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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 ‘/media/volume/teran2_disk/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 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 ... OK
* 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:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-rawDiag.R:7:1'): (code run outside of `test_that()`) ───────────
  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'.
  Backtrace:
      ▆
   1. └─rawDiag::readRaw(rawrr::sampleFilePath()) at test-rawDiag.R:7:1
   2.   └─rawrr::readIndex(rawfile)
   3.     └─rawrr:::.isAssemblyWorking()
   4.       └─rawrr:::.checkRawFileReaderDLLs(FUN)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 9 ]
  Error: Test failures
  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: 1 ERROR
See
  ‘/media/volume/teran2_disk/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 ‘/media/volume/teran2_disk/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()
[1] TRUE
> 
> if (isFALSE(rawrr::.checkDllInMonoPath())){
+   rawrr::installRawFileReaderDLLs()
+ }
removing DLL files in directory '/home/biocbuild/.cache/R/rawrr/rawrrassembly'
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

 ThermoFisher.CommonCore.BackgroundSubtraction.dll 
                                                 0 
                  ThermoFisher.CommonCore.Data.dll 
                                                 0 
ThermoFisher.CommonCore.MassPrecisionEstimator.dll 
                                                 0 
         ThermoFisher.CommonCore.RawFileReader.dll 
                                                 0 
> rawrr::installRawrrExe()
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
[1] 0
>                                                                                                                                                               
> test_check("rawDiag")   
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 9 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-rawDiag.R:7:1'): (code run outside of `test_that()`) ───────────
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'.
Backtrace:
    ▆
 1. └─rawDiag::readRaw(rawrr::sampleFilePath()) at test-rawDiag.R:7:1
 2.   └─rawrr::readIndex(rawfile)
 3.     └─rawrr:::.isAssemblyWorking()
 4.       └─rawrr:::.checkRawFileReaderDLLs(FUN)

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 9 ]
Error: Test failures
Execution halted