.gz
StartedAt: 2021-05-06 04:05:24 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:13:02 -0400 (Thu, 06 May 2021)
EllapsedTime: 457.7 seconds
RetCode: 0
Status:   OK  
CheckDir: musicatk.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:musicatk.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings musicatk_1.0.0.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/musicatk.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.0.0’
* 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 ... OK
* 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 data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
build_standard_table 17.142  1.086  18.252
extract_variants      5.265  0.072   5.349
* 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: OK


Installation output

musicatk.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL musicatk
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘musicatk’ ...
** using staged installation
** R
** data
** 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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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 0 | SKIP 0 | PASS 7 ]
> 
> proc.time()
   user  system elapsed 
 19.064   0.845  21.209 

Example timings

musicatk.Rcheck/musicatk-Ex.timings

nameusersystemelapsed
add_flank_to_variants4.2070.1904.402
add_variant_type0.0360.0080.044
annotate_replication_strand0.8770.0341.007
annotate_transcript_strand1.8880.0662.001
annotate_variant_length0.0230.0070.030
annotate_variant_type0.0090.0040.013
auto_predict_grid2.7720.0912.866
build_custom_table2.3810.0222.406
build_standard_table17.142 1.08618.252
combine_count_tables3.8520.2204.076
combine_predict_grid2.7940.0512.848
compare_cosmic_v23.2110.0393.253
compare_cosmic_v31.3670.0091.376
compare_results1.8950.0111.909
cosmic_v2_subtype_map0.0010.0010.002
create_musica1.0640.1291.277
create_umap4.5270.0714.595
discover_signatures1.0090.0831.095
drop_annotation0.0100.0050.015
exposures0.0160.0090.024
extract_count_tables0.0100.0030.013
extract_variants5.2650.0725.349
extract_variants_from_maf0.1470.0030.151
extract_variants_from_maf_file0.1190.0010.119
extract_variants_from_matrix0.1320.0050.138
extract_variants_from_vcf0.7220.0170.741
extract_variants_from_vcf_file0.5470.0060.554
generate_result_grid0.2280.0050.234
musica0.0180.0050.023
name_signatures0.0110.0040.015
pipe0.0050.0010.006
plot_exposures0.2270.0050.232
plot_sample_counts0.4200.0060.426
plot_sample_reconstruction_error0.7990.0060.805
plot_signatures0.7920.0050.799
plot_umap3.6040.0643.663
predict_exposure1.4770.1171.598
rc0.0020.0010.003
samp_annot0.0200.0070.028
sample_names0.0080.0030.011
select_genome000
signatures0.0170.0090.026
subset_musica_by_annotation0.0110.0040.014
subset_musica_by_counts0.0110.0050.016
subset_variant_by_type0.0160.0060.021
subset_variants_by_samples0.0120.0030.015
table_name0.0070.0030.010
tables0.0190.0060.026
umap0.0140.0050.019
variants0.0210.0080.030