##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:rawDiag.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings rawDiag_1.0.0.tar.gz
###
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##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/rawDiag.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘rawDiag/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rawDiag’ 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 ‘rawDiag’ 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 code 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘rawDiag-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: is.rawDiag
> ### Title: Is an Object an rawDiag Object?
> ### Aliases: is.rawDiag
> 
> ### ** Examples
> 
> rawrr::sampleFilePath() |> rawDiag::readRaw() |> rawDiag::is.rawDiag()
reading index for sample.raw...
'ThermoFisher.CommonCore.Data.dll' is missing.
'ThermoFisher.CommonCore.MassPrecisionEstimator.dll' is missing.
'ThermoFisher.CommonCore.RawFileReader.dll' is missing.
Error in .checkRawFileReaderDLLs(FUN) : 
  'ThermoFisher.CommonCore.*.dll' files are not available on the system.
Run 'rawrr::installRawFileReaderDLLs()' or setenv MONO_PATH to the location where the assemblies are located.
For more information, type '?ThermoFisher'.
Calls: <Anonymous> ... .isAssemblyWorking -> .checkRawFileReaderDLLs -> FUN
Execution halted
* 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:
   38.           ├─base::withCallingHandlers(...)
   39.           ├─base::withVisible(.func())
   40.           └─shiny (local) .func()
   41.             ├─shiny::..stacktraceon..(`<reactive>`(...))
   42.             └─rawDiag (local) `<reactive>`(...)
   43.               ├─base::Reduce(...)
   44.               ├─BiocParallel::bplapply(...)
   45.               └─BiocParallel::bplapply(...)
   46.                 ├─BiocParallel::bplapply(...)
   47.                 └─BiocParallel::bplapply(...)
   48.                   └─BiocParallel:::.bpinit(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘rawDiag.Rmd’ using rmarkdown
trying URL 'https://github.com/thermofisherlsms/RawFileReader/raw/main/Libs/Net471//ThermoFisher.CommonCore.BackgroundSubtraction.dll'
Content type 'application/octet-stream' length 44544 bytes (43 KB)
==================================================
downloaded 43 KB

trying URL 'https://github.com/thermofisherlsms/RawFileReader/raw/main/Libs/Net471//ThermoFisher.CommonCore.Data.dll'
Content type 'application/octet-stream' length 406016 bytes (396 KB)
==================================================
downloaded 396 KB

trying URL 'https://github.com/thermofisherlsms/RawFileReader/raw/main/Libs/Net471//ThermoFisher.CommonCore.MassPrecisionEstimator.dll'
Content type 'application/octet-stream' length 11264 bytes (11 KB)
==================================================
downloaded 11 KB

trying URL 'https://github.com/thermofisherlsms/RawFileReader/raw/main/Libs/Net471//ThermoFisher.CommonCore.RawFileReader.dll'
Content type 'application/octet-stream' length 654336 bytes (639 KB)
==================================================
downloaded 639 KB

trying URL 'https://github.com/fgcz/rawrr/releases/download/1.9.2/rawrr.1.9.2.exe'
Content type 'application/octet-stream' length 28672 bytes (28 KB)
==================================================
downloaded 28 KB


Quitting from lines 223-239 [fetchFromExperimentHub] (rawDiag.Rmd)
Error: processing vignette 'rawDiag.Rmd' failed with diagnostics:
package 'AnnotationHub' could not be loaded
--- failed re-building ‘rawDiag.Rmd’

SUMMARY: processing the following file failed:
  ‘rawDiag.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/rawDiag.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL rawDiag
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘rawDiag’ ...
** using staged installation
** R
** 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 (rawDiag)

R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

> #R                                                                                                                                                            
>                                                                                                                                                               
> library(testthat)                                                                                                                                             
>                                                                                                                                                               
> suppressPackageStartupMessages(library(rawDiag))                                                                                                                
>                                                                                                                                                               
> test_check("rawDiag")   
Cannot open assembly '/home/biocbuild/.cache/R/rawrr/rawrrassembly/rawrr.exe': File does not contain a valid CIL image.
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-rawDiag.R:7:1'): (code run outside of `test_that()`) ───────────
Error in `.isAssemblyWorking()`: 'rawrr.exe' not found.
Run 'rawrr::installRawrrExe()'. For more information, type '?rawrr.exe'.
Backtrace:
    ▆
 1. └─rawDiag::readRaw(rawrr::sampleFilePath()) at test-rawDiag.R:7:1
 2.   └─rawrr::readIndex(rawfile)
 3.     └─rawrr:::.isAssemblyWorking()
── Error ('test-rawDiagServerModule.R:10:3'): (code run outside of `test_that()`) ──
<bplist_error/bperror/error/condition>
Error: BiocParallel errors
  1 remote errors, element index: 1
  0 unevaluated and other errors
  first remote error:
Error in if (rvs != "No RAW file specified!") {: argument is of length zero

Backtrace:
     ▆
  1. ├─shiny::testServer(...) at test-rawDiagServerModule.R:5:1
  2. │ ├─shiny:::withMockContext(...)
  3. │ │ ├─shiny::isolate(...)
  4. │ │ │ ├─shiny::..stacktraceoff..(...)
  5. │ │ │ └─ctx$run(...)
  6. │ │ │   ├─promises::with_promise_domain(...)
  7. │ │ │   │ └─domain$wrapSync(expr)
  8. │ │ │   ├─shiny::withReactiveDomain(...)
  9. │ │ │   │ └─promises::with_promise_domain(...)
 10. │ │ │   │   └─domain$wrapSync(expr)
 11. │ │ │   │     └─base::force(expr)
 12. │ │ │   └─env$runWith(self, func)
 13. │ │ │     └─shiny (local) contextFunc()
 14. │ │ │       └─shiny::..stacktraceon..(expr)
 15. │ │ ├─shiny::withReactiveDomain(...)
 16. │ │ │ └─promises::with_promise_domain(...)
 17. │ │ │   └─domain$wrapSync(expr)
 18. │ │ │     └─base::force(expr)
 19. │ │ └─withr::with_options(...)
 20. │ │   └─base::force(code)
 21. │ └─rlang::eval_tidy(quosure, mask, rlang::caller_env())
 22. ├─testthat::expect_true(is.data.frame(data())) at test-rawDiagServerModule.R:10:3
 23. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 24. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 25. ├─base::is.data.frame(data())
 26. └─shiny (local) data()
 27.   ├─shiny::..stacktraceoff..(self$.updateValue())
 28.   └─self$.updateValue()
 29.     └─ctx$run(...)
 30.       ├─promises::with_promise_domain(...)
 31.       │ └─domain$wrapSync(expr)
 32.       ├─shiny::withReactiveDomain(...)
 33.       │ └─promises::with_promise_domain(...)
 34.       │   └─domain$wrapSync(expr)
 35.       │     └─base::force(expr)
 36.       └─env$runWith(self, func)
 37.         └─shiny (local) contextFunc()
 38.           ├─base::withCallingHandlers(...)
 39.           ├─base::withVisible(.func())
 40.           └─shiny (local) .func()
 41.             ├─shiny::..stacktraceon..(`<reactive>`(...))
 42.             └─rawDiag (local) `<reactive>`(...)
 43.               ├─base::Reduce(...)
 44.               ├─BiocParallel::bplapply(...)
 45.               └─BiocParallel::bplapply(...)
 46.                 ├─BiocParallel::bplapply(...)
 47.                 └─BiocParallel::bplapply(...)
 48.                   └─BiocParallel:::.bpinit(...)

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ]
Error: Test failures
Execution halted