This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by cdo configure 1.6.3, which was generated by GNU Autoconf 2.68. Invocation command line was $ ./configure --with-netcdf=/usr/ --with-hdf5=/usr/ ## --------- ## ## Platform. ## ## --------- ## hostname = NaLe uname -m = i686 uname -r = 1.7.28(0.271/5/3) uname -s = CYGWIN_NT-6.1-WOW64 uname -v = 2014-02-09 21:06 /usr/bin/uname -p = unknown /bin/uname -X = unknown /bin/arch = i686 /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown /usr/bin/hostinfo = unknown /bin/machine = unknown /usr/bin/oslevel = unknown /bin/universe = unknown PATH: /usr/local/bin PATH: /usr/bin PATH: /cygdrive/c/Program Files (x86)/AMD APP/bin/x86_64 PATH: /cygdrive/c/Program Files (x86)/AMD APP/bin/x86 PATH: /cygdrive/c/Program Files (x86)/Intel/iCLS Client PATH: /cygdrive/c/Program Files/Intel/iCLS Client PATH: /cygdrive/c/Windows/system32 PATH: /cygdrive/c/Windows PATH: /cygdrive/c/Windows/System32/Wbem PATH: /cygdrive/c/Windows/System32/WindowsPowerShell/v1.0 PATH: /cygdrive/c/Program Files/Intel/Intel(R) Management Engine Components/DAL PATH: /cygdrive/c/Program Files/Intel/Intel(R) Management Engine Components/IPT PATH: /cygdrive/c/Program Files (x86)/Intel/Intel(R) Management Engine Components/DAL PATH: /cygdrive/c/Program Files (x86)/Intel/Intel(R) Management Engine Components/IPT PATH: /cygdrive/c/Program Files (x86)/ATI Technologies/ATI.ACE/Core-Static PATH: /cygdrive/c/Program Files (x86)/Common Files/DHI/MIKEZero PATH: /cygdrive/c/Program Files/MATLAB/R2010a/runtime/win64 PATH: /cygdrive/c/Program Files/MATLAB/R2010a/bin PATH: /cygdrive/c/Program Files (x86)/MiKTeX 2.9/miktex/bin PATH: /cygdrive/c/Program Files (x86)/OpenVPN/bin PATH: /usr/bin PATH: /usr/bin PATH: /usr/local/bin PATH: /usr/lib PATH: /usr/lib ## ----------- ## ## Core tests. ## ## ----------- ## configure:2573: checking build system type configure:2587: result: i686-pc-cygwin configure:2607: checking host system type configure:2620: result: i686-pc-cygwin configure:2658: checking for a BSD-compatible install configure:2726: result: /usr/bin/install -c configure:2737: checking whether build environment is sane configure:2787: result: yes configure:2928: checking for a thread-safe mkdir -p configure:2967: result: /usr/bin/mkdir -p configure:2980: checking for gawk configure:2996: found /usr/bin/gawk configure:3007: result: gawk configure:3018: checking whether make sets $(MAKE) configure:3040: result: yes configure:3123: checking whether to enable maintainer-specific portions of Makefiles configure:3132: result: no configure:3147: setting up libtool configure:3195: checking how to print strings configure:3222: result: printf configure:3255: checking for style of include used by make configure:3283: result: GNU configure:3354: checking for gcc configure:3370: found /usr/bin/gcc configure:3381: result: gcc configure:3610: checking for C compiler version configure:3619: gcc --version >&5 gcc (GCC) 4.8.2 Copyright (C) 2013 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. configure:3630: $? = 0 configure:3619: gcc -v >&5 Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-pc-cygwin/4.8.2/lto-wrapper.exe Target: i686-pc-cygwin Configured with: /cygdrive/i/szsz/tmpp/gcc4/gcc-4.8.2-2/src/gcc-4.8.2/configure --srcdir=/cygdrive/i/szsz/tmpp/gcc4/gcc-4.8.2-2/src/gcc-4.8.2 --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --libexecdir=/usr/libexec --datadir=/usr/share --localstatedir=/var --sysconfdir=/etc --libdir=/usr/lib --datarootdir=/usr/share --docdir=/usr/share/doc/gcc --htmldir=/usr/share/doc/gcc/html -C --build=i686-pc-cygwin --host=i686-pc-cygwin --target=i686-pc-cygwin --without-libiconv-prefix --without-libintl-prefix --enable-shared --enable-shared-libgcc --enable-static --enable-version-specific-runtime-libs --enable-bootstrap --disable-__cxa_atexit --with-dwarf2 --with-arch=i686 --with-tune=generic --disable-sjlj-exceptions --enable-languages=ada,c,c++,fortran,java,lto,objc,obj-c++ --enable-graphite --enable-threads=posix --enable-libatomic --enable-libgomp --disable-libitm --enable-libquadmath --enable-libquadmath-support --enable-libssp --enable-libada --enable-libjava --enable-libgcj-sublibs --disable-java-awt --disable-symvers --with-ecj-jar=/usr/share/java/ecj.jar --with-gnu-ld --with-gnu-as --with-cloog-include=/usr/include/cloog-isl --without-libiconv-prefix --without-libintl-prefix --with-system-zlib --libexecdir=/usr/lib Thread model: posix gcc version 4.8.2 (GCC) configure:3630: $? = 0 configure:3619: gcc -V >&5 gcc: error: unrecognized command line option '-V' gcc: fatal error: no input files compilation terminated. configure:3630: $? = 1 configure:3619: gcc -qversion >&5 gcc: error: unrecognized command line option '-qversion' gcc: fatal error: no input files compilation terminated. configure:3630: $? = 1 configure:3650: checking whether the C compiler works configure:3672: gcc conftest.c >&5 configure:3676: $? = 0 configure:3724: result: yes configure:3727: checking for C compiler default output file name configure:3729: result: a.exe configure:3735: checking for suffix of executables configure:3742: gcc -o conftest.exe conftest.c >&5 configure:3746: $? = 0 configure:3768: result: .exe configure:3790: checking whether we are cross compiling configure:3798: gcc -o conftest.exe conftest.c >&5 configure:3802: $? = 0 configure:3809: ./conftest.exe configure:3813: $? = 0 configure:3828: result: no configure:3833: checking for suffix of object files configure:3855: gcc -c conftest.c >&5 configure:3859: $? = 0 configure:3880: result: o configure:3884: checking whether we are using the GNU C compiler configure:3903: gcc -c conftest.c >&5 configure:3903: $? = 0 configure:3912: result: yes configure:3921: checking whether gcc accepts -g configure:3941: gcc -c -g conftest.c >&5 configure:3941: $? = 0 configure:3982: result: yes configure:3999: checking for gcc option to accept ISO C89 configure:4063: gcc -c -g -O2 conftest.c >&5 configure:4063: $? = 0 configure:4076: result: none needed configure:4098: checking dependency style of gcc configure:4209: result: gcc3 configure:4224: checking for a sed that does not truncate output configure:4288: result: /usr/bin/sed configure:4306: checking for grep that handles long lines and -e configure:4364: result: /usr/bin/grep configure:4369: checking for egrep configure:4431: result: /usr/bin/grep -E configure:4436: checking for fgrep configure:4498: result: /usr/bin/grep -F configure:4533: checking for ld used by gcc configure:4600: result: /usr/i686-pc-cygwin/bin/ld.exe configure:4607: checking if the linker (/usr/i686-pc-cygwin/bin/ld.exe) is GNU ld configure:4622: result: yes configure:4634: checking for BSD- or MS-compatible name lister (nm) configure:4683: result: /usr/bin/nm -B configure:4813: checking the name lister (/usr/bin/nm -B) interface configure:4820: gcc -c -g -O2 conftest.c >&5 configure:4823: /usr/bin/nm -B "conftest.o" configure:4826: output 00000000 b .bss 00000000 d .data 00000000 N .debug_abbrev 00000000 N .debug_aranges 00000000 N .debug_info 00000000 N .debug_line 00000000 r .rdata$zzz 00000000 t .text 00000000 B _some_variable configure:4833: result: BSD nm configure:4836: checking whether ln -s works configure:4840: result: yes configure:4848: checking the maximum length of command line arguments configure:4973: result: 8192 configure:4990: checking whether the shell understands some XSI constructs configure:5000: result: yes configure:5004: checking whether the shell understands "+=" configure:5010: result: yes configure:5045: checking for /usr/i686-pc-cygwin/bin/ld.exe option to reload object files configure:5052: result: -r configure:5121: checking for objdump configure:5137: found /usr/bin/objdump configure:5148: result: objdump configure:5180: checking how to recognize dependent libraries configure:5382: result: file_magic ^x86 archive import|^x86 DLL configure:5442: checking for ar configure:5458: found /usr/bin/ar configure:5469: result: ar configure:5547: checking for strip configure:5563: found /usr/bin/strip configure:5574: result: strip configure:5646: checking for ranlib configure:5662: found /usr/bin/ranlib configure:5673: result: ranlib configure:5775: checking command to parse /usr/bin/nm -B output from gcc object configure:5893: gcc -c -g -O2 conftest.c >&5 configure:5896: $? = 0 configure:5900: /usr/bin/nm -B conftest.o \| sed -n -e 's/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p' \> conftest.nm configure:5903: $? = 0 cannot find nm_test_var in conftest.nm configure:5893: gcc -c -g -O2 conftest.c >&5 configure:5896: $? = 0 configure:5900: /usr/bin/nm -B conftest.o \| sed -n -e 's/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*_\([_A-Za-z][_A-Za-z0-9]*\)$/\1 _\2 \2/p' \> conftest.nm configure:5903: $? = 0 configure:5957: gcc -o conftest.exe -g -O2 conftest.c conftstm.o >&5 configure:5960: $? = 0 configure:5998: result: ok configure:6839: checking how to run the C preprocessor configure:6870: gcc -E conftest.c configure:6870: $? = 0 configure:6884: gcc -E conftest.c conftest.c:11:28: fatal error: ac_nonexistent.h: No such file or directory #include ^ compilation terminated. configure:6884: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.6.3" | #define PACKAGE_STRING "cdo 1.6.3" | #define PACKAGE_BUGREPORT "http://code.zmaw.de/projects/cdo" | #define PACKAGE_URL "" | #define PACKAGE "cdo" | #define VERSION "1.6.3" | /* end confdefs.h. */ | #include configure:6909: result: gcc -E configure:6929: gcc -E conftest.c configure:6929: $? = 0 configure:6943: gcc -E conftest.c conftest.c:11:28: fatal error: ac_nonexistent.h: No such file or directory #include ^ compilation terminated. configure:6943: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.6.3" | #define PACKAGE_STRING "cdo 1.6.3" | #define PACKAGE_BUGREPORT "http://code.zmaw.de/projects/cdo" | #define PACKAGE_URL "" | #define PACKAGE "cdo" | #define VERSION "1.6.3" | /* end confdefs.h. */ | #include configure:6972: checking for ANSI C header files configure:6992: gcc -c -g -O2 conftest.c >&5 configure:6992: $? = 0 configure:7065: gcc -o conftest.exe -g -O2 conftest.c >&5 configure:7065: $? = 0 configure:7065: ./conftest.exe configure:7065: $? = 0 configure:7076: result: yes configure:7089: checking for sys/types.h configure:7089: gcc -c -g -O2 conftest.c >&5 configure:7089: $? = 0 configure:7089: result: yes configure:7089: checking for sys/stat.h configure:7089: gcc -c -g -O2 conftest.c >&5 configure:7089: $? = 0 configure:7089: result: yes configure:7089: checking for stdlib.h configure:7089: gcc -c -g -O2 conftest.c >&5 configure:7089: $? = 0 configure:7089: result: yes configure:7089: checking for string.h configure:7089: gcc -c -g -O2 conftest.c >&5 configure:7089: $? = 0 configure:7089: result: yes configure:7089: checking for memory.h configure:7089: gcc -c -g -O2 conftest.c >&5 configure:7089: $? = 0 configure:7089: result: yes configure:7089: checking for strings.h configure:7089: gcc -c -g -O2 conftest.c >&5 configure:7089: $? = 0 configure:7089: result: yes configure:7089: checking for inttypes.h configure:7089: gcc -c -g -O2 conftest.c >&5 configure:7089: $? = 0 configure:7089: result: yes configure:7089: checking for stdint.h configure:7089: gcc -c -g -O2 conftest.c >&5 configure:7089: $? = 0 configure:7089: result: yes configure:7089: checking for unistd.h configure:7089: gcc -c -g -O2 conftest.c >&5 configure:7089: $? = 0 configure:7089: result: yes configure:7103: checking for dlfcn.h configure:7103: gcc -c -g -O2 conftest.c >&5 configure:7103: $? = 0 configure:7103: result: yes configure:7290: checking for objdir configure:7305: result: .libs configure:7576: checking if gcc supports -fno-rtti -fno-exceptions configure:7594: gcc -c -g -O2 -fno-rtti -fno-exceptions conftest.c >&5 cc1: warning: command line option '-fno-rtti' is valid for C++/ObjC++ but not for C [enabled by default] configure:7598: $? = 0 configure:7611: result: no configure:7631: checking for gcc option to produce PIC configure:7916: result: -DDLL_EXPORT -DPIC configure:7928: checking if gcc PIC flag -DDLL_EXPORT -DPIC works configure:7946: gcc -c -g -O2 -DDLL_EXPORT -DPIC -DPIC conftest.c >&5 configure:7950: $? = 0 configure:7963: result: yes configure:7987: checking if gcc static flag -static works configure:8015: result: yes configure:8030: checking if gcc supports -c -o file.o configure:8051: gcc -c -g -O2 -o out/conftest2.o conftest.c >&5 configure:8055: $? = 0 configure:8077: result: yes configure:8085: checking if gcc supports -c -o file.o configure:8132: result: yes configure:8165: checking whether the gcc linker (/usr/i686-pc-cygwin/bin/ld.exe) supports shared libraries configure:9240: result: yes configure:9277: checking whether -lc should be explicitly linked in configure:9285: gcc -c -g -O2 conftest.c >&5 configure:9288: $? = 0 configure:9303: gcc -shared conftest.o -v -o ./conftest -Wl,--enable-auto-image-base -Xlinker --out-implib -Xlinker conftest 2\>\&1 \| /usr/bin/grep -lc \>/dev/null 2\>\&1 configure:9306: $? = 1 configure:9320: result: yes configure:9485: checking dynamic linker characteristics configure:10162: result: Win32 ld.exe configure:10269: checking how to hardcode library paths into programs configure:10294: result: immediate configure:10834: checking whether stripping libraries is possible configure:10839: result: yes configure:10874: checking if libtool supports shared libraries configure:10876: result: yes configure:10879: checking whether to build shared libraries configure:10900: result: yes configure:10903: checking whether to build static libraries configure:10907: result: yes configure:10987: checking for gcc configure:11014: result: gcc configure:11036: checking for gcc option to accept ISO C99 configure:11185: gcc -c -g -O2 conftest.c >&5 conftest.c:73:29: error: expected ';', ',' or ')' before 'text' test_restrict (ccp restrict text) ^ conftest.c: In function 'main': conftest.c:127:18: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'newvar' char *restrict newvar = "Another string"; ^ conftest.c:127:18: error: 'newvar' undeclared (first use in this function) conftest.c:127:18: note: each undeclared identifier is reported only once for each function it appears in conftest.c:137:3: error: 'for' loop initial declarations are only allowed in C99 mode for (int i = 0; i < ia->datasize; ++i) ^ conftest.c:137:3: note: use option -std=c99 or -std=gnu99 to compile your code configure:11185: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.6.3" | #define PACKAGE_STRING "cdo 1.6.3" | #define PACKAGE_BUGREPORT "http://code.zmaw.de/projects/cdo" | #define PACKAGE_URL "" | #define PACKAGE "cdo" | #define VERSION "1.6.3" | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | /* end confdefs.h. */ | #include | #include | #include | #include | #include | | // Check varargs macros. These examples are taken from C99 6.10.3.5. | #define debug(...) fprintf (stderr, __VA_ARGS__) | #define showlist(...) puts (#__VA_ARGS__) | #define report(test,...) ((test) ? puts (#test) : printf (__VA_ARGS__)) | static void | test_varargs_macros (void) | { | int x = 1234; | int y = 5678; | debug ("Flag"); | debug ("X = %d\n", x); | showlist (The first, second, and third items.); | report (x>y, "x is %d but y is %d", x, y); | } | | // Check long long types. | #define BIG64 18446744073709551615ull | #define BIG32 4294967295ul | #define BIG_OK (BIG64 / BIG32 == 4294967297ull && BIG64 % BIG32 == 0) | #if !BIG_OK | your preprocessor is broken; | #endif | #if BIG_OK | #else | your preprocessor is broken; | #endif | static long long int bignum = -9223372036854775807LL; | static unsigned long long int ubignum = BIG64; | | struct incomplete_array | { | int datasize; | double data[]; | }; | | struct named_init { | int number; | const wchar_t *name; | double average; | }; | | typedef const char *ccp; | | static inline int | test_restrict (ccp restrict text) | { | // See if C++-style comments work. | // Iterate through items via the restricted pointer. | // Also check for declarations in for loops. | for (unsigned int i = 0; *(text+i) != '\0'; ++i) | continue; | return 0; | } | | // Check varargs and va_copy. | static void | test_varargs (const char *format, ...) | { | va_list args; | va_start (args, format); | va_list args_copy; | va_copy (args_copy, args); | | const char *str; | int number; | float fnumber; | | while (*format) | { | switch (*format++) | { | case 's': // string | str = va_arg (args_copy, const char *); | break; | case 'd': // int | number = va_arg (args_copy, int); | break; | case 'f': // float | fnumber = va_arg (args_copy, double); | break; | default: | break; | } | } | va_end (args_copy); | va_end (args); | } | | int | main () | { | | // Check bool. | _Bool success = false; | | // Check restrict. | if (test_restrict ("String literal") == 0) | success = true; | char *restrict newvar = "Another string"; | | // Check varargs. | test_varargs ("s, d' f .", "string", 65, 34.234); | test_varargs_macros (); | | // Check flexible array members. | struct incomplete_array *ia = | malloc (sizeof (struct incomplete_array) + (sizeof (double) * 10)); | ia->datasize = 10; | for (int i = 0; i < ia->datasize; ++i) | ia->data[i] = i * 1.234; | | // Check named initializers. | struct named_init ni = { | .number = 34, | .name = L"Test wide string", | .average = 543.34343, | }; | | ni.number = 58; | | int dynamic_array[ni.number]; | dynamic_array[ni.number - 1] = 543; | | // work around unused variable warnings | return (!success || bignum == 0LL || ubignum == 0uLL || newvar[0] == 'x' | || dynamic_array[ni.number - 1] != 543); | | ; | return 0; | } configure:11185: gcc -std=gnu99 -c -g -O2 conftest.c >&5 configure:11185: $? = 0 configure:11205: result: -std=gnu99 configure:11214: checking whether gcc -std=gnu99 and cc understand -c and -o together configure:11245: gcc -std=gnu99 -c conftest.c -o conftest2.o >&5 configure:11249: $? = 0 configure:11255: gcc -std=gnu99 -c conftest.c -o conftest2.o >&5 configure:11259: $? = 0 configure:11270: cc -c conftest.c >&5 configure:11274: $? = 0 configure:11282: cc -c conftest.c -o conftest2.o >&5 configure:11286: $? = 0 configure:11292: cc -c conftest.c -o conftest2.o >&5 configure:11296: $? = 0 configure:11314: result: yes configure:11382: checking for ar configure:11409: result: ar configure:11566: checking for ld configure:11593: result: /usr/i686-pc-cygwin/bin/ld.exe configure:11658: checking for nm configure:11685: result: /usr/bin/nm -B configure:11750: checking for ar configure:11777: result: ar configure:11842: checking for as configure:11858: found /usr/bin/as configure:11869: result: as configure:11934: checking for dlltool configure:11950: found /usr/bin/dlltool configure:11961: result: dlltool configure:12026: checking for objdump configure:12053: result: objdump configure:12118: checking for strip configure:12145: result: strip configure:12210: checking for ranlib configure:12237: result: ranlib configure:12318: checking for g++ configure:12334: found /usr/bin/g++ configure:12345: result: g++ configure:12372: checking for C++ compiler version configure:12381: g++ --version >&5 g++ (GCC) 4.8.2 Copyright (C) 2013 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. configure:12392: $? = 0 configure:12381: g++ -v >&5 Using built-in specs. COLLECT_GCC=g++ COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-pc-cygwin/4.8.2/lto-wrapper.exe Target: i686-pc-cygwin Configured with: /cygdrive/i/szsz/tmpp/gcc4/gcc-4.8.2-2/src/gcc-4.8.2/configure --srcdir=/cygdrive/i/szsz/tmpp/gcc4/gcc-4.8.2-2/src/gcc-4.8.2 --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --libexecdir=/usr/libexec --datadir=/usr/share --localstatedir=/var --sysconfdir=/etc --libdir=/usr/lib --datarootdir=/usr/share --docdir=/usr/share/doc/gcc --htmldir=/usr/share/doc/gcc/html -C --build=i686-pc-cygwin --host=i686-pc-cygwin --target=i686-pc-cygwin --without-libiconv-prefix --without-libintl-prefix --enable-shared --enable-shared-libgcc --enable-static --enable-version-specific-runtime-libs --enable-bootstrap --disable-__cxa_atexit --with-dwarf2 --with-arch=i686 --with-tune=generic --disable-sjlj-exceptions --enable-languages=ada,c,c++,fortran,java,lto,objc,obj-c++ --enable-graphite --enable-threads=posix --enable-libatomic --enable-libgomp --disable-libitm --enable-libquadmath --enable-libquadmath-support --enable-libssp --enable-libada --enable-libjava --enable-libgcj-sublibs --disable-java-awt --disable-symvers --with-ecj-jar=/usr/share/java/ecj.jar --with-gnu-ld --with-gnu-as --with-cloog-include=/usr/include/cloog-isl --without-libiconv-prefix --without-libintl-prefix --with-system-zlib --libexecdir=/usr/lib Thread model: posix gcc version 4.8.2 (GCC) configure:12392: $? = 0 configure:12381: g++ -V >&5 g++: error: unrecognized command line option '-V' g++: fatal error: no input files compilation terminated. configure:12392: $? = 1 configure:12381: g++ -qversion >&5 g++: error: unrecognized command line option '-qversion' g++: fatal error: no input files compilation terminated. configure:12392: $? = 1 configure:12396: checking whether we are using the GNU C++ compiler configure:12415: g++ -c conftest.cpp >&5 configure:12415: $? = 0 configure:12424: result: yes configure:12433: checking whether g++ accepts -g configure:12453: g++ -c -g conftest.cpp >&5 configure:12453: $? = 0 configure:12494: result: yes configure:12519: checking dependency style of g++ configure:12630: result: gcc3 configure:12653: checking how to run the C++ preprocessor configure:12680: g++ -E conftest.cpp configure:12680: $? = 0 configure:12694: g++ -E conftest.cpp conftest.cpp:23:28: fatal error: ac_nonexistent.h: No such file or directory #include ^ compilation terminated. configure:12694: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.6.3" | #define PACKAGE_STRING "cdo 1.6.3" | #define PACKAGE_BUGREPORT "http://code.zmaw.de/projects/cdo" | #define PACKAGE_URL "" | #define PACKAGE "cdo" | #define VERSION "1.6.3" | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | /* end confdefs.h. */ | #include configure:12719: result: g++ -E configure:12739: g++ -E conftest.cpp configure:12739: $? = 0 configure:12753: g++ -E conftest.cpp conftest.cpp:23:28: fatal error: ac_nonexistent.h: No such file or directory #include ^ compilation terminated. configure:12753: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.6.3" | #define PACKAGE_STRING "cdo 1.6.3" | #define PACKAGE_BUGREPORT "http://code.zmaw.de/projects/cdo" | #define PACKAGE_URL "" | #define PACKAGE "cdo" | #define VERSION "1.6.3" | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | /* end confdefs.h. */ | #include configure:12921: checking for ld used by g++ configure:12988: result: /usr/i686-pc-cygwin/bin/ld.exe configure:12995: checking if the linker (/usr/i686-pc-cygwin/bin/ld.exe) is GNU ld configure:13010: result: yes configure:13065: checking whether the g++ linker (/usr/i686-pc-cygwin/bin/ld.exe) supports shared libraries configure:13997: result: yes configure:14025: g++ -c -g -O2 conftest.cpp >&5 configure:14028: $? = 0 configure:14210: checking for g++ option to produce PIC configure:14532: result: -DDLL_EXPORT -DPIC configure:14541: checking if g++ PIC flag -DDLL_EXPORT -DPIC works configure:14559: g++ -c -g -O2 -DDLL_EXPORT -DPIC -DPIC conftest.cpp >&5 configure:14563: $? = 0 configure:14576: result: yes configure:14597: checking if g++ static flag -static works configure:14625: result: yes configure:14637: checking if g++ supports -c -o file.o configure:14658: g++ -c -g -O2 -o out/conftest2.o conftest.cpp >&5 configure:14662: $? = 0 configure:14684: result: yes configure:14689: checking if g++ supports -c -o file.o configure:14736: result: yes configure:14766: checking whether the g++ linker (/usr/i686-pc-cygwin/bin/ld.exe) supports shared libraries configure:14794: result: yes configure:14937: checking dynamic linker characteristics configure:15548: result: Win32 ld.exe configure:15601: checking how to hardcode library paths into programs configure:15626: result: immediate configure:15677: checking for special C compiler options needed for large files configure:15722: result: no configure:15728: checking for _FILE_OFFSET_BITS value needed for large files configure:15753: gcc -std=gnu99 -c -g -O2 conftest.c >&5 configure:15753: $? = 0 configure:15785: result: no configure:15876: checking for stdlib.h configure:15876: result: yes configure:15876: checking for unistd.h configure:15876: result: yes configure:15876: checking for sys/param.h configure:15876: gcc -std=gnu99 -c -g -O2 conftest.c >&5 configure:15876: $? = 0 configure:15876: result: yes configure:15896: checking for getpagesize configure:15896: gcc -std=gnu99 -o conftest.exe -g -O2 conftest.c >&5 configure:15896: $? = 0 configure:15896: result: yes configure:15905: checking for working mmap configure:16052: gcc -std=gnu99 -o conftest.exe -g -O2 conftest.c >&5 configure:16052: $? = 0 configure:16052: ./conftest.exe configure:16052: $? = 0 configure:16062: result: yes configure:16073: checking for malloc in -lmalloc configure:16098: gcc -std=gnu99 -o conftest.exe -g -O2 conftest.c -lmalloc >&5 conftest.c:35:6: warning: conflicting types for built-in function 'malloc' [enabled by default] char malloc (); ^ /usr/lib/gcc/i686-pc-cygwin/4.8.2/../../../../i686-pc-cygwin/bin/ld: cannot find -lmalloc collect2: error: ld returned 1 exit status configure:16098: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.6.3" | #define PACKAGE_STRING "cdo 1.6.3" | #define PACKAGE_BUGREPORT "http://code.zmaw.de/projects/cdo" | #define PACKAGE_URL "" | #define PACKAGE "cdo" | #define VERSION "1.6.3" | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | #define HAVE_STDLIB_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MMAP 1 | /* end confdefs.h. */ | | /* Override any GCC internal prototype to avoid an error. | Use char because int might match the return type of a GCC | builtin and then its argument prototype would still apply. */ | #ifdef __cplusplus | extern "C" | #endif | char malloc (); | int | main () | { | return malloc (); | ; | return 0; | } configure:16107: result: no configure:16120: checking for struct stat.st_blksize configure:16120: gcc -std=gnu99 -c -g -O2 conftest.c >&5 configure:16120: $? = 0 configure:16120: result: yes configure:16134: checking sys/resource.h usability configure:16134: gcc -std=gnu99 -c -g -O2 conftest.c >&5 configure:16134: $? = 0 configure:16134: result: yes configure:16134: checking sys/resource.h presence configure:16134: gcc -E conftest.c configure:16134: $? = 0 configure:16134: result: yes configure:16134: checking for sys/resource.h configure:16134: result: yes configure:16146: checking sys/times.h usability configure:16146: gcc -std=gnu99 -c -g -O2 conftest.c >&5 configure:16146: $? = 0 configure:16146: result: yes configure:16146: checking sys/times.h presence configure:16146: gcc -E conftest.c configure:16146: $? = 0 configure:16146: result: yes configure:16146: checking for sys/times.h configure:16146: result: yes configure:16158: checking malloc.h usability configure:16158: gcc -std=gnu99 -c -g -O2 conftest.c >&5 configure:16158: $? = 0 configure:16158: result: yes configure:16158: checking malloc.h presence configure:16158: gcc -E conftest.c configure:16158: $? = 0 configure:16158: result: yes configure:16158: checking for malloc.h configure:16158: result: yes configure:16170: checking glob.h usability configure:16170: gcc -std=gnu99 -c -g -O2 conftest.c >&5 configure:16170: $? = 0 configure:16170: result: yes configure:16170: checking glob.h presence configure:16170: gcc -E conftest.c configure:16170: $? = 0 configure:16170: result: yes configure:16170: checking for glob.h configure:16170: result: yes configure:16184: checking for mallinfo configure:16184: gcc -std=gnu99 -o conftest.exe -g -O2 conftest.c >&5 configure:16184: $? = 0 configure:16184: result: yes configure:16195: checking whether isnan is declared configure:16195: gcc -std=gnu99 -c -g -O2 conftest.c >&5 configure:16195: $? = 0 configure:16195: result: yes configure:16210: checking for getrlimit configure:16210: gcc -std=gnu99 -o conftest.exe -g -O2 conftest.c >&5 configure:16210: $? = 0 configure:16210: result: yes configure:16221: checking for gethostname configure:16221: gcc -std=gnu99 -o conftest.exe -g -O2 conftest.c >&5 configure:16221: $? = 0 configure:16221: result: yes configure:16289: checking for floor in -lm configure:16314: gcc -std=gnu99 -o conftest.exe -g -O2 conftest.c -lm >&5 conftest.c:48:6: warning: conflicting types for built-in function 'floor' [enabled by default] char floor (); ^ configure:16314: $? = 0 configure:16323: result: yes configure:16336: checking for DATA support configure:16353: result: yes configure:16550: checking for the pthreads library -lpthreads configure:16588: gcc -std=gnu99 -o conftest.exe -g -O2 conftest.c -lpthreads -lm >&5 /usr/lib/gcc/i686-pc-cygwin/4.8.2/../../../../i686-pc-cygwin/bin/ld: cannot find -lpthreads collect2: error: ld returned 1 exit status configure:16588: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.6.3" | #define PACKAGE_STRING "cdo 1.6.3" | #define PACKAGE_BUGREPORT "http://code.zmaw.de/projects/cdo" | #define PACKAGE_URL "" | #define PACKAGE "cdo" | #define VERSION "1.6.3" | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | #define HAVE_STDLIB_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MMAP 1 | #define HAVE_STRUCT_STAT_ST_BLKSIZE 1 | #define HAVE_SYS_RESOURCE_H 1 | #define HAVE_SYS_TIMES_H 1 | #define HAVE_MALLOC_H 1 | #define HAVE_GLOB_H 1 | #define HAVE_MALLINFO 1 | #define HAVE_DECL_ISNAN 1 | #define HAVE_GETRLIMIT 1 | #define HAVE_GETHOSTNAME 1 | #define COMP_VERSION "gcc (GCC) 4.8.2" | #define USER_NAME "DELL" | #define HOST_NAME "NaLe" | #define SYSTEM_TYPE "i686-pc-cygwin" | #define HAVE_LIBM 1 | #define ENABLE_DATA 1 | /* end confdefs.h. */ | #include | static void routine(void* a) {a=0;} | static void* start_routine(void* a) {return a;} | int | main () | { | pthread_t th; pthread_attr_t attr; | pthread_create(&th,0,start_routine,0); | pthread_join(th, 0); | pthread_attr_init(&attr); | pthread_cleanup_push(routine, 0); | pthread_cleanup_pop(0); | ; | return 0; | } configure:16597: result: no configure:16495: checking whether pthreads work without any flags configure:16588: gcc -std=gnu99 -o conftest.exe -g -O2 conftest.c -lm >&5 configure:16588: $? = 0 configure:16597: result: yes configure:16616: checking for joinable pthread attribute configure:16631: gcc -std=gnu99 -o conftest.exe -g -O2 conftest.c -lm >&5 configure:16631: $? = 0 configure:16637: result: PTHREAD_CREATE_JOINABLE configure:16647: checking if more special flags are required for pthreads configure:16654: result: no configure:16975: checking zlib.h usability configure:16975: gcc -std=gnu99 -c -g -O2 conftest.c >&5 configure:16975: $? = 0 configure:16975: result: yes configure:16975: checking zlib.h presence configure:16975: gcc -E conftest.c configure:16975: $? = 0 configure:16975: result: yes configure:16975: checking for zlib.h configure:16975: result: yes configure:16985: checking for library containing deflate configure:17016: gcc -std=gnu99 -o conftest.exe -g -O2 conftest.c -lm >&5 /tmp/ccp3hOK2.o: In function `main': /cygdrive/e/setups/cdo_cygwin/cdo-1.6.3/conftest.c:56: undefined reference to `deflate' collect2: error: ld returned 1 exit status configure:17016: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.6.3" | #define PACKAGE_STRING "cdo 1.6.3" | #define PACKAGE_BUGREPORT "http://code.zmaw.de/projects/cdo" | #define PACKAGE_URL "" | #define PACKAGE "cdo" | #define VERSION "1.6.3" | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | #define HAVE_STDLIB_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MMAP 1 | #define HAVE_STRUCT_STAT_ST_BLKSIZE 1 | #define HAVE_SYS_RESOURCE_H 1 | #define HAVE_SYS_TIMES_H 1 | #define HAVE_MALLOC_H 1 | #define HAVE_GLOB_H 1 | #define HAVE_MALLINFO 1 | #define HAVE_DECL_ISNAN 1 | #define HAVE_GETRLIMIT 1 | #define HAVE_GETHOSTNAME 1 | #define COMP_VERSION "gcc (GCC) 4.8.2" | #define USER_NAME "DELL" | #define HOST_NAME "NaLe" | #define SYSTEM_TYPE "i686-pc-cygwin" | #define HAVE_LIBM 1 | #define ENABLE_DATA 1 | #define HAVE_LIBPTHREAD 1 | #define HAVE_ZLIB_H 1 | /* end confdefs.h. */ | | /* Override any GCC internal prototype to avoid an error. | Use char because int might match the return type of a GCC | builtin and then its argument prototype would still apply. */ | #ifdef __cplusplus | extern "C" | #endif | char deflate (); | int | main () | { | return deflate (); | ; | return 0; | } configure:17016: gcc -std=gnu99 -o conftest.exe -g -O2 conftest.c -lz -lm >&5 configure:17016: $? = 0 configure:17033: result: -lz configure:17223: checking for szlib library configure:17225: result: suppressed configure:17391: checking hdf5.h usability configure:17391: gcc -std=gnu99 -c -g -O2 -I/usr//include conftest.c >&5 conftest.c:79:18: fatal error: hdf5.h: No such file or directory #include ^ compilation terminated. configure:17391: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.6.3" | #define PACKAGE_STRING "cdo 1.6.3" | #define PACKAGE_BUGREPORT "http://code.zmaw.de/projects/cdo" | #define PACKAGE_URL "" | #define PACKAGE "cdo" | #define VERSION "1.6.3" | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | #define HAVE_STDLIB_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MMAP 1 | #define HAVE_STRUCT_STAT_ST_BLKSIZE 1 | #define HAVE_SYS_RESOURCE_H 1 | #define HAVE_SYS_TIMES_H 1 | #define HAVE_MALLOC_H 1 | #define HAVE_GLOB_H 1 | #define HAVE_MALLINFO 1 | #define HAVE_DECL_ISNAN 1 | #define HAVE_GETRLIMIT 1 | #define HAVE_GETHOSTNAME 1 | #define COMP_VERSION "gcc (GCC) 4.8.2" | #define USER_NAME "DELL" | #define HOST_NAME "NaLe" | #define SYSTEM_TYPE "i686-pc-cygwin" | #define HAVE_LIBM 1 | #define ENABLE_DATA 1 | #define HAVE_LIBPTHREAD 1 | #define HAVE_ZLIB_H 1 | #define HAVE_LIBZ 1 | /* end confdefs.h. */ | #include | #ifdef HAVE_SYS_TYPES_H | # include | #endif | #ifdef HAVE_SYS_STAT_H | # include | #endif | #ifdef STDC_HEADERS | # include | # include | #else | # ifdef HAVE_STDLIB_H | # include | # endif | #endif | #ifdef HAVE_STRING_H | # if !defined STDC_HEADERS && defined HAVE_MEMORY_H | # include | # endif | # include | #endif | #ifdef HAVE_STRINGS_H | # include | #endif | #ifdef HAVE_INTTYPES_H | # include | #endif | #ifdef HAVE_STDINT_H | # include | #endif | #ifdef HAVE_UNISTD_H | # include | #endif | #include configure:17391: result: no configure:17391: checking hdf5.h presence configure:17391: gcc -E -I/usr//include conftest.c conftest.c:46:18: fatal error: hdf5.h: No such file or directory #include ^ compilation terminated. configure:17391: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.6.3" | #define PACKAGE_STRING "cdo 1.6.3" | #define PACKAGE_BUGREPORT "http://code.zmaw.de/projects/cdo" | #define PACKAGE_URL "" | #define PACKAGE "cdo" | #define VERSION "1.6.3" | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | #define HAVE_STDLIB_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MMAP 1 | #define HAVE_STRUCT_STAT_ST_BLKSIZE 1 | #define HAVE_SYS_RESOURCE_H 1 | #define HAVE_SYS_TIMES_H 1 | #define HAVE_MALLOC_H 1 | #define HAVE_GLOB_H 1 | #define HAVE_MALLINFO 1 | #define HAVE_DECL_ISNAN 1 | #define HAVE_GETRLIMIT 1 | #define HAVE_GETHOSTNAME 1 | #define COMP_VERSION "gcc (GCC) 4.8.2" | #define USER_NAME "DELL" | #define HOST_NAME "NaLe" | #define SYSTEM_TYPE "i686-pc-cygwin" | #define HAVE_LIBM 1 | #define ENABLE_DATA 1 | #define HAVE_LIBPTHREAD 1 | #define HAVE_ZLIB_H 1 | #define HAVE_LIBZ 1 | /* end confdefs.h. */ | #include configure:17391: result: no configure:17391: checking for hdf5.h configure:17391: result: no configure:17401: checking for library containing H5Fopen configure:17432: gcc -std=gnu99 -o conftest.exe -g -O2 -I/usr//include -L/usr//lib conftest.c -lz -lm >&5 /tmp/ccnU3NWQ.o: In function `main': /cygdrive/e/setups/cdo_cygwin/cdo-1.6.3/conftest.c:57: undefined reference to `H5Fopen' collect2: error: ld returned 1 exit status configure:17432: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.6.3" | #define PACKAGE_STRING "cdo 1.6.3" | #define PACKAGE_BUGREPORT "http://code.zmaw.de/projects/cdo" | #define PACKAGE_URL "" | #define PACKAGE "cdo" | #define VERSION "1.6.3" | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | #define HAVE_STDLIB_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MMAP 1 | #define HAVE_STRUCT_STAT_ST_BLKSIZE 1 | #define HAVE_SYS_RESOURCE_H 1 | #define HAVE_SYS_TIMES_H 1 | #define HAVE_MALLOC_H 1 | #define HAVE_GLOB_H 1 | #define HAVE_MALLINFO 1 | #define HAVE_DECL_ISNAN 1 | #define HAVE_GETRLIMIT 1 | #define HAVE_GETHOSTNAME 1 | #define COMP_VERSION "gcc (GCC) 4.8.2" | #define USER_NAME "DELL" | #define HOST_NAME "NaLe" | #define SYSTEM_TYPE "i686-pc-cygwin" | #define HAVE_LIBM 1 | #define ENABLE_DATA 1 | #define HAVE_LIBPTHREAD 1 | #define HAVE_ZLIB_H 1 | #define HAVE_LIBZ 1 | /* end confdefs.h. */ | | /* Override any GCC internal prototype to avoid an error. | Use char because int might match the return type of a GCC | builtin and then its argument prototype would still apply. */ | #ifdef __cplusplus | extern "C" | #endif | char H5Fopen (); | int | main () | { | return H5Fopen (); | ; | return 0; | } configure:17432: gcc -std=gnu99 -o conftest.exe -g -O2 -I/usr//include -L/usr//lib conftest.c -lhdf5 -lz -lm >&5 /usr/lib/gcc/i686-pc-cygwin/4.8.2/../../../../i686-pc-cygwin/bin/ld: cannot find -lhdf5 collect2: error: ld returned 1 exit status configure:17432: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.6.3" | #define PACKAGE_STRING "cdo 1.6.3" | #define PACKAGE_BUGREPORT "http://code.zmaw.de/projects/cdo" | #define PACKAGE_URL "" | #define PACKAGE "cdo" | #define VERSION "1.6.3" | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | #define HAVE_STDLIB_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MMAP 1 | #define HAVE_STRUCT_STAT_ST_BLKSIZE 1 | #define HAVE_SYS_RESOURCE_H 1 | #define HAVE_SYS_TIMES_H 1 | #define HAVE_MALLOC_H 1 | #define HAVE_GLOB_H 1 | #define HAVE_MALLINFO 1 | #define HAVE_DECL_ISNAN 1 | #define HAVE_GETRLIMIT 1 | #define HAVE_GETHOSTNAME 1 | #define COMP_VERSION "gcc (GCC) 4.8.2" | #define USER_NAME "DELL" | #define HOST_NAME "NaLe" | #define SYSTEM_TYPE "i686-pc-cygwin" | #define HAVE_LIBM 1 | #define ENABLE_DATA 1 | #define HAVE_LIBPTHREAD 1 | #define HAVE_ZLIB_H 1 | #define HAVE_LIBZ 1 | /* end confdefs.h. */ | | /* Override any GCC internal prototype to avoid an error. | Use char because int might match the return type of a GCC | builtin and then its argument prototype would still apply. */ | #ifdef __cplusplus | extern "C" | #endif | char H5Fopen (); | int | main () | { | return H5Fopen (); | ; | return 0; | } configure:17449: result: no configure:17458: error: Cannot link to hdf5! It is required for netCDF4. ## ---------------- ## ## Cache variables. ## ## ---------------- ## ac_cv_build=i686-pc-cygwin ac_cv_c_compiler_gnu=yes ac_cv_cxx_compiler_gnu=yes ac_cv_env_CCC_set= ac_cv_env_CCC_value= ac_cv_env_CC_set= ac_cv_env_CC_value= ac_cv_env_CFLAGS_set= ac_cv_env_CFLAGS_value= ac_cv_env_CPPFLAGS_set= ac_cv_env_CPPFLAGS_value= ac_cv_env_CPP_set= ac_cv_env_CPP_value= ac_cv_env_CXXCPP_set= ac_cv_env_CXXCPP_value= ac_cv_env_CXXFLAGS_set= ac_cv_env_CXXFLAGS_value= ac_cv_env_CXX_set= ac_cv_env_CXX_value= ac_cv_env_LDFLAGS_set= ac_cv_env_LDFLAGS_value= ac_cv_env_LIBS_set= ac_cv_env_LIBS_value= ac_cv_env_build_alias_set= ac_cv_env_build_alias_value= ac_cv_env_host_alias_set= ac_cv_env_host_alias_value= ac_cv_env_target_alias_set= ac_cv_env_target_alias_value= ac_cv_exeext=.exe ac_cv_func_gethostname=yes ac_cv_func_getpagesize=yes ac_cv_func_getrlimit=yes ac_cv_func_mallinfo=yes ac_cv_func_mmap_fixed_mapped=yes ac_cv_have_decl_isnan=yes ac_cv_header_dlfcn_h=yes ac_cv_header_glob_h=yes ac_cv_header_hdf5_h=no ac_cv_header_inttypes_h=yes ac_cv_header_malloc_h=yes ac_cv_header_memory_h=yes ac_cv_header_stdc=yes ac_cv_header_stdint_h=yes ac_cv_header_stdlib_h=yes ac_cv_header_string_h=yes ac_cv_header_strings_h=yes ac_cv_header_sys_param_h=yes ac_cv_header_sys_resource_h=yes ac_cv_header_sys_stat_h=yes ac_cv_header_sys_times_h=yes ac_cv_header_sys_types_h=yes ac_cv_header_unistd_h=yes ac_cv_header_zlib_h=yes ac_cv_host=i686-pc-cygwin ac_cv_lib_m_floor=yes ac_cv_lib_malloc_malloc=no ac_cv_member_struct_stat_st_blksize=yes ac_cv_objext=o ac_cv_path_EGREP='/usr/bin/grep -E' ac_cv_path_FGREP='/usr/bin/grep -F' ac_cv_path_GREP=/usr/bin/grep ac_cv_path_SED=/usr/bin/sed ac_cv_path_install='/usr/bin/install -c' ac_cv_path_mkdir=/usr/bin/mkdir ac_cv_prog_AWK=gawk ac_cv_prog_CPP='gcc -E' ac_cv_prog_CXXCPP='g++ -E' ac_cv_prog_ac_ct_AR=ar ac_cv_prog_ac_ct_AS=as ac_cv_prog_ac_ct_CC=gcc ac_cv_prog_ac_ct_CXX=g++ ac_cv_prog_ac_ct_DLLTOOL=dlltool ac_cv_prog_ac_ct_LD=/usr/i686-pc-cygwin/bin/ld.exe ac_cv_prog_ac_ct_NM='/usr/bin/nm -B' ac_cv_prog_ac_ct_OBJDUMP=objdump ac_cv_prog_ac_ct_RANLIB=ranlib ac_cv_prog_ac_ct_STRIP=strip ac_cv_prog_cc_c89= ac_cv_prog_cc_c99=-std=gnu99 ac_cv_prog_cc_g=yes ac_cv_prog_cc_gcc_c_o=yes ac_cv_prog_cxx_g=yes ac_cv_prog_make_make_set=yes ac_cv_search_H5Fopen=no ac_cv_search_deflate=-lz ac_cv_sys_file_offset_bits=no ac_cv_sys_largefile_CC=no am_cv_CC_dependencies_compiler_type=gcc3 am_cv_CXX_dependencies_compiler_type=gcc3 lt_cv_archive_cmds_need_lc=yes lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL' lt_cv_file_magic_cmd=func_win32_libid lt_cv_file_magic_test_file= lt_cv_ld_reload_flag=-r lt_cv_nm_interface='BSD nm' lt_cv_objdir=.libs lt_cv_path_LD=/usr/i686-pc-cygwin/bin/ld.exe lt_cv_path_LDCXX=/usr/i686-pc-cygwin/bin/ld.exe lt_cv_path_NM='/usr/bin/nm -B' lt_cv_prog_compiler_c_o=yes lt_cv_prog_compiler_c_o_CXX=yes lt_cv_prog_compiler_pic_works=yes lt_cv_prog_compiler_pic_works_CXX=yes lt_cv_prog_compiler_rtti_exceptions=no lt_cv_prog_compiler_static_works=yes lt_cv_prog_compiler_static_works_CXX=yes lt_cv_prog_gnu_ld=yes lt_cv_prog_gnu_ldcxx=yes lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*_\([_A-Za-z][_A-Za-z0-9]*\)$/\1 _\2 \2/p'\''' lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '\''s/^: \([^ ]*\) $/ {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/ {"\2", (void *) \&\2},/p'\''' lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='sed -n -e '\''s/^: \([^ ]*\) $/ {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \(lib[^ ]*\)$/ {"\2", (void *) \&\2},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/ {"lib\2", (void *) \&\2},/p'\''' lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^T .* \(.*\)$/extern int \1();/p'\'' -e '\''s/^[ABCDGIRSTW]* .* \(.*\)$/extern char \1;/p'\''' lt_cv_sys_max_cmd_len=8192 ## ----------------- ## ## Output variables. ## ## ----------------- ## ACLOCAL='${SHELL} /cygdrive/e/setups/cdo_cygwin/cdo-1.6.3/config/missing --run aclocal-1.11' AMDEPBACKSLASH='\' AMDEP_FALSE='#' AMDEP_TRUE='' AMTAR='$${TAR-tar}' AR='ar' AS='as' AUTOCONF='${SHELL} /cygdrive/e/setups/cdo_cygwin/cdo-1.6.3/config/missing --run autoconf' AUTOHEADER='${SHELL} /cygdrive/e/setups/cdo_cygwin/cdo-1.6.3/config/missing --run autoheader' AUTOMAKE='${SHELL} /cygdrive/e/setups/cdo_cygwin/cdo-1.6.3/config/missing --run automake-1.11' AWK='gawk' CC='gcc -std=gnu99' CCDEPMODE='depmode=gcc3' CFLAGS='-g -O2 ' CLDFLAGS='' CLIBS='' CPP='gcc -E' CPPFLAGS='-I/usr//include ' CURL_INCLUDE='' CURL_LDFLAGS='' CXX='g++' CXXCPP='g++ -E' CXXDEPMODE='depmode=gcc3' CXXFLAGS='-g -O2' CYGPATH_W='cygpath -w' DEFS='' DEPDIR='.deps' DLLTOOL='dlltool' DSYMUTIL='' DUMPBIN='' ECHO_C='' ECHO_N='-n' ECHO_T='' EGREP='/usr/bin/grep -E' ENABLE_ALL_STATIC_FALSE='' ENABLE_ALL_STATIC_TRUE='' ENABLE_CDI_LIB='' ENABLE_CDI_LIB_FALSE='' ENABLE_CDI_LIB_TRUE='' ENABLE_CGRIBEX='' ENABLE_DATA='yes' ENABLE_EXTRA='' ENABLE_GRIB='' ENABLE_IEG='' ENABLE_MAGICS_FALSE='' ENABLE_MAGICS_TRUE='' ENABLE_SERVICE='' EXEEXT='.exe' FCFLAGS='' FGREP='/usr/bin/grep -F' GREP='/usr/bin/grep' GRIB_API_INCLUDE='' GRIB_API_LIBS='' HDF5_INCLUDE='' HDF5_LIBS='' HDF5_ROOT='/usr/' HOST_NAME='NaLe' INCLUDES='' INSTALL_DATA='${INSTALL} -m 644' INSTALL_PROGRAM='${INSTALL}' INSTALL_SCRIPT='${INSTALL}' INSTALL_STRIP_PROGRAM='$(install_sh) -c -s' JASPER_LIBS='' LD='/usr/i686-pc-cygwin/bin/ld.exe' LDFLAGS='-L/usr//lib ' LIBOBJS='' LIBS='-lz -lm ' LIBTOOL='$(SHELL) $(top_builddir)/libtool' LIPO='' LN_S='ln -s' LTLIBOBJS='' MAGICS_INCLUDE='' MAGICS_LIBS='' MAGICS_ROOT='' MAINT='#' MAINTAINER_MODE_FALSE='' MAINTAINER_MODE_TRUE='#' MAKEINFO='${SHELL} /cygdrive/e/setups/cdo_cygwin/cdo-1.6.3/config/missing --run makeinfo' MKDIR_P='/usr/bin/mkdir -p' NC_CONFIG='' NETCDF_INCLUDE='' NETCDF_LIBS='' NETCDF_ROOT='' NM='/usr/bin/nm -B' NMEDIT='' OBJDUMP='objdump' OBJEXT='o' OTOOL64='' OTOOL='' PACKAGE='cdo' PACKAGE_BUGREPORT='http://code.zmaw.de/projects/cdo' PACKAGE_NAME='cdo' PACKAGE_STRING='cdo 1.6.3' PACKAGE_TARNAME='cdo' PACKAGE_URL='' PACKAGE_VERSION='1.6.3' PATH_SEPARATOR=':' PROJ_INCLUDE='' PROJ_LDFLAGS='' PTHREAD_CC='gcc -std=gnu99' PTHREAD_CFLAGS='' PTHREAD_LIBS='' RANLIB='ranlib' SED='/usr/bin/sed' SET_MAKE='' SHELL='/bin/sh' STRIP='strip' SYSTEM_TYPE='i686-pc-cygwin' SZLIB_INCLUDE='' SZLIB_LIBS='' THREADS_INCLUDE='' THREADS_LIBS='' UDUNITS_INCLUDE='' UDUNITS_LDFLAGS='' USER_NAME='DELL' VERSION='1.6.3' XML2_LIBS='' ZLIB_INCLUDE='' ZLIB_LIBS=' -lz' ac_ct_CC='gcc' ac_ct_CXX='g++' ac_ct_DUMPBIN='' am__EXEEXT_FALSE='' am__EXEEXT_TRUE='' am__fastdepCC_FALSE='#' am__fastdepCC_TRUE='' am__fastdepCXX_FALSE='#' am__fastdepCXX_TRUE='' am__include='include' am__isrc='' am__leading_dot='.' am__nodep='_no' am__quote='' am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -' ax_pthread_config='' bindir='${exec_prefix}/bin' build='i686-pc-cygwin' build_alias='' build_cpu='i686' build_os='cygwin' build_vendor='pc' datadir='${datarootdir}' datarootdir='${prefix}/share' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' dvidir='${docdir}' exec_prefix='NONE' host='i686-pc-cygwin' host_alias='' host_cpu='i686' host_os='cygwin' host_vendor='pc' htmldir='${docdir}' includedir='${prefix}/include' infodir='${datarootdir}/info' install_sh='${SHELL} /cygdrive/e/setups/cdo_cygwin/cdo-1.6.3/config/install-sh' libdir='${exec_prefix}/lib' libexecdir='${exec_prefix}/libexec' localedir='${datarootdir}/locale' localstatedir='${prefix}/var' mandir='${datarootdir}/man' mkdir_p='/usr/bin/mkdir -p' oldincludedir='/usr/include' pdfdir='${docdir}' prefix='NONE' program_transform_name='s,x,x,' psdir='${docdir}' sbindir='${exec_prefix}/sbin' sharedstatedir='${prefix}/com' subdirs='' sysconfdir='${prefix}/etc' target_alias='' ## ----------- ## ## confdefs.h. ## ## ----------- ## /* confdefs.h */ #define PACKAGE_NAME "cdo" #define PACKAGE_TARNAME "cdo" #define PACKAGE_VERSION "1.6.3" #define PACKAGE_STRING "cdo 1.6.3" #define PACKAGE_BUGREPORT "http://code.zmaw.de/projects/cdo" #define PACKAGE_URL "" #define PACKAGE "cdo" #define VERSION "1.6.3" #define STDC_HEADERS 1 #define HAVE_SYS_TYPES_H 1 #define HAVE_SYS_STAT_H 1 #define HAVE_STDLIB_H 1 #define HAVE_STRING_H 1 #define HAVE_MEMORY_H 1 #define HAVE_STRINGS_H 1 #define HAVE_INTTYPES_H 1 #define HAVE_STDINT_H 1 #define HAVE_UNISTD_H 1 #define HAVE_DLFCN_H 1 #define LT_OBJDIR ".libs/" #define HAVE_STDLIB_H 1 #define HAVE_UNISTD_H 1 #define HAVE_SYS_PARAM_H 1 #define HAVE_GETPAGESIZE 1 #define HAVE_MMAP 1 #define HAVE_STRUCT_STAT_ST_BLKSIZE 1 #define HAVE_SYS_RESOURCE_H 1 #define HAVE_SYS_TIMES_H 1 #define HAVE_MALLOC_H 1 #define HAVE_GLOB_H 1 #define HAVE_MALLINFO 1 #define HAVE_DECL_ISNAN 1 #define HAVE_GETRLIMIT 1 #define HAVE_GETHOSTNAME 1 #define COMP_VERSION "gcc (GCC) 4.8.2" #define USER_NAME "DELL" #define HOST_NAME "NaLe" #define SYSTEM_TYPE "i686-pc-cygwin" #define HAVE_LIBM 1 #define ENABLE_DATA 1 #define HAVE_LIBPTHREAD 1 #define HAVE_ZLIB_H 1 #define HAVE_LIBZ 1 configure: exit 1