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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:rawDiag.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings rawDiag_1.1.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/rawDiag.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘1.1.4’
* 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: readRaw
> ### Title: Reads selected raw file trailer information for rawDiag plot
> ###   functions
> ### Aliases: readRaw rawDiag
> 
> ### ** Examples
> 
> rawrr::sampleFilePath() |>
+   rawDiag::readRaw()
reading index for sample.raw...
determining ElapsedScanTimesec ...
reading trailer LM m/z-Correction (ppm) ...
reading trailer AGC ...
reading trailer AGC PS Mode ...
reading trailer FT Resolution ...
reading trailer Ion Injection Time (ms) ...
reading TIC ...
reading BasePeakIntensity ...
'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:
  
  MD5 96e3a4cc1b7caaf92890d85ed4c72f77 /home/biocbuild/.cache/R/rawrr/rawrrassembly/rawrr.exe
  
  =================================================================
  	External Debugger Dump:
  =================================================================
  mono_gdb_render_native_backtraces not supported on this platform, unable to find gdb or lldb
  Aborted (core dumped)
  Error in if (rvs != "No RAW file specified!") { : 
    the condition has length > 1
  Calls: <Anonymous> -> isFALSE -> <Anonymous>
  In addition: Warning message:
  In system2(Sys.which("mono"), args = c(shQuote(exe)), stdout = TRUE) :
    running command ''/usr/bin/mono' '/home/biocbuild/.cache/R/rawrr/rawrrassembly/rawrr.exe'' had status 134
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/rawDiag.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL rawDiag
###
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* installing to library ‘/home/biocbuild/bbs-3.20-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 4.4.1 (2024-06-14) -- "Race for Your Life"
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))                                                                                                                
> 
> rawDiag::checkRawrr()
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

MD5 96e3a4cc1b7caaf92890d85ed4c72f77 /home/biocbuild/.cache/R/rawrr/rawrrassembly/rawrr.exe

=================================================================
	External Debugger Dump:
=================================================================
mono_gdb_render_native_backtraces not supported on this platform, unable to find gdb or lldb
Aborted (core dumped)
Error in if (rvs != "No RAW file specified!") { : 
  the condition has length > 1
Calls: <Anonymous> -> isFALSE -> <Anonymous>
In addition: Warning message:
In system2(Sys.which("mono"), args = c(shQuote(exe)), stdout = TRUE) :
  running command ''/usr/bin/mono' '/home/biocbuild/.cache/R/rawrr/rawrrassembly/rawrr.exe'' had status 134
Execution halted