path: root/sasfit.patch

diff -aurN SASfit-0.94.7.pristine/src/cmake/CPackConfig.cmake SASfit-0.94.7/src/cmake/CPackConfig.cmake
--- SASfit-0.94.7.pristine/src/cmake/CPackConfig.cmake	1970-01-01 01:00:00.000000000 +0100
+++ SASfit-0.94.7/src/cmake/CPackConfig.cmake	2016-11-04 09:06:20.235958749 +0100
@@ -0,0 +1,40 @@
+# src/cmake/CPackConfig.cmake
+#
+# Copyright (c) 2008-2011, Paul Scherrer Institute (PSI)
+#
+# This file is part of SASfit.
+#
+# SASfit is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# SASfit is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with SASfit.  If not, see <http://www.gnu.org/licenses/>.
+
+# Author(s) of this file:
+#   Ingo Bressler (ingo.bressler@bam.de)
+
+SET(CPACK_CMAKE_GENERATOR "Unix Makefiles")
+set(CPACK_PACKAGE_DESCRIPTION_FILE "../Readme.txt")
+set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "SASfit is a SAS tool")
+set(CPACK_PACKAGE_EXECUTABLES "sasfit")
+set(CPACK_PACKAGE_INSTALL_DIRECTORY "sasfit 0.94.7")
+set(CPACK_PACKAGE_NAME "SASfit")
+set(CPACK_PACKAGE_VENDOR "PSI")
+set(CPACK_PACKAGE_VERSION "0.94.7")
+set(CPACK_PACKAGE_VERSION_MAJOR "0")
+set(CPACK_PACKAGE_VERSION_MINOR "94.7")
+set(CPACK_INSTALLED_DIRECTORIES "/home/wachaandras/aur/sasfit/src/sasfit_0.94.7_linux_x86_64;.")
+set(CPACK_PACKAGE_FILE_NAME "sasfit_0.94.7_linux_x86_64")
+if(NOT WIN32)
+	set(CPACK_GENERATOR "TBZ2")
+else(NOT WIN32)
+	set(CPACK_GENERATOR "ZIP")
+endif(NOT WIN32)
+
diff -aurN SASfit-0.94.7.pristine/src/cmake/create_source_package.list SASfit-0.94.7/src/cmake/create_source_package.list
--- SASfit-0.94.7.pristine/src/cmake/create_source_package.list	2016-04-25 09:27:08.000000000 +0200
+++ SASfit-0.94.7/src/cmake/create_source_package.list	2016-11-04 09:05:58.046930712 +0100
@@ -178,183 +178,6 @@
 doc/images/missing.png
 src/doc/footer.html
 src/doc/mainpage.h
-src/f2c/CMakeLists.txt
-src/f2c/abort_.c
-src/f2c/arith.h
-src/f2c/arithchk.c
-src/f2c/backspac.c
-src/f2c/c_abs.c
-src/f2c/c_cos.c
-src/f2c/c_div.c
-src/f2c/c_exp.c
-src/f2c/c_log.c
-src/f2c/c_sin.c
-src/f2c/c_sqrt.c
-src/f2c/cabs.c
-src/f2c/close.c
-src/f2c/COPYRIGHT
-src/f2c/d_abs.c
-src/f2c/d_acos.c
-src/f2c/d_asin.c
-src/f2c/d_atan.c
-src/f2c/d_atn2.c
-src/f2c/d_cnjg.c
-src/f2c/d_cos.c
-src/f2c/d_cosh.c
-src/f2c/d_dim.c
-src/f2c/d_exp.c
-src/f2c/d_imag.c
-src/f2c/d_int.c
-src/f2c/d_lg10.c
-src/f2c/d_log.c
-src/f2c/d_mod.c
-src/f2c/d_nint.c
-src/f2c/d_prod.c
-src/f2c/d_sign.c
-src/f2c/d_sin.c
-src/f2c/d_sinh.c
-src/f2c/d_sqrt.c
-src/f2c/d_tan.c
-src/f2c/d_tanh.c
-src/f2c/derf_.c
-src/f2c/derfc_.c
-src/f2c/dfe.c
-src/f2c/dolio.c
-src/f2c/dtime_.c
-src/f2c/due.c
-src/f2c/ef1asc_.c
-src/f2c/ef1cmc_.c
-src/f2c/endfile.c
-src/f2c/erf_.c
-src/f2c/erfc_.c
-src/f2c/err.c
-src/f2c/etime_.c
-src/f2c/exit_.c
-src/f2c/f2c.h
-src/f2c/f2c.lib
-src/f2c/f2c_math.h
-src/f2c/f77_aloc.c
-src/f2c/f77vers.c
-src/f2c/fio.h
-src/f2c/fmt.c
-src/f2c/fmt.h
-src/f2c/fmtlib.c
-src/f2c/fp.h
-src/f2c/ftell64_.c
-src/f2c/ftell_.c
-src/f2c/getarg_.c
-src/f2c/getenv_.c
-src/f2c/h_abs.c
-src/f2c/h_dim.c
-src/f2c/h_dnnt.c
-src/f2c/h_indx.c
-src/f2c/h_len.c
-src/f2c/h_mod.c
-src/f2c/h_nint.c
-src/f2c/h_sign.c
-src/f2c/hl_ge.c
-src/f2c/hl_gt.c
-src/f2c/hl_le.c
-src/f2c/hl_lt.c
-src/f2c/i77vers.c
-src/f2c/i_abs.c
-src/f2c/i_dim.c
-src/f2c/i_dnnt.c
-src/f2c/i_indx.c
-src/f2c/i_len.c
-src/f2c/i_mod.c
-src/f2c/i_nint.c
-src/f2c/i_sign.c
-src/f2c/iargc_.c
-src/f2c/iio.c
-src/f2c/ilnw.c
-src/f2c/inquire.c
-src/f2c/l_ge.c
-src/f2c/l_gt.c
-src/f2c/l_le.c
-src/f2c/l_lt.c
-src/f2c/lbitbits.c
-src/f2c/lbitshft.c
-src/f2c/lio.h
-src/f2c/lread.c
-src/f2c/lwrite.c
-src/f2c/main.c
-src/f2c/open.c
-src/f2c/pow_ci.c
-src/f2c/pow_dd.c
-src/f2c/pow_di.c
-src/f2c/pow_hh.c
-src/f2c/pow_ii.c
-src/f2c/pow_qq.c
-src/f2c/pow_ri.c
-src/f2c/pow_zi.c
-src/f2c/pow_zz.c
-src/f2c/qbitbits.c
-src/f2c/qbitshft.c
-src/f2c/r_abs.c
-src/f2c/r_acos.c
-src/f2c/r_asin.c
-src/f2c/r_atan.c
-src/f2c/r_atn2.c
-src/f2c/r_cnjg.c
-src/f2c/r_cos.c
-src/f2c/r_cosh.c
-src/f2c/r_dim.c
-src/f2c/r_exp.c
-src/f2c/r_imag.c
-src/f2c/r_int.c
-src/f2c/r_lg10.c
-src/f2c/r_log.c
-src/f2c/r_mod.c
-src/f2c/r_nint.c
-src/f2c/r_sign.c
-src/f2c/r_sin.c
-src/f2c/r_sinh.c
-src/f2c/r_sqrt.c
-src/f2c/r_tan.c
-src/f2c/r_tanh.c
-src/f2c/rawio.h
-src/f2c/rdfmt.c
-src/f2c/rewind.c
-src/f2c/rsfe.c
-src/f2c/rsli.c
-src/f2c/rsne.c
-src/f2c/s_cat.c
-src/f2c/s_cmp.c
-src/f2c/s_copy.c
-src/f2c/s_paus.c
-src/f2c/s_rnge.c
-src/f2c/s_stop.c
-src/f2c/sfe.c
-src/f2c/sig_die.c
-src/f2c/signal1.h
-src/f2c/signal_.c
-src/f2c/signbit.c
-src/f2c/sue.c
-src/f2c/sysdep1.h
-src/f2c/system_.c
-src/f2c/typesize.c
-src/f2c/uio.c
-src/f2c/uninit.c
-src/f2c/util.c
-src/f2c/wref.c
-src/f2c/wrtfmt.c
-src/f2c/wsfe.c
-src/f2c/wsle.c
-src/f2c/wsne.c
-src/f2c/xwsne.c
-src/f2c/z_abs.c
-src/f2c/z_cos.c
-src/f2c/z_div.c
-src/f2c/z_exp.c
-src/f2c/z_log.c
-src/f2c/z_sin.c
-src/f2c/z_sqrt.c
-src/f2c/sasfit_wofz.c
-src/fftw/CMakeLists.txt
-src/fftw/fftw-3.3.3.tar.gz
-src/gsl/gsl-1.16.tar.gz
-src/tcl/tcl-8.4.13.tar.gz
 src/sasfit_common/CMakeLists.txt
 src/sasfit_common/include/bool.h
 src/sasfit_common/include/sasfit_common.h
diff -aurN SASfit-0.94.7.pristine/src/cmake/Findf2c.cmake SASfit-0.94.7/src/cmake/Findf2c.cmake
--- SASfit-0.94.7.pristine/src/cmake/Findf2c.cmake	2016-04-25 09:27:08.000000000 +0200
+++ SASfit-0.94.7/src/cmake/Findf2c.cmake	2016-11-04 09:05:58.046930712 +0100
@@ -36,35 +36,7 @@
 #                              against.
 # f2c_FOUND        - Do not attempt to use if "no" or undefined.
 
-GET_FILENAME_COMPONENT(CURRENT_DIR ${CMAKE_CURRENT_LIST_FILE} PATH)
-GET_FILENAME_COMPONENT(CURRENT_DIR "${CURRENT_DIR}/.." ABSOLUTE)
-
-FIND_PATH(f2c_INCLUDE_DIR f2c.h
-    ${CURRENT_DIR}/f2c/
-    NO_DEFAULT_PATH
-)
-  
-FIND_LIBRARY(f2c_LIBRARY f2c
-    ${CURRENT_DIR}/f2c/lib/
-    ${CURRENT_DIR}/f2c/lib/debug/
-    ${CURRENT_DIR}/f2c/lib/release/
-)
-
-SET(f2c_INCLUDE_DIRS ${f2c_INCLUDE_DIR})
-SET(f2c_LIBRARIES ${f2c_LIBRARY})
-
-IF(f2c_INCLUDE_DIR)
-  SET(f2c_FOUND "YES")
-  IF(NOT f2c_LIBRARY)
-    MESSAGE(STATUS "f2c library not found!")
-  ENDIF(NOT f2c_LIBRARY)
-ELSE(f2c_INCLUDE_DIR)
-  MESSAGE(STATUS "f2c include dir not found!")
-ENDIF(f2c_INCLUDE_DIR)
-
-MESSAGE(STATUS "found f2c inc: ${f2c_INCLUDE_DIRS}")
-
-IF(NOT f2c_FOUND)
-    MESSAGE(SEND_ERROR "The f2c library was not found. For adjustments use ${CMAKE_CURRENT_LIST_FILE}.")
-ENDIF(NOT f2c_FOUND)
+set(f2c_FOUND TRUE)
+set(f2c_INCLUDE_DIRS /usr/include)
+set(f2c_LIBRARIES /usr/lib/libf2c.so)
 
diff -aurN SASfit-0.94.7.pristine/src/cmake/FindFFTW.cmake SASfit-0.94.7/src/cmake/FindFFTW.cmake
--- SASfit-0.94.7.pristine/src/cmake/FindFFTW.cmake	2016-04-25 09:27:08.000000000 +0200
+++ SASfit-0.94.7/src/cmake/FindFFTW.cmake	2016-11-04 09:05:58.046930712 +0100
@@ -45,32 +45,6 @@
 # FFTW_EXE_LINKER_FLAGS = rpath on Unix
 
 message("find FFTW")
-get_package_dir(${SASFIT_ROOT_DIR}/src/fftw)
-
-# file include dir of custom build library
-FIND_PATH(FFTW_INCLUDE_DIRS
-        NAMES fftw3.h
-        PATHS ${SOURCE_DIR}
-        PATH_SUFFIXES include
-        NO_DEFAULT_PATH
-        DOC "FFTW header include dir"
-)
-
-# get library dirs
-FIND_FILE(FFTW_STATIC_LIB
-        NAMES libfftw3.a
-        PATHS ${SOURCE_DIR}
-        PATH_SUFFIXES lib
-        NO_DEFAULT_PATH
-        DOC "FFTW static library"
-)
-
-if(FFTW_STATIC_LIB)
-        set(FFTW_LIBRARIES ${FFTW_STATIC_LIB})
-endif()
-
-set(FFTW_FOUND FALSE)
-if(IS_DIRECTORY ${FFTW_INCLUDE_DIRS} AND FFTW_LIBRARIES)
-    set(FFTW_FOUND TRUE)
-endif()
-
+set(FFTW_FOUND TRUE)
+set(FFTW_LIBRARIES /usr/lib/libfftw3.so)
+set(FFTW_INCLUDE_DIRS /usr/include)
diff -aurN SASfit-0.94.7.pristine/src/cmake/FindGSL.cmake SASfit-0.94.7/src/cmake/FindGSL.cmake
--- SASfit-0.94.7.pristine/src/cmake/FindGSL.cmake	2016-04-25 09:27:08.000000000 +0200
+++ SASfit-0.94.7/src/cmake/FindGSL.cmake	2016-11-04 09:05:58.056930272 +0100
@@ -20,71 +20,6 @@
 # 
 # GSL_INCLUDE_DIRS     = where to find headers 
 
-get_package_dir(${SASFIT_ROOT_DIR}/src/gsl)
-
-# file include dir of custom build library
-FIND_PATH(GSL_INCLUDE_DIRS
-    NAMES gsl/gsl_math.h
-    PATHS ${SOURCE_DIR}
-    PATH_SUFFIXES include
-    NO_DEFAULT_PATH
-    DOC "GSL header include dir"
-)
-
-# get library dirs
-FIND_LIBRARY(GSL_LIBRARY
-	NAMES gsl libgsl
-    PATHS ${SOURCE_DIR}
-	PATH_SUFFIXES lib
-    NO_DEFAULT_PATH
-	DOC "GSL library dir"
-)
-
-FIND_FILE(GSL_STATIC_LIBRARY
-	NAMES gsl.a libgsl.a
-    PATHS ${SOURCE_DIR}
-	PATH_SUFFIXES lib
-    NO_DEFAULT_PATH
-	DOC "GSL static library dir"
-)
-
-IF(NOT GSL_LIBRARY)
-	SET(GSL_LIBRARY ${GSL_STATIC_LIBRARY})
-ENDIF()
-
-FIND_LIBRARY(GSLCBLAS_LIBRARY
-	NAMES gslcblas libgslcblas
-    PATHS ${SOURCE_DIR}
-	PATH_SUFFIXES lib
-    NO_DEFAULT_PATH
-	DOC "GSL cblas library dir"
-)
-
-FIND_FILE(GSLCBLAS_STATIC_LIBRARY
-	NAMES gslcblas.a libgslcblas.a
-    PATHS ${SOURCE_DIR}
-	PATH_SUFFIXES lib
-    NO_DEFAULT_PATH
-	DOC "GSL cblas static library dir"
-)
-	
-IF(NOT GSLCBLAS_LIBRARY)
-	SET(GSLCBLAS_LIBRARY ${GSLCBLAS_STATIC_LIBRARY})
-ENDIF()
-
-SET(GSL_LIBRARIES
-  ${GSL_LIBRARY}
-  ${GSLCBLAS_LIBRARY}
-)
-SET(GSL_STATIC_LIBRARIES 
-  ${GSL_STATIC_LIBRARY}
-  ${GSLCBLAS_STATIC_LIBRARY}
-)
-
-set(GSL_FOUND FALSE)
-if(IS_DIRECTORY ${GSL_INCLUDE_DIRS} AND GSL_LIBRARIES)
-    set(GSL_FOUND TRUE)
-endif()
-message("GSL_FOUND: '${GSL_FOUND}'")
-
-# vim: set ts=4 sw=4 sts=4 tw=0:
+set(GSL_INCLUDE_DIRS /usr/include)
+set(GSL_LIBRARIES /usr/lib/libgsl.so /usr/lib/libgslcblas.so /usr/lib/libm.so)
+set(GSL_FOUND TRUE)
diff -aurN SASfit-0.94.7.pristine/src/cmake/Findsundials.cmake SASfit-0.94.7/src/cmake/Findsundials.cmake
--- SASfit-0.94.7.pristine/src/cmake/Findsundials.cmake	2016-04-25 09:27:08.000000000 +0200
+++ SASfit-0.94.7/src/cmake/Findsundials.cmake	2016-11-04 09:05:58.056930272 +0100
@@ -42,31 +42,15 @@
 # sundials_LINK_DIRECTORIES = link directories, useful for rpath on Unix
 # sundials_EXE_LINKER_FLAGS = rpath on Unix
 
-message("find sundials")
-get_package_dir(${SASFIT_ROOT_DIR}/src/sundials)
-
-set(sundials_INCLUDE_DIRS ${SOURCE_DIR}/include)
-
-# search build directory
-file(GLOB sundials_BUILD_DIRS ${SOURCE_DIR}/*/CMakeCache.txt)
-list(LENGTH sundials_BUILD_DIRS NUM_DIRS)
-if(NUM_DIRS GREATER 0)
-        list(GET sundials_BUILD_DIRS 0 sundials_BUILD_DIR)
-        get_filename_component(sundials_BUILD_DIR
-                               "${sundials_BUILD_DIR}" DIRECTORY)
-#        message("sundials_BUILD_DIR: '${sundials_BUILD_DIR}'")
-        list(APPEND sundials_INCLUDE_DIRS ${sundials_BUILD_DIR}/include)
-endif()
-
-file(GLOB sundials_STATIC_LIBS ${sundials_BUILD_DIR}/src/*/*.a)
-
-if(sundials_STATIC_LIBS)
-        set(sundials_LIBRARIES ${sundials_STATIC_LIBS})
-endif()
-
-list(LENGTH sundials_INCLUDE_DIRS NUM_INC_DIRS)
-set(sundials_FOUND FALSE)
-if(NUM_INC_DIRS EQUAL 2 AND sundials_LIBRARIES)
-        set(sundials_FOUND TRUE)
-endif()
 
+set(sundials_INCLUDE_DIRS /usr/include)
+set(sundials_LIBRARIES /usr/lib/libsundials_arkode.so 
+    /usr/lib/libsundials_cvode.so
+    /usr/lib/libsundials_cvodes.so
+    /usr/lib/libsundials_ida.so
+    /usr/lib/libsundials_idas.so
+    /usr/lib/libsundials_kinsol.so
+    /usr/lib/libsundials_nvecparallel.so
+    /usr/lib/libsundials_nvecserial.so
+    /usr/lib/liblapack.so)
+set(sundials_FOUND TRUE)
diff -aurN SASfit-0.94.7.pristine/src/cmake/FindTCL.cmake SASfit-0.94.7/src/cmake/FindTCL.cmake
--- SASfit-0.94.7.pristine/src/cmake/FindTCL.cmake	2016-04-25 09:27:08.000000000 +0200
+++ SASfit-0.94.7/src/cmake/FindTCL.cmake	2016-11-04 09:05:58.056930272 +0100
@@ -9,53 +9,9 @@
 # TCL_LIBRARIES   = full path to the libraries
 # TCL_INCLUDE_DIRS     = where to find headers 
 
-message("find TCL")
-get_package_dir(${SASFIT_ROOT_DIR}/src/tcl)
-
-# file include dir of custom build library
-FIND_PATH(TCL_INCLUDE_DIRS
-    NAMES tcl.h
-    PATHS ${SOURCE_DIR}
-    PATH_SUFFIXES include
-    NO_DEFAULT_PATH
-    DOC "TCL include dir"
-)
-
-FIND_FILE(TCL_STATIC_LIB
-    NAMES libtcl8.4.a libtcl84s.a
-    PATHS ${SOURCE_DIR}
-    PATH_SUFFIXES lib
-    NO_DEFAULT_PATH
-    DOC "TCL static library"
-)
-
-FIND_FILE(TCL_STATIC_STUBS_LIB
-    NAMES libtclstub8.4.a libtclstub84s.a
-    PATHS ${SOURCE_DIR}
-    PATH_SUFFIXES lib
-    NO_DEFAULT_PATH
-    DOC "TCL static stubs library"
-)
 
-find_program(TCL_SH
-    NAMES tclsh tclsh84 tclsh84s tclsh8.4
-    PATHS ${SOURCE_DIR}
-    PATH_SUFFIXES bin
-    NO_DEFAULT_PATH
-    DOC "TCL interpreter program"
-)
-
-if(TCL_LIBRARY OR TCL_STATIC_LIB OR TCL_STATIC_STUBS_LIB)
-    SET(TCL_LIBRARIES
-        ${TCL_LIBRARY}
-        ${TCL_STATIC_LIB}
-        ${TCL_STATIC_STUBS_LIB}
-    )
-endif()
-
-set(TCL_FOUND FALSE)
-if(IS_DIRECTORY "${TCL_INCLUDE_DIRS}" AND TCL_LIBRARIES AND TCL_SH)
-    set(TCL_FOUND TRUE)
-endif()
+message("find TCL")
 
-# vim: set ts=4 sw=4 sts=4 tw=0:
+set(TCL_INCLUDE_DIRS /usr/include)
+set(TCL_LIBRARIES /usr/lib/libtcl.so /usr/lib/libtclstub8.6.a)
+set(TCL_FOUND TRUE)
diff -aurN SASfit-0.94.7.pristine/src/cmake/SasfitCmakeUtils.cmake SASfit-0.94.7/src/cmake/SasfitCmakeUtils.cmake
--- SASfit-0.94.7.pristine/src/cmake/SasfitCmakeUtils.cmake	2016-04-25 09:27:08.000000000 +0200
+++ SASfit-0.94.7/src/cmake/SasfitCmakeUtils.cmake	2016-11-04 09:05:58.056930272 +0100
@@ -496,10 +496,10 @@
         # avoid modifying LD_LIBRARY_PATH,
         # using dyn.lib.loader in sasfit.sh instead
         list(APPEND PREREQ
-            "/lib/*-linux-gnu/ld-[0-9].[0-9][0-9].so"
-            "/lib/*-linux-gnu/libpthread.so.[0-9]"
-            "/usr/lib/*-linux-gnu/libXrender.so.[0-9]"
-            "/usr/lib/*-linux-gnu/libXfixes.so.[0-9]"
+            "/lib/ld-[0-9].[0-9][0-9].so"
+            "/lib/libpthread.so.[0-9]"
+            "/usr/lib/libXrender.so.[0-9]"
+            "/usr/lib/libXfixes.so.[0-9]"
             )
     elseif(WIN32)
         find_library(pthread_LIB pthread-2)
diff -aurN SASfit-0.94.7.pristine/src/CMakeLists.txt SASfit-0.94.7/src/CMakeLists.txt
--- SASfit-0.94.7.pristine/src/CMakeLists.txt	2016-04-25 09:27:08.000000000 +0200
+++ SASfit-0.94.7/src/CMakeLists.txt	2016-11-04 09:05:58.056930272 +0100
@@ -1,5 +1,7 @@
 cmake_minimum_required(VERSION 2.6.2)
 
+set(CMAKE_C_FLAGS "-fPIC")
+
 if(CMAKE_HOST_APPLE)
         set(CMAKE_C_COMPILER /usr/bin/gcc)
         set(CMAKE_CXX_COMPILER /usr/bin/g++)
@@ -234,7 +236,7 @@
 
 target_link_libraries(sasfit
         ${TCL_LIBRARIES}
-        ${GSL_STATIC_LIBRARIES}
+        ${GSL_LIBRARIES}
         ${FFTW_LIBRARIES}
         ${sundials_LIBRARIES}
         ${OpenMP_LIB}