Merge pull request #81 from cpanse/master

#75 replace mono by dotnet

Author: cpanse

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rawrr
 Type: Package
 Title: Direct Access to Orbitrap Data and Beyond
-Version: 1.15.1
+Version: 1.15.3
 Authors@R: c(person("Christian", "Panse",
         email = "[email protected]",
         role = c("aut", "cre"),
@@ -25,20 +25,20 @@ Suggests:
     rmarkdown,
     tartare (>= 1.5),
     testthat
-Description: This package wraps the functionality
-    of the RawFileReader .NET assembly. Within the R environment,
+Description: This package wraps the functionality of the 
+    Thermo Fisher Scientic RawFileReader .NET 8.0 assembly.
+    Within the R environment,
     spectra and chromatograms are represented by S3 objects.
     The package provides basic functions to download and install
     the required third-party libraries.
     The package is developed, tested, and used at the Functional
     Genomics Center Zurich, Switzerland.
 License: GPL-3
-SystemRequirements: mono-runtime 4.x or higher (including System.Data library)
-    on Linux/macOS, .Net Framework (>= 4.5.1) on Microsoft Windows.
+SystemRequirements: .NET 8.0 
 URL: https://github.com/fgcz/rawrr/
 BugReports: https://github.com/fgcz/rawrr/issues
 Encoding: UTF-8
 NeedsCompilation: no
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 biocViews: MassSpectrometry, Proteomics, Metabolomics, Infrastructure, Software
 VignetteBuilder: knitr

INSTALL

@@ -1,83 +1,73 @@
 # System requirements
 
-## Linux (debian:10/ubuntu:20.04)
+The `rawrr` executable will run out of the box. 
 
-In case you prefer to compile `rawrr.exe` from C# source code, please install
-the mono compiler and xbuild by installing the following Linux packages:
+I you want to build on your own follow the text below.
 
-```{sh}
-sudo apt-get install mono-mcs mono-xbuild
-```
+## Compile and Link yourself
 
-Otherwise, to execute the precompiled code, the following Linux packages are
-sufficient:
+In case you prefer to compile `rawrr.exe` from C# source code, please install
+the .NET 8.0
 
-```{sh}
-sudo apt-get install mono-runtime libmono-system-data4.0-cil -y
-```
+### Linux (debian:10/ubuntu:20.04) (debian:12/ubuntu:24)
 
-## macOS (Catalina/BigSur)
 
+```{sh}
+## DEPRECIATED: sudo apt-get install mono-mcs mono-xbuild
+sudo apt-get install dotnet-sdk-8.0
 ```
-brew install mono
-```
-
-or install from
 
-https://www.mono-project.com/
+### macOS (Catalina/BigSur/.../Sequoia)
 
-## Microsoft Windows
+https://dotnet.microsoft.com/en-us/download
 
-Running the `rawrr.exe` will run out of the box.
+### Microsoft Windows
 
-If the native C# compiler is not available install mono from:
+https://dotnet.microsoft.com/en-us/download
 
-https://www.mono-project.com/
+## Install the .NET assemblies 
 
+assemblies aka Common Intermediate Language bytecode
 
-# Install the .NET assemblies 
+In general, ThermoFisher.CommonCore dlls can be obtained through:
 
-assemblies aka Common Intermediate Language bytecode
+https://github.com/thermofisherlsms/RawFileReader
 
-the following files are required in 
-`r tools::R_user_dir("rawrr", which='cache')`
-or in the `MONO_PATH`
+or 
 
-```
-ThermoFisher.CommonCore.Data.dll
-ThermoFisher.CommonCore.MassPrecisionEstimator.dll
-ThermoFisher.CommonCore.RawFileReader.dll
-```
+by contacting Jim Shofstahl using
 
-The download and install can be done on all platforms using the command:
-`r rawrr::installRawFileReaderDLLs()`
+[email protected]
 
-The in the package included C# source code that can compile into a rawrr.exe
-file by calling `r rawrr:::buildRawrrExe()`. (is executed when the package
-is loaded)
 
-if no C# compile and build tool is available, run
+## build
 
-`r rawrr::installRawrrExe()` to download the rawrr.exe assembly.
+* source nuget pkgs
 
-On Windows, the decimal symbol has to be configured as a '.'!
+* add libraries
 
-In general, ThermoFisher.CommonCore dlls can be obtained through:
+* (cross)-dcompile and link
 
-https://github.com/thermofisherlsms/RawFileReader
+```
+dotnet publish rawrr-dotnet.csproj --os osx -a x64 --output /Users/cp/Library/Caches/org.R-project.R/R/rawrr/rawrrassembly/osx-x64
+dotnet publish rawrr-dotnet.csproj --os win -a x64 --output /Users/cp/Library/Caches/org.R-project.R/R/rawrr/rawrrassembly/win-x64
+dotnet publish rawrr-dotnet.csproj --os linux -a x64 --output /Users/cp/Library/Caches/org.R-project.R/R/rawrr/rawrrassembly/linux-x64
 
-or 
 
-by contacting Jim Shofstahl using
+## generates a ~110MB BLOB
+dotnet publish -c Release -r linux-x64 -p PublishReadyToRun=true
+dotnet publish -c Release -r win-x64 -p PublishReadyToRun=true
+```
 
-[email protected]
 
+## Docker
 
 The `Dockerfile` performing `R CMD build` and `R CMD check` requires
 
 ```
 from bioconductor/bioconductor_docker:devel
 run apt-get update && apt-get install mono-mcs mono-xbuild -y
-run apt-get install texlive-base texlive-latex-extra texinfo texlive-fonts-extra -y
+run apt-get install dotnet-sdk-8.0
 run R -q -e "BiocManager::install(c('BiocStyle', 'ExperimentHub', 'knitr', 'protViz', 'rmarkdown', 'tartare', 'testthat'))"
 ```
+

NAMESPACE

@@ -6,13 +6,10 @@ S3method(plot,rawrrSpectrum)
 S3method(print,rawrrSpectrum)
 S3method(summary,rawrrChromatogram)
 S3method(summary,rawrrSpectrum)
-export(.checkDllInMonoPath)
-export(.thermofisherlsmsUrl)
 export(basePeak)
 export(buildRawrrExe)
 export(dependentScan)
 export(faimsVoltageOn)
-export(installRawFileReaderDLLs)
 export(installRawrrExe)
 export(is.rawrrChromatogram)
 export(is.rawrrSpectrum)
@@ -39,8 +36,10 @@ importFrom(graphics,text)
 importFrom(stats,lm)
 importFrom(stats,na.omit)
 importFrom(stats,predict)
+importFrom(tools,R_user_dir)
 importFrom(utils,download.file)
 importFrom(utils,head)
+importFrom(utils,object.size)
 importFrom(utils,packageVersion)
 importFrom(utils,read.csv2)
 importFrom(utils,read.table)

R/benchmark.R

@@ -0,0 +1,22 @@
+#R
+
+#' @importFrom utils object.size
+# f <- "/Users/cp/Library/Caches/org.R-project.R/R/ExperimentHub/46314c3933e2_4590.raw"
+.benchmark <- function(f){
+   stopifnot(file.exists(f))
+
+   rawrr::readFileHeader(f)$`Number of scans` -> n 
+
+   2**(seq(0, floor(log(n, 2)))) |>
+            lapply(FUN = function(i){
+                sample(n, size = i) |> sort() -> idx
+                message("Reading ", i, "random scans from ", f)
+		start.time <- Sys.time()
+		rawrr::readSpectrum(f, scan = idx) -> S
+		end.time <- Sys.time()
+                message("in ", end.time - start.time)
+		data.frame(count = i,
+                    size = object.size(S) |> as.integer(),
+                    runTimeInSec = as.double(difftime(end.time, start.time, units='secs')))
+	}) |> Reduce(f = rbind)
+}