#75

fgcz · Oct 29, 2024 · 5444985 · 5444985
1 parent 5e5b736
commit 5444985
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Showing 5 changed files with 52 additions and 8 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: rawrr
 Type: Package
 Title: Direct Access to Orbitrap Data and Beyond
-Version: 1.15.0
+Version: 1.15.1
 Authors@R: c(person("Christian", "Panse",
         email = "[email protected]",
         role = c("aut", "cre"),

diff --git a/R/dotNetAssembly.R b/R/dotNetAssembly.R
@@ -24,7 +24,7 @@
 
     # execute rawrr.exe assembly and keep output string
     rvs <-  "?"
-    if (Sys.info()['sysname'] %in% c("Darwin", "Linux")){
+    if (Sys.info()['sysname'] %in% c("Darwin", "Linux") && !exists('RAWRRDOTNET')){
       if (file.exists(exe) && Sys.which('mono') != ""){
         rvs <- system2(Sys.which('mono'), args = c(shQuote(exe)),
                        stdout = TRUE)
@@ -113,6 +113,18 @@ rawrrAssemblyPath <- function(){
 
 .rawrrAssembly <- function(){
   f <- file.path(rawrrAssemblyPath(), 'rawrr.exe')
+
+    if (exists('RAWRRDOTNET')){
+       if (Sys.info()['sysname'] == "Darwin"){
+           file.path(rawrr::rawrrAssemblyPath(), 'osx-x64', 'rawrr') -> f
+       } else if (Sys.info()['sysname'] == "Linux"){
+           file.path(rawrr::rawrrAssemblyPath(), 'linux-x64', 'rawrr') -> f
+       } else {
+           file.path(rawrr::rawrrAssemblyPath(), 'win-x64', 'rawrr.exe') -> f
+       }
+       message("Using '", f, "' ...")
+    }
+
   return(f)
 }
 

diff --git a/R/rawrr.R b/R/rawrr.R
@@ -87,7 +87,9 @@
 
     mono <- if(Sys.info()['sysname'] %in% c("Darwin", "Linux")) TRUE else FALSE
     exe <- .rawrrAssembly()
-
+
+
+
     tfi <- tempfile(tmpdir=tmpdir, fileext = ".txt")
     tfo <- tempfile(tmpdir=tmpdir, fileext = ".R")
     tfstdout <- tempfile(tmpdir=tmpdir, fileext = ".stdout")
@@ -97,8 +99,9 @@
     if(isFALSE(file.exists(tfi))){
             stop(paste0("No input file '", tfi, "' available!"))
     }
+
 
-    if (mono){
+    if (mono && !exists('RAWRRDOTNET')){
       if (system2(command = "/usr/bin/which", args = c("mono"),
             stderr = FALSE, stdout = FALSE) != 0){
         stop("mono is not available; please check https://www.mono-project.com/")
@@ -252,7 +255,8 @@ readIndex <- function (rawfile)
     TRUE
   else FALSE
   exe <- .rawrrAssembly()
-  if (mono) {
+
+  if (mono && !exists('RAWRRDOTNET')){
     con <- textConnection(system2(Sys.which("mono"),
                                   args = c(shQuote(exe),
                                            shQuote(rawfile), "index"),
@@ -283,13 +287,15 @@ filter <- function(rawfile, filter = "ms", precision = 10, tmpdir=tempdir()){
   .checkRawFile(rawfile)
   mono <- if(Sys.info()['sysname'] %in% c("Darwin", "Linux")) TRUE else FALSE
   exe <- .rawrrAssembly()
+
 
   tfstderr <- tempfile(tmpdir=tmpdir)
   tfo <- tempfile(tmpdir=tmpdir, fileext = ".txt")
   tfstdout <- tempfile(tmpdir=tmpdir)
 
   cmd <- exe
 
+  if (exists('RAWRRDOTNET')){ mono <<- FALSE}
   if (mono){
     rvs <- system2(Sys.which("mono"),
                    args = c(shQuote(exe), shQuote(rawfile),
@@ -621,6 +627,7 @@ readSpectrum <- function(rawfile, scan = NULL, tmpdir = tempdir(),
 
   mono <- if(Sys.info()['sysname'] %in% c("Darwin", "Linux")) TRUE else FALSE
   exe <- .rawrrAssembly()
+
 
   tfstdout <- tempfile(fileext = ".stdout", tmpdir = tmpdir)
   tfstderr <- tempfile(fileext = ".stderr", tmpdir = tmpdir)
@@ -629,7 +636,7 @@ readSpectrum <- function(rawfile, scan = NULL, tmpdir = tempdir(),
 
   system2args <- c(shQuote(rawfile), "chromatogram", shQuote(filter), tfcsv)
 
-  if (mono){
+  if (mono && !exists('RAWRRDOTNET')){
     rvs <- system2("mono", args = c(shQuote(exe), system2args), stdout=tfstdout, stderr=tfstderr)
   }else{
     rvs <- system2(exe, args = system2args, stdout=tfstdout, stderr=tfstderr)
@@ -1589,12 +1596,13 @@ readTrailer <- function(rawfile, label = NULL) {
 
   mono <- if(Sys.info()['sysname'] %in% c("Darwin", "Linux")) TRUE else FALSE
   exe <- .rawrrAssembly()
+
 
   cmd <- exe
 
   if (is.null(label)){
     # should return all available trailer label
-    if (mono){
+    if (mono && !exists('RAWRRDOTNET')){
       con <- textConnection(system2(Sys.which("mono"),
                                     args = c(shQuote(exe), shQuote(rawfile), "trailer"),
                                     stdout = TRUE))
@@ -1605,7 +1613,7 @@ readTrailer <- function(rawfile, label = NULL) {
     }
   }else{
     # use case for providing a trailer label
-    if (mono){
+    if (mono && !exists('RAWRRDOTNET')){
       con <- textConnection(system2(Sys.which("mono"),
                                     args = c(shQuote(exe), shQuote(rawfile),
                                              "trailer",  shQuote(label)),

diff --git a/inst/rawrrassembly/README.md b/inst/rawrrassembly/README.md
@@ -20,3 +20,10 @@ rawrr.exe <rawfile> chromatogram
 ```
 
 
+## Howto build
+
+```
+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
+```
diff --git a/inst/rawrrassembly/rawrr-dotnet.csproj b/inst/rawrrassembly/rawrr-dotnet.csproj
@@ -0,0 +1,17 @@
+<Project Sdk="Microsoft.NET.Sdk">
+
+  <PropertyGroup>
+    <OutputType>Exe</OutputType>
+    <TargetFramework>net8.0</TargetFramework> <!-- Or net7.0, depending on your setup -->
+    <AssemblyName>rawrr</AssemblyName>
+    <PublishSingleFile>true</PublishSingleFile> 
+    <SelfContained>true</SelfContained> 
+  </PropertyGroup>
+
+  <ItemGroup>
+    <PackageReference Include="ThermoFisher.CommonCore.BackgroundSubtraction" Version="8.0.6" />
+    <PackageReference Include="Thermofisher.CommonCore.MassPrecisionEstimator" Version="8.0.6" />
+    <PackageReference Include="ThermoFisher.CommonCore.RawFileReader" Version="8.0.6" />
+  </ItemGroup>
+</Project>
+