Fixes for windows build

statisticalbiotechnology · May 24, 2019 · edb9d0b · edb9d0b
1 parent c190c5b
commit edb9d0b
Show file tree

Hide file tree

Showing 5 changed files with 64 additions and 19 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -82,10 +82,16 @@ endforeach()
 # COMPILING DINOSAUR
 #############################################################################
 
-execute_process(COMMAND mvn package -Pconf -DskipTests -Ddir=${CMAKE_CURRENT_BINARY_DIR}/dinosaur WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/ext/dinosaur RESULT_VARIABLE MVN_RESULT)
+if (MSVC)
+  set(MVN_CMD mvn.cmd)
+else (MSVC)
+  set(MVN_CMD mvn)
+endif (MSVC)
+
+execute_process(COMMAND ${MVN_CMD} package -Pconf -DskipTests -Ddir=${CMAKE_CURRENT_BINARY_DIR}/dinosaur WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/ext/dinosaur OUTPUT_FILE ${CMAKE_CURRENT_BINARY_DIR}/dinosaur_maven_stdout.txt ERROR_FILE ${CMAKE_CURRENT_BINARY_DIR}/dinosaur_maven_stderr.txt RESULT_VARIABLE MVN_RESULT)
 
 if(NOT "${MVN_RESULT}" STREQUAL "0")
-  message(FATAL_ERROR "Cannot create module Dinosaur, mvn execution failed")
+  message(FATAL_ERROR "Cannot create module Dinosaur, mvn execution failed: ${MVN_RESULT}")
 endif()
 
 install(FILES ${CMAKE_CURRENT_BINARY_DIR}/dinosaur/Dinosaur-1.1.3.free.jar ${CMAKE_SOURCE_DIR}/ext/advParams_dinosaur_targeted.txt DESTINATION ${JAR_PATH})

diff --git a/admin/builders/nativew32_build.bat b/admin/builders/nativew32_build.bat
@@ -149,6 +149,25 @@ if not exist "%PWIZ_DIR%\lib" (
   for /r pwiz %%x in (*.hpp, *.h) do copy "%%x" include\ /Y > NUL
 )
 
+set MVN_BASE=apache-maven-3.6.1
+set MVN_URL=http://ftp.unicamp.br/pub/apache/maven/maven-3/3.6.1/binaries/%MVN_BASE%-bin.zip
+if not exist "%INSTALL_DIR%\%MVN_BASE%" (
+  echo Downloading and installing CMake
+  call :downloadfile %MVN_URL% %INSTALL_DIR%\mvn.zip
+  %ZIP_EXE% x "%INSTALL_DIR%\mvn.zip" -o"%INSTALL_DIR%" > NUL
+)
+setlocal
+set PATH=%PATH%;%INSTALL_DIR%\%MVN_BASE%\bin
+
+set JAVA_BASE=openjdk-8u212-b04
+set JAVA_URL=https://github.com/AdoptOpenJDK/openjdk8-upstream-binaries/releases/download/jdk8u212-b04/OpenJDK8u-x64_windows_8u212b04.zip
+if not exist "%INSTALL_DIR%\%JAVA_BASE%" (
+  echo Downloading and installing Java JDK   
+  call :downloadfile %JAVA_URL% %INSTALL_DIR%\java.zip
+  %ZIP_EXE% x "%INSTALL_DIR%\java.zip" -o"%INSTALL_DIR%" > NUL
+)
+set JAVA_HOME=%INSTALL_DIR%\%JAVA_BASE%
+
 ::: Needed for CPack :::
 set NSIS_DIR=%INSTALL_DIR%\nsis
 set NSIS_URL=https://sourceforge.net/projects/nsis/files/NSIS 3/3.04/nsis-3.04-setup.exe/download
@@ -157,7 +176,6 @@ if not exist "%NSIS_DIR%" (
   call :downloadfile "%NSIS_URL%" %INSTALL_DIR%\nsis.exe
   "%INSTALL_DIR%\nsis.exe" /S /D=%INSTALL_DIR%\nsis
 )
-setlocal
 set PATH=%PATH%;%INSTALL_DIR%\nsis
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::::::
@@ -176,7 +194,7 @@ if not exist "%BUILD_DIR%" (md "%BUILD_DIR%")
 if not exist "%BUILD_DIR%\quandenser" (md "%BUILD_DIR%\quandenser")
 cd /D "%BUILD_DIR%\quandenser....."
 echo cmake quandenser.....
-%CMAKE_EXE% -G "Visual Studio %MSVC_VER%" -DBOOST_ROOT="%PWIZ_DIR%\libraries\boost_1_56_0" -DZLIB_INCLUDE_DIR="%PWIZ_DIR%\libraries\zlib-1.2.3" -DCMAKE_PREFIX_PATH="%PWIZ_DIR%" "%SRC_DIR%\quandenser"
+%CMAKE_EXE% -G "Visual Studio %MSVC_VER%" -DBOOST_ROOT="%PWIZ_DIR%\libraries\boost_1_67_0" -DZLIB_INCLUDE_DIR="%PWIZ_DIR%\libraries\zlib-1.2.3" -DCMAKE_PREFIX_PATH="%PWIZ_DIR%" "%SRC_DIR%\quandenser"
 
 echo build quandenser (this will take a few minutes).....
 msbuild PACKAGE.vcxproj /p:VCTargetsPath="%VCTARGET%" /p:Configuration=%BUILD_TYPE% /m
@@ -188,7 +206,7 @@ msbuild PACKAGE.vcxproj /p:VCTargetsPath="%VCTARGET%" /p:Configuration=%BUILD_TY
 if not exist "%BUILD_DIR%\quandenser-vendor-support" (md "%BUILD_DIR%\quandenser-vendor-support")
 cd /D "%BUILD_DIR%\quandenser-vendor-support"
 echo cmake quandenser with vendor support.....
-%CMAKE_EXE% -G "Visual Studio %MSVC_VER%" -DBOOST_ROOT="%PWIZ_DIR%\libraries\boost_1_56_0" -DZLIB_INCLUDE_DIR="%PWIZ_DIR%\libraries\zlib-1.2.3" -DCMAKE_PREFIX_PATH="%PWIZ_DIR%" -DVENDOR_SUPPORT=ON "%SRC_DIR%\quandenser"
+%CMAKE_EXE% -G "Visual Studio %MSVC_VER%" -DBOOST_ROOT="%PWIZ_DIR%\libraries\boost_1_67_0" -DZLIB_INCLUDE_DIR="%PWIZ_DIR%\libraries\zlib-1.2.3" -DCMAKE_PREFIX_PATH="%PWIZ_DIR%" -DVENDOR_SUPPORT=ON "%SRC_DIR%\quandenser"
 
 echo build quandenser with vendor support (this will take a few minutes).....
 msbuild PACKAGE.vcxproj /p:VCTargetsPath="%VCTARGET%" /p:Configuration=%BUILD_TYPE% /m

diff --git a/admin/builders/nativew64_build.bat b/admin/builders/nativew64_build.bat
@@ -156,6 +156,25 @@ if not exist "%PWIZ_DIR%\lib" (
   for /r pwiz %%x in (*.hpp, *.h) do copy "%%x" include\ /Y > NUL
 )
 
+set MVN_BASE=apache-maven-3.6.1
+set MVN_URL=http://ftp.unicamp.br/pub/apache/maven/maven-3/3.6.1/binaries/%MVN_BASE%-bin.zip
+if not exist "%INSTALL_DIR%\%MVN_BASE%" (
+  echo Downloading and installing CMake
+  call :downloadfile %MVN_URL% %INSTALL_DIR%\mvn.zip
+  %ZIP_EXE% x "%INSTALL_DIR%\mvn.zip" -o"%INSTALL_DIR%" > NUL
+)
+setlocal
+set PATH=%PATH%;%INSTALL_DIR%\%MVN_BASE%\bin
+
+set JAVA_BASE=openjdk-8u212-b04
+set JAVA_URL=https://github.com/AdoptOpenJDK/openjdk8-upstream-binaries/releases/download/jdk8u212-b04/OpenJDK8u-x64_windows_8u212b04.zip
+if not exist "%INSTALL_DIR%\%JAVA_BASE%" (
+  echo Downloading and installing Java JDK   
+  call :downloadfile %JAVA_URL% %INSTALL_DIR%\java.zip
+  %ZIP_EXE% x "%INSTALL_DIR%\java.zip" -o"%INSTALL_DIR%" > NUL
+)
+set JAVA_HOME=%INSTALL_DIR%\%JAVA_BASE%
+
 ::: Needed for CPack :::
 set NSIS_DIR=%INSTALL_DIR%\nsis
 set NSIS_URL=https://sourceforge.net/projects/nsis/files/NSIS 3/3.04/nsis-3.04-setup.exe/download
@@ -164,7 +183,6 @@ if not exist "%NSIS_DIR%" (
   call :downloadfile "%NSIS_URL%" %INSTALL_DIR%\nsis.exe
   "%INSTALL_DIR%\nsis.exe" /S /D=%INSTALL_DIR%\nsis
 )
-setlocal
 set PATH=%PATH%;%INSTALL_DIR%\nsis
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::::::
@@ -183,7 +201,7 @@ if not exist "%BUILD_DIR%" (md "%BUILD_DIR%")
 if not exist "%BUILD_DIR%\quandenser" (md "%BUILD_DIR%\quandenser")
 cd /D "%BUILD_DIR%\quandenser"
 echo cmake quandenser.....
-%CMAKE_EXE% -G "Visual Studio %MSVC_VER% Win64" -DBOOST_ROOT="%PWIZ_DIR%\libraries\boost_1_56_0" -DZLIB_INCLUDE_DIR="%PWIZ_DIR%\libraries\zlib-1.2.3" -DCMAKE_PREFIX_PATH="%PWIZ_DIR%" "%SRC_DIR%\quandenser"
+%CMAKE_EXE% -G "Visual Studio %MSVC_VER% Win64" -DBOOST_ROOT="%PWIZ_DIR%\libraries\boost_1_67_0" -DZLIB_INCLUDE_DIR="%PWIZ_DIR%\libraries\zlib-1.2.3" -DCMAKE_PREFIX_PATH="%PWIZ_DIR%" "%SRC_DIR%\quandenser"
 
 echo build quandenser (this will take a few minutes).....
 msbuild PACKAGE.vcxproj /p:VCTargetsPath="%VCTARGET%" /p:Configuration=%BUILD_TYPE% /m
@@ -195,7 +213,7 @@ msbuild PACKAGE.vcxproj /p:VCTargetsPath="%VCTARGET%" /p:Configuration=%BUILD_TY
 if not exist "%BUILD_DIR%\quandenser-vendor-support" (md "%BUILD_DIR%\quandenser-vendor-support")
 cd /D "%BUILD_DIR%\quandenser-vendor-support"
 echo cmake quandenser with vendor support.....
-%CMAKE_EXE% -G "Visual Studio %MSVC_VER% Win64" -DBOOST_ROOT="%PWIZ_DIR%\libraries\boost_1_56_0" -DZLIB_INCLUDE_DIR="%PWIZ_DIR%\libraries\zlib-1.2.3" -DCMAKE_PREFIX_PATH="%PWIZ_DIR%" -DVENDOR_SUPPORT=ON "%SRC_DIR%\quandenser"
+%CMAKE_EXE% -G "Visual Studio %MSVC_VER% Win64" -DBOOST_ROOT="%PWIZ_DIR%\libraries\boost_1_67_0" -DZLIB_INCLUDE_DIR="%PWIZ_DIR%\libraries\zlib-1.2.3" -DCMAKE_PREFIX_PATH="%PWIZ_DIR%" -DVENDOR_SUPPORT=ON "%SRC_DIR%\quandenser"
 
 echo build quandenser with vendor support (this will take a few minutes).....
 msbuild PACKAGE.vcxproj /p:VCTargetsPath="%VCTARGET%" /p:Configuration=%BUILD_TYPE% /m

diff --git a/cmake/FindProteoWizard.cmake b/cmake/FindProteoWizard.cmake
@@ -6,10 +6,16 @@
 # PROTEOWIZARD_LIBRARIES, the libraries to link against to use xercesc.
 # PROTEOWIZARD_FOUND, If false, don't try to use xercesc.
 
-function(_pwiz_find_library _name)
-    find_library(${_name} NAMES ${ARGN})
-    mark_as_advanced(${_name})
-endfunction()
+set(PWIZ_LIBRARIES "")
+
+macro(_pwiz_find_library _name)
+  find_library(${_name} NAMES ${ARGN})
+  mark_as_advanced(${_name})
+  if(NOT ${_name})
+    message(FATAL_ERROR "${_name} library not found")
+  endif()
+  list(APPEND PWIZ_LIBRARIES ${${_name}})
+endmacro()
 
 FIND_PATH(PWIZ_INCLUDE_DIR pwiz )
 
@@ -22,9 +28,6 @@ _pwiz_find_library(PWIZ_UTILITY_MINIXML_LIBRARY pwiz_utility_minimxml)
 _pwiz_find_library(PWIZ_DATA_MSDATA_VERSION_LIBRARY pwiz_data_msdata_version)
 _pwiz_find_library(PWIZ_SHA1_LIBRARY SHA1)
 
-set(PWIZ_LIBRARIES "")
-list(APPEND PWIZ_LIBRARIES ${PWIZ_DATA_MSDATA_LIBRARY} ${PWIZ_DATA_COMMON_LIBRARY} ${PWIZ_UTILITY_MISC_LIBRARY} ${PWIZ_UTILITY_MINIXML_LIBRARY} ${PWIZ_DATA_MSDATA_VERSION_LIBRARY} ${PWIZ_SHA1_LIBRARY})
-
 #/home/matthew/build-32bit/tools/proteowizard/lib/baf2sql_c.dll
 #/home/matthew/build-32bit/tools/proteowizard/lib/cdt.dll
 #/home/matthew/build-32bit/tools/proteowizard/lib/MassLynxRaw.dll
@@ -34,7 +37,6 @@ if(MSVC)
   _pwiz_find_library(HDF5_LIBRARY hdf5)
   _pwiz_find_library(SQLITE3PP_LIBRARY sqlite3pp)
   _pwiz_find_library(SQLITE3_LIBRARY sqlite3)
-  list(APPEND PWIZ_LIBRARIES ${PWIZ_DATA_MSDATA_MZ5_LIBRARY} ${HDF5PP_LIBRARY} ${HDF5_LIBRARY} ${SQLITE3PP_LIBRARY} ${SQLITE3_LIBRARY})
   if (VENDOR_SUPPORT)
     _pwiz_find_library(PWIZ_DATA_VENDOR_LIBRARY pwiz_data_vendor_readers)
     _pwiz_find_library(PWIZ_DATA_VENDOR_THERMO_LIBRARY pwiz_reader_thermo)
@@ -43,21 +45,22 @@ if(MSVC)
     _pwiz_find_library(PWIZ_DATA_VENDOR_SHIMADZU_API_LIBRARY pwiz_vendor_api_shimadzu)
     _pwiz_find_library(PWIZ_DATA_VENDOR_UIMF_LIBRARY pwiz_reader_uimf)
     _pwiz_find_library(PWIZ_DATA_VENDOR_UIMF_API_LIBRARY pwiz_vendor_api_uimf)
+    _pwiz_find_library(PWIZ_DATA_VENDOR_UNIFI_LIBRARY pwiz_reader_unifi)
+    _pwiz_find_library(PWIZ_DATA_VENDOR_UNIFI_API_LIBRARY pwiz_vendor_api_unifi)
     _pwiz_find_library(PWIZ_DATA_VENDOR_AGILENT_LIBRARY pwiz_reader_agilent)
     _pwiz_find_library(PWIZ_DATA_VENDOR_AGILENT_API_LIBRARY pwiz_vendor_api_agilent)
     _pwiz_find_library(PWIZ_DATA_VENDOR_WATERS_LIBRARY pwiz_reader_waters)
     _pwiz_find_library(PWIZ_DATA_VENDOR_WATERS_API_LIBRARY MassLynxRaw)
     _pwiz_find_library(PWIZ_DATA_VENDOR_WATERS_IMS_API_LIBRARY cdt)
     _pwiz_find_library(PWIZ_DATA_VENDOR_BRUKER_LIBRARY pwiz_reader_bruker)
     _pwiz_find_library(PWIZ_DATA_VENDOR_BRUKER_BAF2SQL_API_LIBRARY baf2sql_c)
+    _pwiz_find_library(PWIZ_DATA_VENDOR_BRUKER_TIMSDATA_API_LIBRARY timsdata)
     _pwiz_find_library(PWIZ_DATA_VENDOR_BRUKER_API_LIBRARY pwiz_vendor_api_bruker)
     _pwiz_find_library(PWIZ_DATA_VENDOR_ABI_T2D_LIBRARY pwiz_reader_abi_t2d)
     _pwiz_find_library(PWIZ_DATA_VENDOR_ABI_LIBRARY pwiz_reader_abi)
     _pwiz_find_library(PWIZ_DATA_VENDOR_ABI_API_LIBRARY pwiz_vendor_api_abi)
-    list(APPEND PWIZ_LIBRARIES ${PWIZ_DATA_VENDOR_LIBRARY} ${PWIZ_DATA_VENDOR_THERMO_LIBRARY} ${PWIZ_DATA_VENDOR_THERMO_API_LIBRARY} ${PWIZ_DATA_VENDOR_SHIMADZU_LIBRARY} ${PWIZ_DATA_VENDOR_SHIMADZU_API_LIBRARY} ${PWIZ_DATA_VENDOR_UIMF_LIBRARY} ${PWIZ_DATA_VENDOR_UIMF_API_LIBRARY} ${PWIZ_DATA_VENDOR_AGILENT_LIBRARY} ${PWIZ_DATA_VENDOR_AGILENT_API_LIBRARY} ${PWIZ_DATA_VENDOR_WATERS_LIBRARY} ${PWIZ_DATA_VENDOR_WATERS_API_LIBRARY} ${PWIZ_DATA_VENDOR_WATERS_IMS_API_LIBRARY} ${PWIZ_DATA_VENDOR_BRUKER_LIBRARY} ${PWIZ_DATA_VENDOR_BRUKER_API_LIBRARY} ${PWIZ_DATA_VENDOR_BRUKER_BAF2SQL_API_LIBRARY} ${PWIZ_DATA_VENDOR_ABI_T2D_LIBRARY} ${PWIZ_DATA_VENDOR_ABI_T2D_API_LIBRARY} ${PWIZ_DATA_VENDOR_ABI_LIBRARY} ${PWIZ_DATA_VENDOR_ABI_API_LIBRARY})
     if (NOT CMAKE_GENERATOR MATCHES ".*Win64.*")
       _pwiz_find_library(PWIZ_DATA_VENDOR_ABI_T2D_API_LIBRARY pwiz_vendor_api_abi_t2d)
-      list(APPEND PWIZ_LIBRARIES ${PWIZ_DATA_VENDOR_ABI_T2D_API_LIBRARY})
     endif()
   endif (VENDOR_SUPPORT)
 endif(MSVC)

diff --git a/src/DinosaurFeatureList.h b/src/DinosaurFeatureList.h
@@ -20,7 +20,7 @@
 #include <vector>
 #include <sstream>
 
-#include <boost/unordered_map.hpp>
+#include <boost/unordered/unordered_map.hpp>
 
 #include "percolator/src/DataSet.h"