Well your header search path is seriously messed up, no wonder that you can't find system headers. Whats the output of
xcode-select --print-path You might want to try pointing Xcode to the right path, e.g. (assuming that it is in /Applications/Xcode.app): xcode-select --switch /Applications/Xcode.app/Contents/Developer/ and check if that fixes the header seach path On Friday, June 19, 2015 at 2:16:27 AM UTC+2, la...@math.luc.edu wrote: > > > > On Thursday, June 18, 2015 at 5:30:14 PM UTC-5, Volker Braun wrote: > > There is something fishy even before the failure when I diff it with my > log (see below): Your clang doesn't support C89 and misses ANSI C headers. > > > > Do you have anything in /usr/local installed? > > > lots. e.g., 'texlive' and 'mysql' directories. > in 'bin' one finds ps2pdf, etc. > in 'include' one finds graphviz and aspell.h > (i seem to be using the texlive. 'which latex' points to > /usr/texbin/latex, but tracing down the symbolic links, it comes back to > this texlive directory.) > > I will answer the other question from your other post here... > > weehawken:sage-devel lauve$ clang++ -E -x c++ - -v < /dev/null > > Apple LLVM version 6.1.0 (clang-602.0.53) (based on LLVM 3.6.0svn) > > Target: x86_64-apple-darwin14.3.0 > > Thread model: posix > > "/usr/bin/clang++" -cc1 -triple x86_64-apple-macosx10.10.0 -E > -disable-free -disable-llvm-verifier -main-file-name - -mrelocation-model > pic -pic-level 2 -mdisable-fp-elim -masm-verbose -munwind-tables > -target-cpu core2 -target-linker-version 242 -v -dwarf-column-info > -resource-dir /usr/bin/../lib/clang/6.1.0 -stdlib=libc++ -fdeprecated-macro > -fdebug-compilation-dir /Users/lauve/sage-devel -ferror-limit 19 > -fmessage-length 122 -stack-protector 1 -mstackrealign -fblocks > -fobjc-runtime=macosx-10.10.0 -fencode-extended-block-signature > -fcxx-exceptions -fexceptions -fmax-type-align=16 -fdiagnostics-show-option > -fcolor-diagnostics -o - -x c++ - > > clang -cc1 version 6.1.0 based upon LLVM 3.6.0svn default target > x86_64-apple-darwin14.3.0 > > ignoring nonexistent directory "/usr/bin/../include/c++/v1" > > ignoring nonexistent directory "/usr/include/c++/v1" > > ignoring nonexistent directory "/usr/bin/../lib/clang/6.1.0/include" > > #include "..." search starts here: > > #include <...> search starts here: > > /usr/local/include > > /usr/include > > /System/Library/Frameworks (framework directory) > > /Library/Frameworks (framework directory) > > End of search list. > > # 1 "<stdin>" > > # 1 "<built-in>" 1 > > # 1 "<built-in>" 3 > > # 326 "<built-in>" 3 > > # 1 "<command line>" 1 > > # 1 "<built-in>" 2 > > # 1 "<stdin>" 2 > > > > > > @@ -70,7 +71,7 @@ > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether /usr/bin/clang accepts -g... yes > -checking for /usr/bin/clang option to accept ISO C89... none needed > +checking for /usr/bin/clang option to accept ISO C89... unsupported > checking for style of include used by make... GNU > checking dependency style of /usr/bin/clang... gcc3 > checking how to run the C preprocessor... /usr/bin/clang -E > @@ -82,7 +83,7 @@ > checking for working volatile... yes > checking for main in -lm... yes > checking whether time.h and sys/time.h may both be included... yes > -checking for ANSI C header files... yes > +checking for ANSI C header files... no > checking for sys/types.h... yes > checking for sys/stat.h... yes > checking for stdlib.h... yes > @@ -95,2236 +96,6 @@ > checking for size_t... yes > checking limits.h usability... yes > checking limits.h presence... yes > -checking for limits.h... yes > -checking float.h usability... yes > -checking float.h presence... yes > > > > > > On Thursday, June 18, 2015 at 10:43:10 PM UTC+2, la...@math.luc.edu wrote: > > Re: possibly needing to install Xcode: > I installed it. restarted machine. ran 'make distclean' then ran 'make'. > Same problem. two files (float.h and stdarg.h) that cannot be found, though > they exist. > > 'xcode-select --version' and 'gcc --version' return the same output as I > mentioned before. > > > Here are the logs, in full. > > ~~~~~~~ > ~~~ mpfr > ~~~~~~~~~~~~~~~~~~ > Found local metadata for mpfr-3.1.2.p0 > Found local sources at /Users/lauve/sage-devel/upstream/mpfr-3.1.2.tar.bz2 > Checksum: e70341aa7974b4ba1023c75c750aca68222b0723 vs > e70341aa7974b4ba1023c75c750aca68222b0723 > mpfr-3.1.2.p0 > ==================================================== > Setting up build directory for mpfr-3.1.2.p0 > Finished set up > **************************************************** > Host system: > Darwin weehawken.local 14.3.0 Darwin Kernel Version 14.3.0: Mon Mar 23 > 11:59:05 PDT 2015; root:xnu-2782.20.48~5/RELEASE_X86_64 x86_64 > **************************************************** > C compiler: /usr/bin/clang > C compiler version: > Apple LLVM version 6.1.0 (clang-602.0.53) (based on LLVM 3.6.0svn) > Target: x86_64-apple-darwin14.3.0 > Thread model: posix > **************************************************** > Patching MPFR... > > Now configuring MPFR... > Checking what CC and CFLAGS MPFR would use if they were empty... > Settings chosen by MPFR when configuring with CC and CFLAGS unset: > CC: /usr/bin/gcc > CFLAGS: -Wall -Wmissing-prototypes -Wpointer-arith -m64 -O2 > -march=corei7-avx -mtune=corei7-avx -g > Settings required to properly build MPFR, taking into account SAGE_DEBUG > etc.: > CFLAGS: > LDFLAGS: > ABI: > Settings from the "global" environment: > CC: /usr/bin/clang > CFLAGS: > (CPPFLAGS, CXX and CXXFLAGS are listed below; these don't get modified.) > Using MPFR's settings (plus mandatory ones). > Finally using the following settings: > CC=/usr/bin/clang > CFLAGS=-Wall -Wmissing-prototypes -Wpointer-arith -m64 -O2 > -march=corei7-avx -mtune=corei7-avx -g > CPP= > CPPFLAGS= > CXX=/usr/bin/clang++ > CXXFLAGS= > LDFLAGS= > ABI= > (These settings may still get overridden by 'configure' or Makefiles.) > > Configuring MPFR with the following options: > --prefix="/Users/lauve/sage-devel/local" > --libdir="/Users/lauve/sage-devel/local/lib" > --with-gmp="/Users/lauve/sage-devel/local" > --disable-thread-safe > You can set MPFR_CONFIGURE to pass additional parameters. > checking for a BSD-compatible install... /usr/bin/install -c > checking whether build environment is sane... yes > checking for a thread-safe mkdir -p... ./install-sh -c -d > checking for gawk... no > checking for mawk... no > checking for nawk... no > checking for awk... awk > checking whether make sets $(MAKE)... yes > checking whether to enable maintainer-specific portions of Makefiles... yes > checking build system type... x86_64-apple-darwin14.3.0 > checking host system type... x86_64-apple-darwin14.3.0 > checking for grep that handles long lines and -e... /usr/bin/grep > checking for egrep... /usr/bin/grep -E > checking for a sed that does not truncate output... /usr/bin/sed > checking for gcc... /usr/bin/clang > checking whether the C compiler works... yes > checking for C compiler default output file name... a.out > checking for suffix of executables... > checking whether we are cross compiling... no > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether /usr/bin/clang accepts -g... yes > checking for /usr/bin/clang option to accept ISO C89... unsupported > checking for style of include used by make... GNU > checking dependency style of /usr/bin/clang... gcc3 > checking how to run the C preprocessor... /usr/bin/clang -E > checking for ICC... no > checking whether /usr/bin/clang and cc understand -c and -o together... > rm: conftest.dSYM: is a directory > yes > checking if the compiler understands -Wl,-search_paths_first... yes > checking for an ANSI C-conforming const... yes > checking for working volatile... yes > checking for main in -lm... yes > checking whether time.h and sys/time.h may both be included... yes > checking for ANSI C header files... no > checking for sys/types.h... yes > checking for sys/stat.h... yes > checking for stdlib.h... yes > checking for string.h... yes > checking for memory.h... yes > checking for strings.h... yes > checking for inttypes.h... yes > checking for stdint.h... yes > checking for unistd.h... yes > checking for size_t... yes > checking limits.h usability... yes > checking limits.h presence... yes > checking for limits.h... yes > checking float.h usability... no > checking float.h presence... no > checking for float.h... no > configure: error: float.h not found > Error configuring MPFR. > See above for the options passed to it, and the file > > /Users/lauve/sage-devel/local/var/tmp/sage/build/mpfr-3.1.2.p0/src/config.log > for details. > > real 0m26.664s > user 0m10.775s > sys 0m9.652s > ************************************************************************ > Error installing package mpfr-3.1.2.p0 > ************************************************************************ > Please email sage-devel (http://groups.google.com/group/sage-devel) > explaining the problem and including the relevant part of the log file > /Users/lauve/sage-devel/logs/pkgs/mpfr-3.1.2.p0.log > Describe your computer, operating system, etc. > If you want to try to fix the problem yourself, *don't* just cd to > /Users/lauve/sage-devel/local/var/tmp/sage/build/mpfr-3.1.2.p0 and type > 'make' or whatever is appropriate. > Instead, the following commands setup all environment variables > correctly and load a subshell for you to debug the error: > (cd '/Users/lauve/sage-devel/local/var/tmp/sage/build/mpfr-3.1.2.p0' && > '/Users/lauve/sage-devel/sage' --sh) > When you are done debugging, you can type "exit" to leave the subshell. > ************************************************************************ > > > > > > ~~~~~~~ > ~~~ zlib > ~~~~~~~~~~~~~~~~~~ > Found local metadata for zlib-1.2.8.p0 > Found local sources at /Users/lauve/sage-devel/upstream/zlib-1.2.8.tar.bz2 > Checksum: e63277b761e138a75f8c6a9ededb8d95198739a7 vs > e63277b761e138a75f8c6a9ededb8d95198739a7 > zlib-1.2.8.p0 > ==================================================== > Setting up build directory for zlib-1.2.8.p0 > Finished set up > **************************************************** > Host system: > Darwin weehawken.local 14.3.0 Darwin Kernel Version 14.3.0: Mon Mar 23 > 11:59:05 PDT 2015; root:xnu-2782.20.48~5/RELEASE_X86_64 x86_64 > **************************************************** > C compiler: /usr/bin/clang > C compiler version: > Apple LLVM version 6.1.0 (clang-602.0.53) (based on LLVM 3.6.0svn) > Target: x86_64-apple-darwin14.3.0 > Thread model: posix > **************************************************** > cygwin_symbols.patch > patching file win32/zlib.def > Checking for shared library support... > Building shared library libz.1.2.8.dylib with /usr/bin/clang. > Checking for off64_t... No. > Checking for fseeko... Yes. > Checking for strerror... Yes. > Checking for unistd.h... Yes. > Checking for stdarg.h... No. > Checking whether to use vs[n]printf() or s[n]printf()... using > s[n]printf(). > Checking for snprintf() in stdio.h... Yes. > Checking for return value of snprintf()... Yes. > Checking for attribute(visibility) support... Yes. > /usr/bin/clang -O3 -DHAVE_HIDDEN -I. -c -o example.o test/example.c > /usr/bin/clang -O3 -DHAVE_HIDDEN -c -o adler32.o adler32.c > /usr/bin/clang -O3 -DHAVE_HIDDEN -c -o crc32.o crc32.c > In file included from test/example.c:8: > In file included from ./zlib.h:34: > ./zconf.h:427:14: fatal error: 'stdarg.h' file not found > # include <stdarg.h> /* for va_list */ > ^ > In file included from crc32.c:31: > In file included from ./zutil.h:22: > In file included from ./zlib.h:34: > ./zconf.h:427:14: fatal error: 'stdarg.h' file not found > # include <stdarg.h> /* for va_list */ > ^ > In file included from adler32.c:8: > In file included from ./zutil.h:22: > In file included from ./zlib.h:34: > ./zconf.h:427:14: fatal error: 'stdarg.h' file not found > # include <stdarg.h> /* for va_list */ > ^ > 1 error generated. > make[3]: *** [adler32.o] Error 1 > make[3]: *** Waiting for unfinished jobs.... > 1 error generated. > make[3]: 1 error*** [example.o] Error 1 > generated. > make[3]: *** [crc32.o] Error 1 > Error building zlib. > > real 0m1.231s > user 0m0.485s > sys 0m0.497s > ************************************************************************ > Error installing package zlib-1.2.8.p0 > ************************************************************************ > Please email sage-devel (http://groups.google.com/group/sage-devel) > explaining the problem and including the relevant part of the log file > /Users/lauve/sage-devel/logs/pkgs/zlib-1.2.8.p0.log > Describe your computer, operating system, etc. > If you want to try to fix the problem yourself, *don't* just cd to > /Users/lauve/sage-devel/local/var/tmp/sage/build/zlib-1.2.8.p0 and type > 'make' or whatever is appropriate. > Instead, the following commands setup all environment variables > correctly and load a subshell for you to debug the error: > (cd '/Users/lauve/sage-devel/local/var/tmp/sage/build/zlib-1.2.8.p0' && > '/Users/lauve/sage-devel/sage' --sh) > When you are done debugging, you can type "exit" to leave the subshell. > ************************************************************************ > > > > > > On Thursday, June 18, 2015 at 3:29:17 PM UTC-5, Volker Braun wrote: > > The actual logs of whatever failed > > On Thursday, June 18, 2015 at 8:56:56 PM UTC+2, la...@math.luc.edu wrote: > > will install Xcode and get back to you. in the meantime, did you just want > a directory listing, or the actual logs? > > weehawken:sage-devel lauve$ ls logs/pkgs/ > bzip2-1.0.6.20140317.log mpfr-3.1.2.p0.log pkgconf-0.9.7.log > config.log mpir-2.7.0-alpha12.log zlib-1.2.8.p0.log > > iconv-1.14.log patch-2.7.1.log > > > > On Thursday, June 18, 2015 at 1:27:43 PM UTC-5, Volker Braun wrote: > > I think you need to have XCode installed, even though you shouldn't have > to. > > Can you also post logs (in SAGE_ROOT/logs/pkgs/) > > > On Thursday, June 18, 2015 at 7:29:56 PM UTC+2, la...@math.luc.edu wrote: > > Okay... > I am now running 10.10.3. > to try to get a clean version of tools, I deleted the following three > directories: > * /Applications/Xcode.app > * /Library/Developer/CommandLineTools > * /usr/include/c++ > I ran xcode-select --install from the command line. A pop up asked me to > install. I did. > Now /Library/Developer/CommandLineTools and /usr/include/c++ have returned. > (note that I do not have XCode.app at present) > > Still, in my sage source directory, when I run make -j4, I get errors. > (Setting SAGE_KEEP_BUILT_SPKGS='yes' doesn't eliminate the problem.) > > There are errors in the packages *mpfr-3.1.2.p0* and *zlib-1.2.8.p0*. > > In my logs, the packages seem not to be able to find files that I'm sure > are there: *float.h* and *stdarg.h* > indeed, there is some general checks that flew by earlier in the build > process to the effect, > > checking float.h usability... yes > > checking float.h presence... yes > checking for float.h... yes > > Yet, mpfr cannot find it. Similarly, earlier in the 'make' process, I saw > fly by the line > > checking whether <stdarg.h> exists and works... yes > > > > new output of gcc --version : > > Configured with: --prefix=/Library/Developer/CommandLineTools/usr > --with-gxx-include-dir=/usr/include/c++/4.2.1 > > Apple LLVM version 6.1.0 (clang-602.0.53) (based on LLVM 3.6.0svn) > > Target: x86_64-apple-darwin14.3.0 > > Thread model: posix > > > (note: both of the directories mentioned do exist. The files *float.h* > and *stdarg.h* exist in: > > * /Library/Developer/CommandLineTools/usr/lib/clang/6.1.0/include/ > > * /usr/include/c++/4.2.1/tr1/ > > among other places) > > > output of xcode-select --version : > > xcode-select version 2333 > > > > output of locate stdarg.h : > > /Applications/local/include/c++/4.6.3/tr1/stdarg.h > > > /Applications/local/lib/gcc/x86_64-apple-darwin10.8.0/4.6.3/include/cross-stdarg.h > > > /Applications/local/lib/gcc/x86_64-apple-darwin10.8.0/4.6.3/include/stdarg.h > > > > /Library/Developer/CommandLineTools/Library/PrivateFrameworks/LLDB.framework/Versions/A/Resources/Clang/include/stdarg.h > > /Library/Developer/CommandLineTools/usr/lib/clang/6.1.0/include/stdarg.h > > /Library/Developer/CommandLineTools/usr/lib/llvm-gcc/4.2.1/include/stdarg.h > > /System/Library/Frameworks/Kernel.framework/Versions/A/Headers/stdarg.h > > > /System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/2.0/include/stdarg.h > > /usr/include/c++/4.2.1/tr1/stdarg.h > > > output of locate float.h : > > /Applications/gap4r4/src/float.h > > /Applications/local/include/c++/4.6.3/tr1/float.h > > /Applications/local/lib/gap-4.4.12/src/float.h > > /Applications/local/lib/gcc/x86_64-apple-darwin10.8.0/4.6.3/include/float.h > > > /Library/Developer/CommandLineTools/Library/PrivateFrameworks/LLDB.framework/Versions/A/Resources/Clang/include/float.h > > /Library/Developer/CommandLineTools/usr/lib/clang/6.1.0/include/float.h > > > /System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/2.0/include/float.h > > /usr/include/c++/4.2.1/tr1/float.h > > > > Any further ideas? > > > > On Wednesday, June 10, 2015 at 2:56:55 PM UTC-5, Volker Braun wrote: > > Since Apple declined to fix the "rootpipe" bug in OSX 10.9 I would > recommend to upgrade to OSX 10.10 asap, effectively you don't receive > security fixes any more. > > Even then, why did you not upgrade to command line tools 6.2? They should > still run on OSX 10.9 > > ... -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
