Closed GeraldCNelson closed 3 years ago
moffat
commented
4 years ago Hi @GeraldCNelson,
Did you run
brew tap moffat/sciencebits
before running the install step? Did you pass any other options? what version of homebrew do you have?
You can check your vision of homebrew with brew -v
Cheers, Carlos
GeraldCNelson
commented
4 years ago I did the brew tap process first. No other options. Just copy and pasted from your website.
Brew -v returns
Homebrew 2.2.13-176-g223b66b
Homebrew/homebrew-core (git revision fe68b96; last commit 2020-04-27)
Homebrew/homebrew-cask (git revision 798e5; last commit 2020-04-27)
Gerald C. Nelson Professor Emeritus, UIUC +1 217-390-7888 (cell) +1 970-639-2079 (land line) Skype: jerrynelson http://bit.ly/1arho7d
From: Carlos Moffat notifications@github.com Reply-To: moffat/homebrew-sciencebits reply@reply.github.com Date: Monday, April 27, 2020 at 12:02 PM To: moffat/homebrew-sciencebits homebrew-sciencebits@noreply.github.com Cc: Gerald Nelson nelson.gerald.c@gmail.com, Mention mention@noreply.github.com Subject: Re: [moffat/homebrew-sciencebits] mac installation from home-brew fails (#1)
Hi @GeraldCNelsonhttps://github.com/GeraldCNelson,
Did you run
brew tap moffat/sciencebits
before running the install step? Did you pass any other options? what version of homebrew do you have?
You can check your vision of homebrew with brew -v
Cheers, Carlos
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/moffat/homebrew-sciencebits/issues/1#issuecomment-620142508, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AB6UJMVPNVB3CF6JU2KOLB3ROXCFHANCNFSM4MSEGD6A.
moffat
commented
4 years ago @GeraldCNelson,
Can you send me the files in the log directory? /Users/gcn/Library/Logs/Homebrew/cdo/
Thanks.
GeraldCNelson
commented
4 years ago I have attached the config.log file.
I should add a couple of notes. I already have a version of cdo installed. The results from cdo –version are
Climate Data Operators version 1.9.8 (https://mpimet.mpg.de/cdo)
System: x86_64-apple-darwin19.3.0
CXX Compiler: /usr/bin/clang++ -std=gnu++11 -pipe -Os -stdlib=libc++ -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk -arch x86_64 -D_THREAD_SAFE -pthread
CXX version : unknown
C Compiler: /usr/bin/clang -pipe -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk -arch x86_64 -D_THREAD_SAFE -pthread -D_THREAD_SAFE -D_THREAD_SAFE -pthread
C version : unknown
F77 Compiler: -pipe -Os -m64
Features: 32GB 12threads C++11 DATA PTHREADS HDF5 NC4/HDF5 OPeNDAP UDUNITS2 PROJ CURL FFTW3 SSE4_1
Libraries: HDF5/1.10.6 proj/5.2.0 curl/7.68.0
Filetypes: srv ext ieg grb1 grb2 nc1 nc2 nc4 nc4c nc5
CDI library version : 1.9.8ecCodes library version : 2.16.0
NetCDF library version : 4.7.3 of Jan 7 2020 07:00:01 $
hdf5 library version : 1.10.6
exse library version : 1.4.1
FILE library version : 1.8.3I’m trying to run cdo from R via the system command. Compound commands fail. And I can’t get the -z operation to work. Happy to send the R code if it is of interest. All I’m trying to do is convert CMIP6 data (the ISIMIP version) units to something mere mortals are interested in degrees C instead of Kelvin and precip in terms of mm rather than kgs. I can do all of this with the raster command but was hoping cdo would be quicker.
Gerald C. Nelson Professor Emeritus, UIUC +1 217-390-7888 (cell) +1 970-639-2079 (land line) Skype: jerrynelson http://bit.ly/1arho7d
From: Carlos Moffat notifications@github.com Reply-To: moffat/homebrew-sciencebits reply@reply.github.com Date: Monday, April 27, 2020 at 12:22 PM To: moffat/homebrew-sciencebits homebrew-sciencebits@noreply.github.com Cc: Gerald Nelson nelson.gerald.c@gmail.com, Mention mention@noreply.github.com Subject: Re: [moffat/homebrew-sciencebits] mac installation from home-brew fails (#1)
@GeraldCNelsonhttps://github.com/GeraldCNelson,
Can you send me the files in the log directory? /Users/gcn/Library/Logs/Homebrew/cdo/
Thanks.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/moffat/homebrew-sciencebits/issues/1#issuecomment-620152794, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AB6UJMQH2EJQ2AAWD24U3JDROXEP5ANCNFSM4MSEGD6A.
moffat
commented
4 years ago Hi @GeraldCNelson
Thanks for this info. I can't reproduce this problem, but my guess is that you have a mix of homebrew and non-homebrew libraries/compilers and it's compiling against the wrong thing. It's best to make sure all dependencies (hdf5, netcdf) installed in your system are the brew ones.
I don't see the config.log file.
I'm not an R user so I can't help with that part of the problem, I'm afraid.
Best
GeraldCNelson
commented
4 years ago I’ll work on getting the various dependencies in home brew. I have copied the log file below.
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 1.9.8, which was generated by GNU Autoconf 2.69. Invocation command line was
$ ./configure --disable-debug --disable-dependency-tracking --prefix=/usr/local/Cellar/cdo/1.9.8_1 LIBS=-lhdf5 --with-netcdf=/usr/local/opt/netcdf --with-hdf5=/usr/local/opt/hdf5 --with-szlib=/usr/local/opt/szip
hostname = GCN-MacBook-Pro-7.local uname -m = x86_64 uname -r = 19.4.0 uname -s = Darwin uname -v = Darwin Kernel Version 19.4.0: Wed Mar 4 22:28:40 PST 2020; root:xnu-6153.101.6~15/RELEASE_X86_64
/usr/bin/uname -p = i386 /bin/uname -X = unknown
/bin/arch = unknown /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown /usr/bin/hostinfo = Mach kernel version: Darwin Kernel Version 19.4.0: Wed Mar 4 22:28:40 PST 2020; root:xnu-6153.101.6~15/RELEASE_X86_64 Kernel configured for up to 12 processors. 6 processors are physically available. 12 processors are logically available. Processor type: x86_64h (Intel x86-64h Haswell) Processors active: 0 1 2 3 4 5 6 7 8 9 10 11 Primary memory available: 32.00 gigabytes Default processor set: 467 tasks, 2078 threads, 12 processors Load average: 1.84, Mach factor: 10.15 /bin/machine = unknown /usr/bin/oslevel = unknown /bin/universe = unknown
PATH: /usr/local/Homebrew/Library/Homebrew/shims/mac/super PATH: /usr/local/opt/gcc/bin PATH: /usr/local/opt/hdf5/bin PATH: /usr/local/opt/netcdf/bin PATH: /usr/bin PATH: /bin PATH: /usr/sbin PATH: /sbin
configure:2879: checking build system type configure:2893: result: x86_64-apple-darwin19.4.0 configure:2913: checking host system type configure:2926: result: x86_64-apple-darwin19.4.0 configure:2965: checking for a BSD-compatible install configure:3033: result: /usr/bin/install -c configure:3044: checking whether build environment is sane configure:3099: result: yes configure:3250: checking for a thread-safe mkdir -p configure:3289: result: config/install-sh -c -d configure:3296: checking for gawk configure:3326: result: no configure:3296: checking for mawk configure:3326: result: no configure:3296: checking for nawk configure:3326: result: no configure:3296: checking for awk configure:3312: found /usr/bin/awk configure:3323: result: awk configure:3334: checking whether make sets $(MAKE) configure:3356: result: yes configure:3385: checking whether make supports nested variables configure:3402: result: yes configure:3531: checking whether to enable maintainer-specific portions of Makefiles configure:3540: result: no configure:3559: checking whether make supports the include directive configure:3574: make -f confmf.GNU && cat confinc.out this is the amdoit target configure:3577: $? = 0 configure:3596: result: yes (GNU style) configure:3666: checking for gcc configure:3693: result: clang configure:3922: checking for C compiler version configure:3931: clang --version >&5 Apple clang version 11.0.3 (clang-1103.0.32.59) Target: x86_64-apple-darwin19.4.0 Thread model: posix InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin configure:3942: $? = 0 configure:3931: clang -v >&5 Apple clang version 11.0.3 (clang-1103.0.32.59) Target: x86_64-apple-darwin19.4.0 Thread model: posix InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin configure:3942: $? = 0 configure:3931: clang -V >&5 clang: error: unsupported option '-V -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk' configure:3942: $? = 1 configure:3931: clang -qversion >&5 clang: error: unknown argument '-qversion'; did you mean '--version'? configure:3942: $? = 1 configure:3962: checking whether the C compiler works configure:3984: clang conftest.c -lhdf5 >&5 configure:3988: $? = 0 configure:4036: result: yes configure:4039: checking for C compiler default output file name configure:4041: result: a.out configure:4047: checking for suffix of executables configure:4054: clang -o conftest conftest.c -lhdf5 >&5 configure:4058: $? = 0 configure:4080: result: configure:4102: checking whether we are cross compiling configure:4110: clang -o conftest conftest.c -lhdf5 >&5 configure:4114: $? = 0 configure:4121: ./conftest configure:4125: $? = 0 configure:4140: result: no configure:4145: checking for suffix of object files configure:4167: clang -c conftest.c >&5 configure:4171: $? = 0 configure:4192: result: o configure:4196: checking whether we are using the GNU C compiler configure:4215: clang -c conftest.c >&5 configure:4215: $? = 0 configure:4224: result: yes configure:4233: checking whether clang accepts -g configure:4253: clang -c -g conftest.c >&5 configure:4253: $? = 0 configure:4294: result: yes configure:4311: checking for clang option to accept ISO C89 configure:4374: clang -c -g -O2 conftest.c >&5 configure:4374: $? = 0 configure:4387: result: none needed configure:4412: checking whether clang understands -c and -o together configure:4434: clang -c conftest.c -o conftest2.o configure:4437: $? = 0 configure:4434: clang -c conftest.c -o conftest2.o configure:4437: $? = 0 configure:4449: result: yes configure:4468: checking dependency style of clang configure:4579: result: none configure:4644: checking for ar configure:4660: found /usr/bin/ar configure:4671: result: ar configure:4697: checking the archiver (ar) interface configure:4713: clang -c -g -O2 conftest.c >&5 configure:4713: $? = 0 configure:4715: ar cru libconftest.a conftest.o >&5 configure:4718: $? = 0 configure:4746: result: ar configure:4767: setting up libtool configure:4815: checking how to print strings configure:4842: result: printf configure:4863: checking for a sed that does not truncate output configure:4927: result: /usr/local/Homebrew/Library/Homebrew/shims/mac/super/sed configure:4945: checking for grep that handles long lines and -e configure:5003: result: /usr/bin/grep configure:5008: checking for egrep configure:5070: result: /usr/bin/grep -E configure:5075: checking for fgrep configure:5137: result: /usr/bin/grep -F configure:5172: checking for ld used by clang configure:5239: result: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld configure:5246: checking if the linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) is GNU ld configure:5261: result: no configure:5273: checking for BSD- or MS-compatible name lister (nm) configure:5327: result: /usr/bin/nm -B configure:5457: checking the name lister (/usr/bin/nm -B) interface configure:5464: clang -c -g -O2 conftest.c >&5 configure:5467: /usr/bin/nm -B "conftest.o" configure:5470: output 00000000000001e0 S _some_variable configure:5477: result: BSD nm configure:5480: checking whether ln -s works configure:5484: result: yes configure:5492: checking the maximum length of command line arguments configure:5623: result: 196608 configure:5671: checking how to convert x86_64-apple-darwin19.4.0 file names to x86_64-apple-darwin19.4.0 format configure:5711: result: func_convert_file_noop configure:5718: checking how to convert x86_64-apple-darwin19.4.0 file names to toolchain format configure:5738: result: func_convert_file_noop configure:5745: checking for /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld option to reload object files configure:5752: result: -r configure:5826: checking for objdump configure:5842: found /usr/bin/objdump configure:5853: result: objdump configure:5885: checking how to recognize dependent libraries configure:6085: result: pass_all configure:6170: checking for dlltool configure:6200: result: no configure:6230: checking how to associate runtime and link libraries configure:6257: result: printf %s\n configure:6381: checking for archiver @FILE support configure:6398: clang -c -g -O2 conftest.c >&5 configure:6398: $? = 0 configure:6401: ar cru libconftest.a @conftest.lst >&5 ar: @conftest.lst: No such file or directory configure:6404: $? = 1 configure:6424: result: no configure:6482: checking for strip configure:6498: found /usr/bin/strip configure:6509: result: strip configure:6581: checking for ranlib configure:6597: found /usr/bin/ranlib configure:6608: result: ranlib configure:6710: checking command to parse /usr/bin/nm -B output from clang object configure:6863: clang -c -g -O2 conftest.c >&5 configure:6866: $? = 0 configure:6870: /usr/bin/nm -B conftest.o | sed -n -e 's/^.[ ]([BCDEGRST][BCDEGRST])[ ][ ]([_A-Za-z][_A-Za-z0-9])$/\1 \2 \2/p' | sed '/ gnu_lto/d' > conftest.nm configure:6873: $? = 0 cannot find nm_testvar in conftest.nm configure:6863: clang -c -g -O2 conftest.c >&5 configure:6866: $? = 0 configure:6870: /usr/bin/nm -B conftest.o | sed -n -e 's/^.[ ]([BCDEGRST][BCDEGRST])[ ][ ]*([_A-Za-z][A-Za-z0-9]*)$/\1 \2 \2/p' | sed '/ __gnu_lto/d' > conftest.nm configure:6873: $? = 0 configure:6939: clang -o conftest -g -O2 conftest.c conftstm.o >&5 warning: (x86_64) could not find object file symbol for symbol _main configure:6942: $? = 0 configure:6980: result: ok configure:7027: checking for sysroot configure:7057: result: no configure:7064: checking for a working dd configure:7102: result: /bin/dd configure:7106: checking how to truncate binary pipes configure:7121: result: /bin/dd bs=4096 count=1 configure:7450: checking for mt configure:7480: result: no configure:7500: checking if : is a manifest tool configure:7506: : '-?' configure:7514: result: no configure:7570: checking for dsymutil configure:7586: found /usr/bin/dsymutil configure:7597: result: dsymutil configure:7662: checking for nmedit configure:7678: found /usr/bin/nmedit configure:7689: result: nmedit configure:7754: checking for lipo configure:7770: found /usr/bin/lipo configure:7781: result: lipo configure:7846: checking for otool configure:7862: found /usr/bin/otool configure:7873: result: otool configure:7938: checking for otool64 configure:7968: result: no configure:8013: checking for -single_module linker flag clang -g -O2 -o libconftest.dylib -dynamiclib -Wl,-single_module conftest.c configure:8046: result: yes configure:8049: checking for -exported_symbols_list linker flag configure:8069: clang -o conftest -g -O2 -Wl,-exported_symbols_list,conftest.sym conftest.c -lhdf5 >&5 configure:8069: $? = 0 configure:8079: result: yes configure:8082: checking for -force_load linker flag clang -g -O2 -c -o conftest.o conftest.c ar cru libconftest.a conftest.o ranlib libconftest.a clang -g -O2 -o conftest conftest.c -Wl,-force_load,./libconftest.a configure:8114: result: yes configure:8191: checking how to run the C preprocessor configure:8222: clang -E conftest.c configure:8222: $? = 0 configure:8236: clang -E conftest.c conftest.c:12:10: fatal error: 'ac_nonexistent.h' file not found
^~~~~~~~~~~~~~~~~~1 error generated.
configure:8236: $? = 1
configure: failed program was:
| / confdefs.h /
| #define PACKAGE_NAME "cdo"
| #define PACKAGE_TARNAME "cdo"
| #define PACKAGE_VERSION "1.9.8"
| #define PACKAGE_STRING "cdo 1.9.8"
| #define PACKAGE_BUGREPORT "https://mpimet.mpg.de/cdo"
| #define PACKAGE_URL ""
| #define CDO "1.9.8"
| #define PACKAGE "cdo"
| #define VERSION "1.9.8"
| / end confdefs.h. /
| #include
^~~~~~~~~~~~~~~~~~1 error generated.
configure:8295: $? = 1
configure: failed program was:
| / confdefs.h /
| #define PACKAGE_NAME "cdo"
| #define PACKAGE_TARNAME "cdo"
| #define PACKAGE_VERSION "1.9.8"
| #define PACKAGE_STRING "cdo 1.9.8"
| #define PACKAGE_BUGREPORT "https://mpimet.mpg.de/cdo"
| #define PACKAGE_URL ""
| #define CDO "1.9.8"
| #define PACKAGE "cdo"
| #define VERSION "1.9.8"
| / end confdefs.h. /
| #include
^~~~~~~~~~~~~~~~~~1 error generated.
configure:13674: $? = 1
configure: failed program was:
| / confdefs.h /
| #define PACKAGE_NAME "cdo"
| #define PACKAGE_TARNAME "cdo"
| #define PACKAGE_VERSION "1.9.8"
| #define PACKAGE_STRING "cdo 1.9.8"
| #define PACKAGE_BUGREPORT "https://mpimet.mpg.de/cdo"
| #define PACKAGE_URL ""
| #define CDO "1.9.8"
| #define PACKAGE "cdo"
| #define VERSION "1.9.8"
| #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
^~~~~~~~~~~~~~~~~~1 error generated.
configure:13733: $? = 1
configure: failed program was:
| / confdefs.h /
| #define PACKAGE_NAME "cdo"
| #define PACKAGE_TARNAME "cdo"
| #define PACKAGE_VERSION "1.9.8"
| #define PACKAGE_STRING "cdo 1.9.8"
| #define PACKAGE_BUGREPORT "https://mpimet.mpg.de/cdo"
| #define PACKAGE_URL ""
| #define CDO "1.9.8"
| #define PACKAGE "cdo"
| #define VERSION "1.9.8"
| #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:17056: $? = 0 configure:17045: gfortran -v >&5 Using built-in specs. COLLECT_GCC=gfortran COLLECT_LTO_WRAPPER=/usr/local/Cellar/gcc/9.3.0_1/libexec/gcc/x86_64-apple-darwin19/9.3.0/lto-wrapper Target: x86_64-apple-darwin19 Configured with: ../configure --build=x86_64-apple-darwin19 --prefix=/usr/local/Cellar/gcc/9.3.0_1 --libdir=/usr/local/Cellar/gcc/9.3.0_1/lib/gcc/9 --disable-nls --enable-checking=release --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-9 --with-gmp=/usr/local/opt/gmp --with-mpfr=/usr/local/opt/mpfr --with-mpc=/usr/local/opt/libmpc --with-isl=/usr/local/opt/isl --with-system-zlib --with-pkgversion='Homebrew GCC 9.3.0_1' --with-bugurl=https://github.com/Homebrew/homebrew-core/issues --disable-multilib --with-native-system-header-dir=/usr/include --with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk SED=/usr/bin/sed Thread model: posix gcc version 9.3.0 (Homebrew GCC 9.3.0_1) configure:17056: $? = 0 configure:17045: gfortran -V >&5 gfortran: error: unrecognized command line option '-V' gfortran: fatal error: no input files compilation terminated. configure:17056: $? = 1 configure:17045: gfortran -qversion >&5 gfortran: error: unrecognized command line option '-qversion'; did you mean '--version'? gfortran: fatal error: no input files compilation terminated. configure:17056: $? = 1 configure:17065: checking whether we are using the GNU Fortran 77 compiler configure:17078: gfortran -c conftest.F >&5 configure:17078: $? = 0 configure:17087: result: yes configure:17093: checking whether gfortran accepts -g configure:17104: gfortran -c -g conftest.f >&5 configure:17104: $? = 0 configure:17112: result: yes configure:17241: checking if libtool supports shared libraries configure:17243: result: yes configure:17246: checking whether to build shared libraries configure:17270: result: yes configure:17273: checking whether to build static libraries configure:17277: result: yes configure:17629: checking for gfortran option to produce PIC configure:17636: result: -fno-common configure:17644: checking if gfortran PIC flag -fno-common works configure:17662: gfortran -c -g -O2 -fno-common conftest.f >&5 configure:17666: $? = 0 configure:17679: result: yes configure:17702: checking if gfortran static flag -static works configure:17730: result: no configure:17742: checking if gfortran supports -c -o file.o configure:17763: gfortran -c -g -O2 -o out/conftest2.o conftest.f >&5 configure:17767: $? = 0 configure:17789: result: yes configure:17794: checking if gfortran supports -c -o file.o configure:17841: result: yes configure:17871: checking whether the gfortran linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries configure:19080: result: yes configure:19221: checking dynamic linker characteristics configure:19960: result: darwin19.4.0 dyld configure:20025: checking how to hardcode library paths into programs configure:20050: result: immediate configure:20083: checking for C/C++ restrict keyword configure:20108: clang -c -g -O2 conftest.c >&5 configure:20108: $? = 0 configure:20116: result: __restrict configure:20136: checking whether clang++ supports C++11 features by default configure:20430: clang++ -c -g -O2 conftest.cpp >&5 conftest.cpp:36:2: error: "This is not a C++11 compiler"
| ^ 1 error generated. configure:20430: $? = 1 configure: failed program was: | / confdefs.h / | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.9.8" | #define PACKAGE_STRING "cdo 1.9.8" | #define PACKAGE_BUGREPORT "https://mpimet.mpg.de/cdo" | #define PACKAGE_URL "" | #define CDO "1.9.8" | #define PACKAGE "cdo" | #define VERSION "1.9.8" | #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 restrict __restrict | / end confdefs.h. / |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| // If the compiler admits that it is not ready for C++11, why torture it? | ||||||||||||||||||||||||
| // Hopefully, this will speed up the test. | ||||||||||||||||||||||||
| #ifndef __cplusplus | ||||||||||||||||||||||||
| #error "This is not a C++ compiler" | ||||||||||||||||||||||||
| #elif __cplusplus < 201103L | ||||||||||||||||||||||||
| #error "This is not a C++11 compiler" | ||||||||||||||||||||||||
| #else | ||||||||||||||||||||||||
| namespace cxx11 | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| namespace test_static_assert | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| template |
||||||||||||||||||||||||
| struct check | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| static_assert(sizeof(int) <= sizeof(T), "not big enough"); | ||||||||||||||||||||||||
| }; | ||||||||||||||||||||||||
| } | ||||||||||||||||||||||||
| namespace test_final_override | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| struct Base | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| virtual void f() {} | ||||||||||||||||||||||||
| }; | ||||||||||||||||||||||||
| struct Derived : public Base | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| virtual void f() override {} | ||||||||||||||||||||||||
| }; | ||||||||||||||||||||||||
| } | ||||||||||||||||||||||||
| namespace test_double_right_angle_brackets | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| template < typename T > | ||||||||||||||||||||||||
| struct check {}; | ||||||||||||||||||||||||
| typedef check |
||||||||||||||||||||||||
| typedef check<check |
||||||||||||||||||||||||
| typedef check<check<check |
||||||||||||||||||||||||
| typedef check<check<check<check |
||||||||||||||||||||||||
| } | ||||||||||||||||||||||||
| namespace test_decltype | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| int | ||||||||||||||||||||||||
| f() | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| int a = 1; | ||||||||||||||||||||||||
| decltype(a) b = 2; | ||||||||||||||||||||||||
| return a + b; | ||||||||||||||||||||||||
| } | ||||||||||||||||||||||||
| } | ||||||||||||||||||||||||
| namespace test_type_deduction | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| template < typename T1, typename T2 > | ||||||||||||||||||||||||
| struct is_same | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| static const bool value = false; | ||||||||||||||||||||||||
| }; | ||||||||||||||||||||||||
| template < typename T > | ||||||||||||||||||||||||
| struct is_same<T, T> | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| static const bool value = true; | ||||||||||||||||||||||||
| }; | ||||||||||||||||||||||||
| template < typename T1, typename T2 > | ||||||||||||||||||||||||
| auto | ||||||||||||||||||||||||
| add(T1 a1, T2 a2) -> decltype(a1 + a2) | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| return a1 + a2; | ||||||||||||||||||||||||
| } | ||||||||||||||||||||||||
| int | ||||||||||||||||||||||||
| test(const int c, volatile int v) | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| static_assert(is_same<int, decltype(0)>::value == true, ""); | ||||||||||||||||||||||||
| static_assert(is_same<int, decltype(c)>::value == false, ""); | ||||||||||||||||||||||||
| static_assert(is_same<int, decltype(v)>::value == false, ""); | ||||||||||||||||||||||||
| auto ac = c; | ||||||||||||||||||||||||
| auto av = v; | ||||||||||||||||||||||||
| auto sumi = ac + av + 'x'; | ||||||||||||||||||||||||
| auto sumf = ac + av + 1.0; | ||||||||||||||||||||||||
| static_assert(is_same<int, decltype(ac)>::value == true, ""); | ||||||||||||||||||||||||
| static_assert(is_same<int, decltype(av)>::value == true, ""); | ||||||||||||||||||||||||
| static_assert(is_same<int, decltype(sumi)>::value == true, ""); | ||||||||||||||||||||||||
| static_assert(is_same<int, decltype(sumf)>::value == false, ""); | ||||||||||||||||||||||||
| static_assert(is_same<int, decltype(add(c, v))>::value == true, ""); | ||||||||||||||||||||||||
| return (sumf > 0.0) ? sumi : add(c, v); | ||||||||||||||||||||||||
| } | ||||||||||||||||||||||||
| } | ||||||||||||||||||||||||
| namespace test_noexcept | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| int f() { return 0; } | ||||||||||||||||||||||||
| int g() noexcept { return 0; } | ||||||||||||||||||||||||
| static_assert(noexcept(f()) == false, ""); | ||||||||||||||||||||||||
| static_assert(noexcept(g()) == true, ""); | ||||||||||||||||||||||||
| } | ||||||||||||||||||||||||
| namespace test_constexpr | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| template < typename CharT > | ||||||||||||||||||||||||
| unsigned long constexpr | ||||||||||||||||||||||||
| strlen_c_r(const CharT *const s, const unsigned long acc) noexcept | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| return *s ? strlen_c_r(s + 1, acc + 1) : acc; | ||||||||||||||||||||||||
| } | ||||||||||||||||||||||||
| template < typename CharT > | ||||||||||||||||||||||||
| unsigned long constexpr | ||||||||||||||||||||||||
| strlen_c(const CharT *const s) noexcept | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| return strlen_c_r(s, 0UL); | ||||||||||||||||||||||||
| } | ||||||||||||||||||||||||
| static_assert(strlen_c("") == 0UL, ""); | ||||||||||||||||||||||||
| static_assert(strlen_c("1") == 1UL, ""); | ||||||||||||||||||||||||
| static_assert(strlen_c("example") == 7UL, ""); | ||||||||||||||||||||||||
| static_assert(strlen_c("another\0example") == 7UL, ""); | ||||||||||||||||||||||||
| } | ||||||||||||||||||||||||
| namespace test_rvalue_references | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| template < int N > | ||||||||||||||||||||||||
| struct answer | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| static constexpr int value = N; | ||||||||||||||||||||||||
| }; | ||||||||||||||||||||||||
| answer<1> f(int&) { return answer<1>(); } | ||||||||||||||||||||||||
| answer<2> f(const int&) { return answer<2>(); } | ||||||||||||||||||||||||
| answer<3> f(int&&) { return answer<3>(); } | ||||||||||||||||||||||||
| void | ||||||||||||||||||||||||
| test() | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| int i = 0; | ||||||||||||||||||||||||
| const int c = 0; | ||||||||||||||||||||||||
| static_assert(decltype(f(i))::value == 1, ""); | ||||||||||||||||||||||||
| static_assert(decltype(f(c))::value == 2, ""); | ||||||||||||||||||||||||
| static_assert(decltype(f(0))::value == 3, ""); | ||||||||||||||||||||||||
| } | ||||||||||||||||||||||||
| } | ||||||||||||||||||||||||
| namespace test_uniform_initialization | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| struct test | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| static const int zero {}; | ||||||||||||||||||||||||
| static const int one {1}; | ||||||||||||||||||||||||
| }; | ||||||||||||||||||||||||
| static_assert(test::zero == 0, ""); | ||||||||||||||||||||||||
| static_assert(test::one == 1, ""); | ||||||||||||||||||||||||
| } | ||||||||||||||||||||||||
| namespace test_lambdas | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| void | ||||||||||||||||||||||||
| test1() | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| auto lambda1 = [](){}; | ||||||||||||||||||||||||
| auto lambda2 = lambda1; | ||||||||||||||||||||||||
| lambda1(); | ||||||||||||||||||||||||
| lambda2(); | ||||||||||||||||||||||||
| } | ||||||||||||||||||||||||
| int | ||||||||||||||||||||||||
| test2() | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| auto a = [](int i, int j){ return i + j; }(1, 2); | ||||||||||||||||||||||||
| auto b = []() -> int { return '0'; }(); | ||||||||||||||||||||||||
| auto c = [=](){ return a + b; }(); | ||||||||||||||||||||||||
| auto d = [&](){ return c; }(); | ||||||||||||||||||||||||
| auto e = [a, &b](int x) mutable { | ||||||||||||||||||||||||
| const auto identity = [](int y){ return y; }; | ||||||||||||||||||||||||
| for (auto i = 0; i < a; ++i) | ||||||||||||||||||||||||
| a += b--; | ||||||||||||||||||||||||
| return x + identity(a + b); | ||||||||||||||||||||||||
| }(0); | ||||||||||||||||||||||||
| return a + b + c + d + e; | ||||||||||||||||||||||||
| } | ||||||||||||||||||||||||
| int | ||||||||||||||||||||||||
| test3() | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| const auto nullary = [](){ return 0; }; | ||||||||||||||||||||||||
| const auto unary = [](int x){ return x; }; | ||||||||||||||||||||||||
| using nullary_t = decltype(nullary); | ||||||||||||||||||||||||
| using unary_t = decltype(unary); | ||||||||||||||||||||||||
| const auto higher1st = [](nullary_t f){ return f(); }; | ||||||||||||||||||||||||
| const auto higher2nd = [unary](nullary_t f1){ | ||||||||||||||||||||||||
| return [unary, f1](unary_t f2){ return f2(unary(f1())); }; | ||||||||||||||||||||||||
| }; | ||||||||||||||||||||||||
| return higher1st(nullary) + higher2nd(nullary)(unary); | ||||||||||||||||||||||||
| } | ||||||||||||||||||||||||
| } | ||||||||||||||||||||||||
| namespace test_variadic_templates | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| template |
||||||||||||||||||||||||
| struct sum; | ||||||||||||||||||||||||
| template <int N0, int... N1toN> | ||||||||||||||||||||||||
| struct sum<N0, N1toN...> | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| static constexpr auto value = N0 + sum |
||||||||||||||||||||||||
| }; | ||||||||||||||||||||||||
| template <> | ||||||||||||||||||||||||
| struct sum<> | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| static constexpr auto value = 0; | ||||||||||||||||||||||||
| }; | ||||||||||||||||||||||||
| static_assert(sum<>::value == 0, ""); | ||||||||||||||||||||||||
| static_assert(sum<1>::value == 1, ""); | ||||||||||||||||||||||||
| static_assert(sum<23>::value == 23, ""); | ||||||||||||||||||||||||
| static_assert(sum<1, 2>::value == 3, ""); | ||||||||||||||||||||||||
| static_assert(sum<5, 5, 11>::value == 21, ""); | ||||||||||||||||||||||||
| static_assert(sum<2, 3, 5, 7, 11, 13>::value == 41, ""); | ||||||||||||||||||||||||
| } | ||||||||||||||||||||||||
| // http://stackoverflow.com/questions/13728184/template-aliases-and-sfinae | ||||||||||||||||||||||||
| // Clang 3.1 fails with headers of libstd++ 4.8.3 when using std::function | ||||||||||||||||||||||||
| // because of this. | ||||||||||||||||||||||||
| namespace test_template_alias_sfinae | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| struct foo {}; | ||||||||||||||||||||||||
| template |
||||||||||||||||||||||||
| using member = typename T::member_type; | ||||||||||||||||||||||||
| template |
||||||||||||||||||||||||
| void func(...) {} | ||||||||||||||||||||||||
| template |
||||||||||||||||||||||||
| void func(member |
||||||||||||||||||||||||
| void test(); | ||||||||||||||||||||||||
| void test() { func |
||||||||||||||||||||||||
| } | ||||||||||||||||||||||||
| } // namespace cxx11 | ||||||||||||||||||||||||
| #endif // __cplusplus >= 201103L | ||||||||||||||||||||||||
| configure:20437: result: no configure:20447: checking whether clang++ supports C++11 features with -std=gnu++11 configure:20743: clang++ -std=gnu++11 -c -g -O2 conftest.cpp >&5 configure:20743: $? = 0 configure:20752: result: yes configure:21122: checking for clang option to support OpenMP configure:21137: clang -o conftest -g -O2 conftest.c -lhdf5 >&5 conftest.c:28:2: error: unknown type name 'choke' choke me ^ conftest.c:28:10: error: expected ';' after top level declarator choke me ^ ; 2 errors generated. configure:21137: $? = 1 configure: failed program was: | / confdefs.h / | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.9.8" | #define PACKAGE_STRING "cdo 1.9.8" | #define PACKAGE_BUGREPORT "https://mpimet.mpg.de/cdo" | #define PACKAGE_URL "" | #define CDO "1.9.8" | #define PACKAGE "cdo" | #define VERSION "1.9.8" | #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 restrict __restrict | #define HAVE_CXX11 1 | / end confdefs.h. / |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| #ifndef _OPENMP | |||||||||||||||||||||||||
| choke me | |||||||||||||||||||||||||
| #endif | |||||||||||||||||||||||||
| #include |
|||||||||||||||||||||||||
| int main () { return omp_get_num_threads (); } | |||||||||||||||||||||||||
| configure:21155: clang -o conftest -g -O2 -fopenmp conftest.c -lhdf5 >&5 clang: error: unsupported option '-fopenmp' clang: error: unsupported option '-fopenmp' configure:21155: $? = 1 configure: failed program was: | / confdefs.h / | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.9.8" | #define PACKAGE_STRING "cdo 1.9.8" | #define PACKAGE_BUGREPORT "https://mpimet.mpg.de/cdo" | #define PACKAGE_URL "" | #define CDO "1.9.8" | #define PACKAGE "cdo" | #define VERSION "1.9.8" | #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 restrict __restrict | #define HAVE_CXX11 1 | / end confdefs.h. / |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| #ifndef _OPENMP | |||||||||||||||||||||||||
| choke me | |||||||||||||||||||||||||
| #endif | |||||||||||||||||||||||||
| #include |
|||||||||||||||||||||||||
| int main () { return omp_get_num_threads (); } | |||||||||||||||||||||||||
| configure:21155: clang -o conftest -g -O2 -xopenmp conftest.c -lhdf5 >&5 clang: error: language not recognized: 'openmp' configure:21155: $? = 1 configure: failed program was: | / confdefs.h / | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.9.8" | #define PACKAGE_STRING "cdo 1.9.8" | #define PACKAGE_BUGREPORT "https://mpimet.mpg.de/cdo" | #define PACKAGE_URL "" | #define CDO "1.9.8" | #define PACKAGE "cdo" | #define VERSION "1.9.8" | #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 restrict __restrict | #define HAVE_CXX11 1 | / end confdefs.h. / |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| #ifndef _OPENMP | |||||||||||||||||||||||||
| choke me | |||||||||||||||||||||||||
| #endif | |||||||||||||||||||||||||
| #include |
|||||||||||||||||||||||||
| int main () { return omp_get_num_threads (); } | |||||||||||||||||||||||||
| configure:21155: clang -o conftest -g -O2 -openmp conftest.c -lhdf5 >&5 conftest.c:28:2: error: unknown type name 'choke' choke me ^ conftest.c:28:10: error: expected ';' after top level declarator choke me ^ ; 2 errors generated. configure:21155: $? = 1 configure: failed program was: | / confdefs.h / | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.9.8" | #define PACKAGE_STRING "cdo 1.9.8" | #define PACKAGE_BUGREPORT "https://mpimet.mpg.de/cdo" | #define PACKAGE_URL "" | #define CDO "1.9.8" | #define PACKAGE "cdo" | #define VERSION "1.9.8" | #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 restrict __restrict | #define HAVE_CXX11 1 | / end confdefs.h. / |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| #ifndef _OPENMP | |||||||||||||||||||||||||
| choke me | |||||||||||||||||||||||||
| #endif | |||||||||||||||||||||||||
| #include |
|||||||||||||||||||||||||
| int main () { return omp_get_num_threads (); } | |||||||||||||||||||||||||
| configure:21155: clang -o conftest -g -O2 -mp conftest.c -lhdf5 >&5 clang: error: unknown argument: '-mp' configure:21155: $? = 1 configure: failed program was: | / confdefs.h / | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.9.8" | #define PACKAGE_STRING "cdo 1.9.8" | #define PACKAGE_BUGREPORT "https://mpimet.mpg.de/cdo" | #define PACKAGE_URL "" | #define CDO "1.9.8" | #define PACKAGE "cdo" | #define VERSION "1.9.8" | #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 restrict __restrict | #define HAVE_CXX11 1 | / end confdefs.h. / |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| #ifndef _OPENMP | |||||||||||||||||||||||||
| choke me | |||||||||||||||||||||||||
| #endif | |||||||||||||||||||||||||
| #include |
|||||||||||||||||||||||||
| int main () { return omp_get_num_threads (); } | |||||||||||||||||||||||||
| configure:21155: clang -o conftest -g -O2 -omp conftest.c -lhdf5 >&5 conftest.c:28:2: error: unknown type name 'choke' choke me ^ conftest.c:28:10: error: expected ';' after top level declarator choke me ^ ; 2 errors generated. configure:21155: $? = 1 configure: failed program was: | / confdefs.h / | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.9.8" | #define PACKAGE_STRING "cdo 1.9.8" | #define PACKAGE_BUGREPORT "https://mpimet.mpg.de/cdo" | #define PACKAGE_URL "" | #define CDO "1.9.8" | #define PACKAGE "cdo" | #define VERSION "1.9.8" | #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 restrict __restrict | #define HAVE_CXX11 1 | / end confdefs.h. / |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| #ifndef _OPENMP | |||||||||||||||||||||||||
| choke me | |||||||||||||||||||||||||
| #endif | |||||||||||||||||||||||||
| #include |
|||||||||||||||||||||||||
| int main () { return omp_get_num_threads (); } | |||||||||||||||||||||||||
| configure:21155: clang -o conftest -g -O2 -qsmp=omp conftest.c -lhdf5 >&5 clang: error: unknown argument: '-qsmp=omp' configure:21155: $? = 1 configure: failed program was: | / confdefs.h / | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.9.8" | #define PACKAGE_STRING "cdo 1.9.8" | #define PACKAGE_BUGREPORT "https://mpimet.mpg.de/cdo" | #define PACKAGE_URL "" | #define CDO "1.9.8" | #define PACKAGE "cdo" | #define VERSION "1.9.8" | #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 restrict __restrict | #define HAVE_CXX11 1 | / end confdefs.h. / |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| #ifndef _OPENMP | |||||||||||||||||||||||||
| choke me | |||||||||||||||||||||||||
| #endif | |||||||||||||||||||||||||
| #include |
|||||||||||||||||||||||||
| int main () { return omp_get_num_threads (); } | |||||||||||||||||||||||||
| configure:21155: clang -o conftest -g -O2 -homp conftest.c -lhdf5 >&5 clang: error: unknown argument: '-homp' configure:21155: $? = 1 configure: failed program was: | / confdefs.h / | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.9.8" | #define PACKAGE_STRING "cdo 1.9.8" | #define PACKAGE_BUGREPORT "https://mpimet.mpg.de/cdo" | #define PACKAGE_URL "" | #define CDO "1.9.8" | #define PACKAGE "cdo" | #define VERSION "1.9.8" | #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 restrict __restrict | #define HAVE_CXX11 1 | / end confdefs.h. / |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| #ifndef _OPENMP | |||||||||||||||||||||||||
| choke me | |||||||||||||||||||||||||
| #endif | |||||||||||||||||||||||||
| #include |
|||||||||||||||||||||||||
| int main () { return omp_get_num_threads (); } | |||||||||||||||||||||||||
| configure:21155: clang -o conftest -g -O2 -Popenmp conftest.c -lhdf5 >&5 clang: error: unknown argument '-Popenmp'; did you mean '-fopenmp'? configure:21155: $? = 1 configure: failed program was: | / confdefs.h / | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.9.8" | #define PACKAGE_STRING "cdo 1.9.8" | #define PACKAGE_BUGREPORT "https://mpimet.mpg.de/cdo" | #define PACKAGE_URL "" | #define CDO "1.9.8" | #define PACKAGE "cdo" | #define VERSION "1.9.8" | #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 restrict __restrict | #define HAVE_CXX11 1 | / end confdefs.h. / |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| #ifndef _OPENMP | |||||||||||||||||||||||||
| choke me | |||||||||||||||||||||||||
| #endif | |||||||||||||||||||||||||
| #include |
|||||||||||||||||||||||||
| int main () { return omp_get_num_threads (); } | |||||||||||||||||||||||||
| configure:21155: clang -o conftest -g -O2 --openmp conftest.c -lhdf5 >&5 clang: error: unsupported option '--openmp'; did you mean '-fopenmp'? configure:21155: $? = 1 configure: failed program was: | / confdefs.h / | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.9.8" | #define PACKAGE_STRING "cdo 1.9.8" | #define PACKAGE_BUGREPORT "https://mpimet.mpg.de/cdo" | #define PACKAGE_URL "" | #define CDO "1.9.8" | #define PACKAGE "cdo" | #define VERSION "1.9.8" | #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 restrict __restrict | #define HAVE_CXX11 1 | / end confdefs.h. / |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| #ifndef _OPENMP | |||||||||||||||||||||||||
| choke me | |||||||||||||||||||||||||
| #endif | |||||||||||||||||||||||||
| #include |
|||||||||||||||||||||||||
| int main () { return omp_get_num_threads (); } | |||||||||||||||||||||||||
configure:21169: result: unsupported configure:21223: checking for ar configure:21250: result: ar configure:21407: checking for ld configure:21434: result: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld configure:21499: checking for nm configure:21526: result: /usr/bin/nm -B configure:21591: checking for ar configure:21618: result: ar configure:21683: checking for as configure:21699: found /usr/bin/as configure:21710: result: as configure:21775: checking for dlltool configure:21802: result: false configure:21867: checking for objdump configure:21894: result: objdump configure:21959: checking for strip configure:21986: result: strip configure:22051: checking for ranlib configure:22078: result: ranlib configure:22114: checking for special C compiler options needed for large files configure:22159: result: no configure:22165: checking for _FILE_OFFSET_BITS value needed for large files configure:22190: clang -c -g -O2 conftest.c >&5 configure:22190: $? = 0 configure:22222: result: no configure:22315: checking for stdlib.h configure:22315: result: yes configure:22315: checking for unistd.h configure:22315: result: yes configure:22315: checking for sys/param.h configure:22315: clang -c -g -O2 conftest.c >&5 configure:22315: $? = 0 configure:22315: result: yes configure:22335: checking for getpagesize configure:22335: clang -o conftest -g -O2 conftest.c -lhdf5 >&5 configure:22335: $? = 0 configure:22335: result: yes configure:22344: checking for working mmap configure:22491: clang -o conftest -g -O2 conftest.c -lhdf5 >&5 configure:22491: $? = 0 configure:22491: ./conftest configure:22491: $? = 0 configure:22501: result: yes configure:22512: checking for struct stat.st_blksize configure:22512: clang -c -g -O2 conftest.c >&5 configure:22512: $? = 0 configure:22512: result: yes configure:22526: checking sys/resource.h usability configure:22526: clang -c -g -O2 conftest.c >&5 configure:22526: $? = 0 configure:22526: result: yes configure:22526: checking sys/resource.h presence configure:22526: clang -E conftest.c configure:22526: $? = 0 configure:22526: result: yes configure:22526: checking for sys/resource.h configure:22526: result: yes configure:22538: checking sys/times.h usability configure:22538: clang -c -g -O2 conftest.c >&5 configure:22538: $? = 0 configure:22538: result: yes configure:22538: checking sys/times.h presence configure:22538: clang -E conftest.c configure:22538: $? = 0 configure:22538: result: yes configure:22538: checking for sys/times.h configure:22538: result: yes configure:22550: checking malloc.h usability configure:22550: clang -c -g -O2 conftest.c >&5 conftest.c:67:10: fatal error: 'malloc.h' file not found
^~~~~~~~~~1 error generated.
configure:22550: $? = 1
configure: failed program was:
| / confdefs.h /
| #define PACKAGE_NAME "cdo"
| #define PACKAGE_TARNAME "cdo"
| #define PACKAGE_VERSION "1.9.8"
| #define PACKAGE_STRING "cdo 1.9.8"
| #define PACKAGE_BUGREPORT "https://mpimet.mpg.de/cdo"
| #define PACKAGE_URL ""
| #define CDO "1.9.8"
| #define PACKAGE "cdo"
| #define VERSION "1.9.8"
| #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 restrict __restrict
| #define HAVE_CXX11 1
| #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
| / end confdefs.h. /
| #include
^~~~~~~~~~| 1 error generated. configure:22550: $? = 1 configure: failed program was: | / confdefs.h / | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.9.8" | #define PACKAGE_STRING "cdo 1.9.8" | #define PACKAGE_BUGREPORT "https://mpimet.mpg.de/cdo" | #define PACKAGE_URL "" | #define CDO "1.9.8" | #define PACKAGE "cdo" | #define VERSION "1.9.8" | #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 restrict __restrict | #define HAVE_CXX11 1 | #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 | / end confdefs.h. / | #include |
/ confdefs.h / | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.9.8" | #define PACKAGE_STRING "cdo 1.9.8" | #define PACKAGE_BUGREPORT "https://mpimet.mpg.de/cdo" | #define PACKAGE_URL "" | #define CDO "1.9.8" | #define PACKAGE "cdo" | #define VERSION "1.9.8" | #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 restrict __restrict | #define HAVE_CXX11 1 | #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_GLOB_H 1 | #define HAVE_FNMATCH_H 1 | #define HAVE_WORDEXP_H 1 | #define HAVE_EXECINFO_H 1 | / end confdefs.h. / | /* Define mallinfo to an innocuous variant, in case |
For example, HP-UX 11i |
#define mallinfo innocuous_mallinfo |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| /* System header to define __stub macros and hopefully few prototypes, | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| which can conflict with char mallinfo (); below. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prefer |
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| #ifdef STDC | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| # include |
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| #else | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| # include |
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| #endif | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| #undef mallinfo | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| /* 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 mallinfo (); | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| /* The GNU C library defines this for functions which it implements | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| to always fail with ENOSYS. Some functions are actually named | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| something starting with __ and the normal name is an alias. */ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| #if defined __stub_mallinfo | defined __stub___mallinfo | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| choke me | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| #endif | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| int | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| main () | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| { | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| return mallinfo (); | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| ; | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| return 0; | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| } |
| configure:22612: result: no configure:22623: checking for backtrace configure:22623: clang -o conftest -g -O2 conftest.c -lhdf5 >&5 configure:22623: $? = 0 configure:22623: result: yes configure:22636: checking for getrlimit configure:22636: clang -o conftest -g -O2 conftest.c -lhdf5 >&5 configure:22636: $? = 0 configure:22636: result: yes configure:22711: checking for floor in -lm configure:22736: clang -o conftest -g -O2 conftest.c -lm -lhdf5 >&5 conftest.c:51:6: warning: incompatible redeclaration of library function 'floor' [-Wincompatible-library-redeclaration] char floor (); ^ conftest.c:51:6: note: 'floor' is a builtin with type 'double (double)' 1 warning generated. configure:22736: $? = 0 configure:22745: result: yes configure:22759: checking for feenableexcept configure:22759: clang -o conftest -g -O2 conftest.c -lm -lhdf5 >&5 Undefined symbols for architecture x86_64: "_feenableexcept", referenced from: _main in conftest-f08e41.o ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) configure:22759: $? = 1 configure: failed program was: | / confdefs.h / | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.9.8" | #define PACKAGE_STRING "cdo 1.9.8" | #define PACKAGE_BUGREPORT "https://mpimet.mpg.de/cdo" | #define PACKAGE_URL "" | #define CDO "1.9.8" | #define PACKAGE "cdo" | #define VERSION "1.9.8" | #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 restrict __restrict | #define HAVE_CXX11 1 | #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_GLOB_H 1 | #define HAVE_FNMATCH_H 1 | #define HAVE_WORDEXP_H 1 | #define HAVE_EXECINFO_H 1 | #define HAVE_BACKTRACE 1 | #define HAVE_GETRLIMIT 1 | #define CXX_VERSION "Apple clang version 11.0.3 (clang-1103.0.32.59)" | #define C_VERSION "Apple clang version 11.0.3 (clang-1103.0.32.59)" | #define F77_VERSION "GNU Fortran (Homebrew GCC 9.3.0_1) 9.3.0" | #define SYSTEM_TYPE "x86_64-apple-darwin19.4.0" | #define HAVE_LIBM 1 | / end confdefs.h. / | /* Define feenableexcept to an innocuous variant, in case |
For example, HP-UX 11i |
#define feenableexcept innocuous_feenableexcept |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| /* System header to define __stub macros and hopefully few prototypes, | |||||||||||||||||||||||||||||||||||||||||||||||
| which can conflict with char feenableexcept (); below. | |||||||||||||||||||||||||||||||||||||||||||||||
| Prefer |
|||||||||||||||||||||||||||||||||||||||||||||||
| #ifdef STDC | |||||||||||||||||||||||||||||||||||||||||||||||
| # include |
|||||||||||||||||||||||||||||||||||||||||||||||
| #else | |||||||||||||||||||||||||||||||||||||||||||||||
| # include |
|||||||||||||||||||||||||||||||||||||||||||||||
| #endif | |||||||||||||||||||||||||||||||||||||||||||||||
| #undef feenableexcept | |||||||||||||||||||||||||||||||||||||||||||||||
| /* 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 feenableexcept (); | |||||||||||||||||||||||||||||||||||||||||||||||
| /* The GNU C library defines this for functions which it implements | |||||||||||||||||||||||||||||||||||||||||||||||
| to always fail with ENOSYS. Some functions are actually named | |||||||||||||||||||||||||||||||||||||||||||||||
| something starting with __ and the normal name is an alias. */ | |||||||||||||||||||||||||||||||||||||||||||||||
| #if defined __stub_feenableexcept | defined __stub___feenableexcept | ||||||||||||||||||||||||||||||||||||||||||||||
| choke me | |||||||||||||||||||||||||||||||||||||||||||||||
| #endif | |||||||||||||||||||||||||||||||||||||||||||||||
| int | |||||||||||||||||||||||||||||||||||||||||||||||
| main () | |||||||||||||||||||||||||||||||||||||||||||||||
| { | |||||||||||||||||||||||||||||||||||||||||||||||
| return feenableexcept (); | |||||||||||||||||||||||||||||||||||||||||||||||
| ; | |||||||||||||||||||||||||||||||||||||||||||||||
| return 0; | |||||||||||||||||||||||||||||||||||||||||||||||
| } |
| configure:22759: result: no configure:22769: checking for fenv_t.__control configure:22769: clang -c -g -O2 conftest.c >&5 configure:22769: $? = 0 configure:22769: result: yes configure:22779: checking for fenv_t.__mxcsr configure:22779: clang -c -g -O2 conftest.c >&5 configure:22779: $? = 0 configure:22779: result: yes configure:22802: checking C preprocessor flags for Fortran calling convention cfortran.h configure:22888: result: -DgFortran (probed) configure:22923: checking if C externals constructed with cfortran.h work configure:22983: clang -c -g -O2 -I./src -DgFortran conftest.c >&5 configure:22983: $? = 0 configure:22984: Renaming C object file. configure:22987: $? = 0 configure:23005: gfortran -c -g -O2 conftest.f >&5 configure:23005: $? = 0 configure:23006: Renaming Fortran object file. configure:23009: $? = 0 configure:23065: gfortran -o conftest -g -O2 conftest.f conftest_c.o conftest_f.o -lm -lhdf5 >&5 configure:23065: $? = 0 configure:23065: ./conftest configure:23065: $? = 0 configure:23099: result: yes configure:23153: checking for DATA support configure:23167: result: configure:23319: checking if compiler needs -Werror to reject unknown flags configure:23335: clang -c -g -O2 -Werror -Wunknown-warning-option -Wsizeof-array-argument -DgFortran conftest.c >&5 configure:23335: $? = 0 configure:23336: result: yes configure:23356: checking whether pthreads work with -pthread configure:23444: clang -o conftest -g -O2 -pthread -Werror -DgFortran conftest.c -lm -lhdf5 >&5 configure:23444: $? = 0 configure:23453: result: yes configure:23472: checking for joinable pthread attribute configure:23487: clang -o conftest -g -O2 -pthread -DgFortran conftest.c -lm -lhdf5 >&5 configure:23487: $? = 0 configure:23493: result: PTHREAD_CREATE_JOINABLE configure:23503: checking if more special flags are required for pthreads configure:23518: result: -D_THREAD_SAFE configure:23524: checking for PTHREAD_PRIO_INHERIT configure:23541: clang -o conftest -g -O2 -pthread -DgFortran conftest.c -lm -lhdf5 >&5 configure:23541: $? = 0 configure:23550: result: yes configure:23819: checking szlib.h usability configure:23819: clang -c -g -O2 -D_THREAD_SAFE -pthread -I/usr/local/opt/szip/include -DgFortran conftest.c >&5 configure:23819: $? = 0 configure:23819: result: yes configure:23819: checking szlib.h presence configure:23819: clang -E -I/usr/local/opt/szip/include -DgFortran conftest.c configure:23819: $? = 0 configure:23819: result: yes configure:23819: checking for szlib.h configure:23819: result: yes configure:23829: checking for library containing SZ_BufftoBuffCompress configure:23860: clang -o conftest -g -O2 -D_THREAD_SAFE -pthread -I/usr/local/opt/szip/include -DgFortran -L/usr/local/opt/szip/lib conftest.c -lm -lhdf5 >&5 Undefined symbols for architecture x86_64: "_SZ_BufftoBuffCompress", referenced from: _main in conftest-5cad62.o ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) configure:23860: $? = 1 configure: failed program was: | / confdefs.h / | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.9.8" | #define PACKAGE_STRING "cdo 1.9.8" | #define PACKAGE_BUGREPORT "https://mpimet.mpg.de/cdo" | #define PACKAGE_URL "" | #define CDO "1.9.8" | #define PACKAGE "cdo" | #define VERSION "1.9.8" | #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 restrict __restrict | #define HAVE_CXX11 1 | #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_GLOB_H 1 | #define HAVE_FNMATCH_H 1 | #define HAVE_WORDEXP_H 1 | #define HAVE_EXECINFO_H 1 | #define HAVE_BACKTRACE 1 | #define HAVE_GETRLIMIT 1 | #define CXX_VERSION "Apple clang version 11.0.3 (clang-1103.0.32.59)" | #define C_VERSION "Apple clang version 11.0.3 (clang-1103.0.32.59)" | #define F77_VERSION "GNU Fortran (Homebrew GCC 9.3.0_1) 9.3.0" | #define SYSTEM_TYPE "x86_64-apple-darwin19.4.0" | #define HAVE_LIBM 1 | #define HAVE_FENV_T___CONTROL 1 | #define HAVE_FENV_T___MXCSR 1 | #define HAVE_CF_INTERFACE 1 | #define ENABLE_DATA 1 | #define HAVE_PTHREAD_PRIO_INHERIT 1 | #define HAVE_LIBPTHREAD 1 | #define HAVE_SZLIB_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 SZ_BufftoBuffCompress (); | |||||||||||||||||||||||||||||||||||||||||||||||||||
| int | |||||||||||||||||||||||||||||||||||||||||||||||||||
| main () | |||||||||||||||||||||||||||||||||||||||||||||||||||
| { | |||||||||||||||||||||||||||||||||||||||||||||||||||
| return SZ_BufftoBuffCompress (); | |||||||||||||||||||||||||||||||||||||||||||||||||||
| ; | |||||||||||||||||||||||||||||||||||||||||||||||||||
| return 0; | |||||||||||||||||||||||||||||||||||||||||||||||||||
| } |
| configure:23860: clang -o conftest -g -O2 -D_THREAD_SAFE -pthread -I/usr/local/opt/szip/include -DgFortran -L/usr/local/opt/szip/lib conftest.c -lsz -lm -lhdf5 >&5 configure:23860: $? = 0 configure:23877: result: -lsz configure:24067: checking hdf5.h usability configure:24067: clang -c -g -O2 -D_THREAD_SAFE -pthread -I/usr/local/opt/hdf5/include -I/usr/local/opt/szip/include -DgFortran conftest.c >&5 configure:24067: $? = 0 configure:24067: result: yes configure:24067: checking hdf5.h presence configure:24067: clang -E -I/usr/local/opt/hdf5/include -I/usr/local/opt/szip/include -DgFortran conftest.c configure:24067: $? = 0 configure:24067: result: yes configure:24067: checking for hdf5.h configure:24067: result: yes configure:24077: checking for library containing H5Fopen configure:24108: clang -o conftest -g -O2 -D_THREAD_SAFE -pthread -I/usr/local/opt/hdf5/include -I/usr/local/opt/szip/include -DgFortran -L/usr/local/opt/hdf5/lib -L/usr/local/opt/szip/lib conftest.c -lsz -lm -lhdf5 >&5 configure:24108: $? = 0 configure:24125: result: none required configure:24137: checking for library containing H5DSis_scale configure:24168: clang -o conftest -g -O2 -D_THREAD_SAFE -pthread -I/usr/local/opt/hdf5/include -I/usr/local/opt/szip/include -DgFortran -L/usr/local/opt/hdf5/lib -L/usr/local/opt/szip/lib conftest.c -lsz -lm -lhdf5 >&5 Undefined symbols for architecture x86_64: "_H5DSis_scale", referenced from: _main in conftest-8bb9a2.o ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) configure:24168: $? = 1 configure: failed program was: | / confdefs.h / | #define PACKAGE_NAME "cdo" | #define PACKAGE_TARNAME "cdo" | #define PACKAGE_VERSION "1.9.8" | #define PACKAGE_STRING "cdo 1.9.8" | #define PACKAGE_BUGREPORT "https://mpimet.mpg.de/cdo" | #define PACKAGE_URL "" | #define CDO "1.9.8" | #define PACKAGE "cdo" | #define VERSION "1.9.8" | #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 restrict __restrict | #define HAVE_CXX11 1 | #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_GLOB_H 1 | #define HAVE_FNMATCH_H 1 | #define HAVE_WORDEXP_H 1 | #define HAVE_EXECINFO_H 1 | #define HAVE_BACKTRACE 1 | #define HAVE_GETRLIMIT 1 | #define CXX_VERSION "Apple clang version 11.0.3 (clang-1103.0.32.59)" | #define C_VERSION "Apple clang version 11.0.3 (clang-1103.0.32.59)" | #define F77_VERSION "GNU Fortran (Homebrew GCC 9.3.0_1) 9.3.0" | #define SYSTEM_TYPE "x86_64-apple-darwin19.4.0" | #define HAVE_LIBM 1 | #define HAVE_FENV_T___CONTROL 1 | #define HAVE_FENV_T___MXCSR 1 | #define HAVE_CF_INTERFACE 1 | #define ENABLE_DATA 1 | #define HAVE_PTHREAD_PRIO_INHERIT 1 | #define HAVE_LIBPTHREAD 1 | #define HAVE_SZLIB_H 1 | #define HAVE_LIBSZ 1 | #define HAVE_HDF5_H 1 | #define HAVE_LIBHDF5 1 | / end confdefs.h. / |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| /* Override any GCC internal prototype to avoid an error. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| U |
GeraldCNelson
commented
4 years ago Looks like I have the home brew version of hdf5 and netcdf.
Warning: hdf5 1.12.0 is already installed and up-to-date
To reinstall 1.12.0, run brew reinstall hdf5
GCN-MacBook-Pro-7:ISIMIPData gcn$ brew install netcdf
Warning: netcdf 4.7.4 is already installed and up-to-date
To reinstall 4.7.4, run brew reinstall netcdf
Gerald C. Nelson Professor Emeritus, UIUC +1 217-390-7888 (cell) +1 970-639-2079 (land line) Skype: jerrynelson http://bit.ly/1arho7d
From: Carlos Moffat notifications@github.com Reply-To: moffat/homebrew-sciencebits reply@reply.github.com Date: Monday, April 27, 2020 at 1:14 PM To: moffat/homebrew-sciencebits homebrew-sciencebits@noreply.github.com Cc: Gerald Nelson nelson.gerald.c@gmail.com, Mention mention@noreply.github.com Subject: Re: [moffat/homebrew-sciencebits] mac installation from home-brew fails (#1)
Hi @GeraldCNelsonhttps://github.com/GeraldCNelson
Thanks for this info. I can't reproduce this problem, but my guess is that you have a mix of homebrew and non-homebrew libraries/compilers and it's compiling against the wrong thing. It's best to make sure all dependencies (hdf5, netcdf) installed in your system are the brew ones.
I don't see the config.log file.
I'm not an R user so I can't help with that part of the problem, I'm afraid.
Best
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/moffat/homebrew-sciencebits/issues/1#issuecomment-620178911, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AB6UJMRIDWNHKZKEMKTZ7TLROXKRHANCNFSM4MSEGD6A.
GeraldCNelson
commented
4 years ago There are other files in the logs directory. Would getting them be useful?
Gerald C. Nelson Professor Emeritus, UIUC +1 217-390-7888 (cell) +1 970-639-2079 (land line) Skype: jerrynelson http://bit.ly/1arho7d
From: Carlos Moffat notifications@github.com Reply-To: moffat/homebrew-sciencebits reply@reply.github.com Date: Monday, April 27, 2020 at 12:22 PM To: moffat/homebrew-sciencebits homebrew-sciencebits@noreply.github.com Cc: Gerald Nelson nelson.gerald.c@gmail.com, Mention mention@noreply.github.com Subject: Re: [moffat/homebrew-sciencebits] mac installation from home-brew fails (#1)
@GeraldCNelsonhttps://github.com/GeraldCNelson,
Can you send me the files in the log directory? /Users/gcn/Library/Logs/Homebrew/cdo/
Thanks.
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moffat
commented
4 years ago @GeraldCNelson,
Yes, why don't you email them to me at cmoffat@udel.edu
Cheers.
moffat
commented
3 years ago Hi @GeraldCNelson
I'm happy to report that cdo is now back in 'core', so my formula is obsolete. I'd recommend trying the installation again with that version.
I'm attempting install cdo on my mac with
brew install cdo. In the make install step I get the following errorsAny way around this, other than compiling directly without going through home-brew?