##############################################################################
##############################################################################
###
### 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) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* 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 ... ERROR
Running examples in ‘musicatk-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: extract_variants
> ### Title: Extract variants from mutliple objects
> ### Aliases: extract_variants
> 
> ### ** Examples
> 
> # Get loations of two vcf files and a maf file
> luad_vcf_file <- system.file("extdata", "public_LUAD_TCGA-97-7938.vcf",
+ package = "musicatk")
> lusc_maf_file <- system.file("extdata", "public_TCGA.LUSC.maf",
+ package = "musicatk")
> melanoma_vcfs <- list.files(system.file("extdata", package = "musicatk"),
+   pattern = glob2rx("*SKCM*vcf"), full.names = TRUE)
> 
> # Read all files in at once
> inputs <- c(luad_vcf_file, melanoma_vcfs, lusc_maf_file)
> variants <- extract_variants(inputs = inputs)

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |==============                                                        |  20%Extracted 1 out of 5 inputs: /home/biocbuild/bbs-3.17-bioc/R/library/musicatk/extdata/public_LUAD_TCGA-97-7938.vcf

  |                                                                            
  |============================                                          |  40%Extracted 2 out of 5 inputs: /home/biocbuild/bbs-3.17-bioc/R/library/musicatk/extdata/public_SKCM_TCGA-EE-A3J5-06A-11D-A20D-08.vcf

  |                                                                            
  |==========================================                            |  60%Extracted 3 out of 5 inputs: /home/biocbuild/bbs-3.17-bioc/R/library/musicatk/extdata/public_SKCM_TCGA-ER-A197-06A-32D-A197-08.vcf

  |                                                                            
  |========================================================              |  80%Extracted 4 out of 5 inputs: /home/biocbuild/bbs-3.17-bioc/R/library/musicatk/extdata/public_SKCM_TCGA-ER-A19O-06A-11D-A197-08.vcf

  |                                                                            
  |======================================================================| 100%Extracted 5 out of 5 inputs: /home/biocbuild/bbs-3.17-bioc/R/library/musicatk/extdata/public_TCGA.LUSC.maf
> table(variants$sample)

TCGA-97-7938-01A-11D-2167-08 TCGA-EE-A3J5-06A-11D-A20D-08 
                         121                          123 
TCGA-ER-A197-06A-32D-A197-08 TCGA-ER-A19O-06A-11D-A197-08 
                          13                           52 
TCGA-56-7582-01A-11D-2042-08 TCGA-77-7335-01A-11D-2042-08 
                         199                          283 
TCGA-94-7557-01A-11D-2122-08 
                         120 
> 
> # Run again but renaming samples in first four vcfs
> new_name <- c(paste0("Sample", 1:4), NA)
> variants <- extract_variants(inputs = inputs, rename = new_name)

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |==============                                                        |  20%Extracted 1 out of 5 inputs: /home/biocbuild/bbs-3.17-bioc/R/library/musicatk/extdata/public_LUAD_TCGA-97-7938.vcf
Killed
* 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 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/musicatk.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### 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)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 7/8
  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 
 25.793   0.767  27.456