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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_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/rawDiag.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘rawDiag/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rawDiag’ version ‘1.2.0’
* 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 whether startup messages can be suppressed ... 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: plotPrecursorHeatmap
> ### Title: Precursor Mass versus StartTime MS2 based hexagons
> ### Aliases: plotPrecursorHeatmap PlotPrecursorHeatmap
> 
> ### ** Examples
> 
> rawrr::sampleFilePath() |> rawDiag::readRaw() |> rawDiag::plotPrecursorHeatmap()
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 ...
'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:
  > 
  > rawDiag::checkRawrr()
  
  Unhandled Exception:
  System.IO.FileNotFoundException: Could not load file or assembly 'ThermoFisher.CommonCore.RawFileReader, Version=5.0.0.93, Culture=neutral, PublicKeyToken=1aef06afb5abd953' or one of its dependencies.
  File name: 'ThermoFisher.CommonCore.RawFileReader, Version=5.0.0.93, Culture=neutral, PublicKeyToken=1aef06afb5abd953'
  [ERROR] FATAL UNHANDLED EXCEPTION: System.IO.FileNotFoundException: Could not load file or assembly 'ThermoFisher.CommonCore.RawFileReader, Version=5.0.0.93, Culture=neutral, PublicKeyToken=1aef06afb5abd953' or one of its dependencies.
  File name: 'ThermoFisher.CommonCore.RawFileReader, Version=5.0.0.93, Culture=neutral, PublicKeyToken=1aef06afb5abd953'
  Error in if (rvs != "No RAW file specified!") { : 
    argument is of length zero
  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 1
  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 4.4.2 (2024-10-31) -- "Pile of Leaves"
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()

Unhandled Exception:
System.IO.FileNotFoundException: Could not load file or assembly 'ThermoFisher.CommonCore.RawFileReader, Version=5.0.0.93, Culture=neutral, PublicKeyToken=1aef06afb5abd953' or one of its dependencies.
File name: 'ThermoFisher.CommonCore.RawFileReader, Version=5.0.0.93, Culture=neutral, PublicKeyToken=1aef06afb5abd953'
[ERROR] FATAL UNHANDLED EXCEPTION: System.IO.FileNotFoundException: Could not load file or assembly 'ThermoFisher.CommonCore.RawFileReader, Version=5.0.0.93, Culture=neutral, PublicKeyToken=1aef06afb5abd953' or one of its dependencies.
File name: 'ThermoFisher.CommonCore.RawFileReader, Version=5.0.0.93, Culture=neutral, PublicKeyToken=1aef06afb5abd953'
Error in if (rvs != "No RAW file specified!") { : 
  argument is of length zero
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 1
Execution halted