From 2fb6af9db66d93cb88544e9ae3bb74f05d34d517 Mon Sep 17 00:00:00 2001
From: Avni2000 <77120766+Avni2000@users.noreply.github.com>
Date: Fri, 11 Apr 2025 14:37:18 -0500
Subject: [PATCH 1/3] Update coinor.cmake

---
 libraries.cmake/coinor.cmake | 36 +++++++++++++++++++-----------------
 1 file changed, 19 insertions(+), 17 deletions(-)

diff --git a/libraries.cmake/coinor.cmake b/libraries.cmake/coinor.cmake
index b430c9c..9c129a8 100644
--- a/libraries.cmake/coinor.cmake
+++ b/libraries.cmake/coinor.cmake
@@ -146,24 +146,26 @@ MACRO( OPENMS_CONTRIB_BUILD_COINOR)
 		endif()
 		
     message( STATUS "Configure COIN-OR library (./configure -C --prefix=${PROJECT_BINARY_DIR} ${STATIC_BUILD} ${SHARED_BUILD} --with-lapack=no --with-blas=no ${COINOR_EXTRA_FLAGS} CXX=${CMAKE_CXX_COMPILER} CC=${CMAKE_C_COMPILER})")
-    exec_program("./configure" "${COINOR_DIR}"
-      ARGS 
-      -C 
-      --prefix=${PROJECT_BINARY_DIR}
-      ## Following two lines can be combined with prefix
-      ## But maybe they avoid building the doc into share (wanted?)
-      #--libdir=${CONTRIB_BIN_LIB_DIR} 
-      #--includedir=${CONTRIB_BIN_INCLUDE_DIR}
-      ${STATIC_BUILD}
-      ${SHARED_BUILD}
-      --with-lapack=no
-      --with-blas=no
-      ${COINOR_EXTRA_FLAGS} 
-      CXX=${CMAKE_CXX_COMPILER} 
-      CC=${CMAKE_C_COMPILER}
+#exec_program -> execute_process
+    execute_process(
+      COMMAND 
+        ./configure 
+        -C 
+        --prefix=${PROJECT_BINARY_DIR}
+        ${STATIC_BUILD}
+        ${SHARED_BUILD}
+        --with-lapack=no
+        --with-blas=no
+        ${COINOR_EXTRA_FLAGS_LIST}
+        CXX=${CMAKE_CXX_COMPILER}
+        CC=${CMAKE_C_COMPILER}
+      WORKING_DIRECTORY ${COINOR_DIR}
       OUTPUT_VARIABLE COINOR_CONFIGURE_OUT
-      RETURN_VALUE COINOR_CONFIGURE_SUCCESS
-      )
+      ERROR_VARIABLE COINOR_CONFIGURE_ERR
+      RESULT_VARIABLE COINOR_CONFIGURE_SUCCESS
+    )
+
+     
     
     ## logfile
     file(APPEND ${LOGFILE} ${COINOR_CONFIGURE_OUT})

From ec27b4003c033d0cde5aa84ddeb5196f4198667d Mon Sep 17 00:00:00 2001
From: Avni2000 <77120766+Avni2000@users.noreply.github.com>
Date: Fri, 11 Apr 2025 14:39:39 -0500
Subject: [PATCH 2/3] Update coinor.cmake

ignore
---
 libraries.cmake/coinor.cmake | 1 -
 1 file changed, 1 deletion(-)

diff --git a/libraries.cmake/coinor.cmake b/libraries.cmake/coinor.cmake
index 9c129a8..fd36b69 100644
--- a/libraries.cmake/coinor.cmake
+++ b/libraries.cmake/coinor.cmake
@@ -161,7 +161,6 @@ MACRO( OPENMS_CONTRIB_BUILD_COINOR)
         CC=${CMAKE_C_COMPILER}
       WORKING_DIRECTORY ${COINOR_DIR}
       OUTPUT_VARIABLE COINOR_CONFIGURE_OUT
-      ERROR_VARIABLE COINOR_CONFIGURE_ERR
       RESULT_VARIABLE COINOR_CONFIGURE_SUCCESS
     )
 

From f71a58f289d2bd1c1d4135c9ea0cf0d6e2129122 Mon Sep 17 00:00:00 2001
From: Avni2000 <77120766+Avni2000@users.noreply.github.com>
Date: Fri, 11 Apr 2025 15:15:24 -0500
Subject: [PATCH 3/3] Update coinor.cmake - both done

---
 libraries.cmake/coinor.cmake | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/libraries.cmake/coinor.cmake b/libraries.cmake/coinor.cmake
index fd36b69..78d3964 100644
--- a/libraries.cmake/coinor.cmake
+++ b/libraries.cmake/coinor.cmake
@@ -161,6 +161,7 @@ MACRO( OPENMS_CONTRIB_BUILD_COINOR)
         CC=${CMAKE_C_COMPILER}
       WORKING_DIRECTORY ${COINOR_DIR}
       OUTPUT_VARIABLE COINOR_CONFIGURE_OUT
+      ERROR_VARIABLE COINOR_CONFIGURE_ERR
       RESULT_VARIABLE COINOR_CONFIGURE_SUCCESS
     )
 
@@ -178,13 +179,15 @@ MACRO( OPENMS_CONTRIB_BUILD_COINOR)
 
     ## make install
     message( STATUS "Building and installing COIN-OR library (make install).. ")
-    exec_program(${CMAKE_MAKE_PROGRAM} "${COINOR_DIR}"
-      ARGS 
-      install
-      #-j ${NUMBER_OF_JOBS} # the project has problems with multiple jobs. It tries to create folders at the same time and fails.
-      -j 1
+    execute_process(
+      COMMAND 
+      ${CMAKE_MAKE_PROGRAM}
+      install 
+      "-j1"
+      WORKING_DIRECTORY ${COINOR_DIR} 
+        # Explicitly pass as one argument      
       OUTPUT_VARIABLE COINOR_MAKE_OUT
-      RETURN_VALUE COINOR_MAKE_SUCCESS
+      RESULT_VARIABLE COINOR_MAKE_SUCCESS
       )
 
     ## logfile