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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:dasper.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings dasper_1.4.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/dasper.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'dasper/DESCRIPTION' ... OK
* this is package 'dasper' version '1.4.3'
* 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:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'dasper' can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/dasper.Rcheck/00install.out' for details.
* 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
Unexported object imported by a ':::' call: 'grid:::calcControlPoints'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.classify_junc: no visible binding for global variable 'lend'
.classify_junc: no visible binding for global variable 'rstart'
.coverage_to_plot_get: no visible binding for global variable '.'
.coverage_to_plot_get: no visible binding for global variable
  'case_control'
.get_ref_exons_annot: no visible binding for global variable '.'
.plot_coverage: no visible binding for global variable 'case_control'
.plot_junctions: no visible binding for global variable 'size'
annotate_junc_ref: no visible global function definition for
  'ensemblGenome'
annotate_junc_ref: no visible global function definition for
  'basedir<-'
annotate_junc_ref: no visible global function definition for 'read.gtf'
annotate_junc_ref: no visible global function definition for
  'getSpliceTable'
Undefined global functions or variables:
  . basedir<- case_control ensemblGenome getSpliceTable lend read.gtf
  rstart size
* 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 line endings in shell scripts ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
coverage_process 130.56  22.92  285.81
junction_process  66.42   1.71   69.12
plot_sashimi      40.60   1.28   43.71
ref_load          16.41   0.40   17.49
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    2.   \-testthat::test_dir(...)
    3.     \-testthat:::test_files(...)
    4.       \-testthat:::test_files(...)
    5.         +-testthat::with_reporter(...)
    6.         | \-base::tryCatch(...)
    7.         |   \-base tryCatchList(expr, classes, parentenv, handlers)
    8.         |     \-base tryCatchOne(expr, names, parentenv, handlers[[1L]])
    9.         |       \-base doTryCatch(return(expr), name, parentenv, handler)
   10.         \-testthat:::parallel_event_loop_chunky(queue, reporters)
   11.           \-queue$poll(Inf)
   12.             \-base::lapply(...)
   13.               \-testthat FUN(X[[i]], ...)
   14.                 \-private$handle_error(msg, i)
   15.                   \-rlang::abort(...)
  Execution halted
* 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 ERROR, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/dasper.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch dasper
###
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* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
* installing *source* package 'dasper' ...
** using non-staged installation via StagedInstall field
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'dasper'
    finding HTML links ... done
    coverage_process                        html  
    dasper                                  html  
    deprecated                              html  
    junction_load                           html  
    junction_process                        html  
    junctions_example                       html  
    finding level-2 HTML links ... done

    outlier_process                         html  
    plot_sashimi                            html  
    ref_load                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (dasper)
Making 'packages.html' ... done

R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(dasper)
> 
> test_check("dasper")
Starting 2 test processes


Error:
! testthat subprocess failed to start, stderr:
Error in data$sofile[[paste0("arch-", .Platform$r_arch)]] : 

  subscript out of bounds

Calls: callr_startup_hook -> <Anonymous>

Caused by error:
! R session crashed with exit code 1
Backtrace:
     x
  1. \-testthat::test_check("dasper")
  2.   \-testthat::test_dir(...)
  3.     \-testthat:::test_files(...)
  4.       \-testthat:::test_files(...)
  5.         +-testthat::with_reporter(...)
  6.         | \-base::tryCatch(...)
  7.         |   \-base tryCatchList(expr, classes, parentenv, handlers)
  8.         |     \-base tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9.         |       \-base doTryCatch(return(expr), name, parentenv, handler)
 10.         \-testthat:::parallel_event_loop_chunky(queue, reporters)
 11.           \-queue$poll(Inf)
 12.             \-base::lapply(...)
 13.               \-testthat FUN(X[[i]], ...)
 14.                 \-private$handle_error(msg, i)
 15.                   \-rlang::abort(...)
Execution halted