In the newest gcc 4.9.1 package, after ./configure I ran make, and it failed with error message:
checking for x86_64-unknown-linux-gnu-gcc... /root/tar/gcc-4.9.1/host-x86_64-unknown-linux-gnu/gcc/xgcc -B/root/tar/gcc-4.9.1/host-x86_64-unknown-linux-gnu/gcc/ -B/usr/local/x86_64-unknown-linux-gnu/bin/ -B/usr/local/x86_64-unknown-linux-gnu/lib/ -isystem /usr/local/x86_64-unknown-linux-gnu/include -isystem /usr/local/x86_64-unknown-linux-gnu/sys-include
checking for suffix of object files... configure: error: in `/root/tar/gcc-4.9.1/x86_64-unknown-linux-gnu/libgcc':
configure: error: cannot compute suffix of object files: cannot compile
See `config.log' for more details.
I checked the config.log in the x86_64-unknown-linux-gnu/libgcc/, and it said,
configure:3389: /root/tar/gcc-4.9.1/host-x86_64-unknown-linux-gnu/gcc/xgcc -B/root/tar/gcc-4.9.1/host-x86_64-unknown-linux-gnu/gcc/ -B/usr/local/x86_64-unknown-linux-gnu/bin/ -B/usr/local/x86_64-unknown-linux-gnu/lib/ -isystem /usr/local/x86_64-unknown-linux-gnu/include -isystem /usr/local/x86_64-unknown-linux-gnu/sys-include -o conftest -g -O2 conftest.c >&5
/root/tar/gcc-4.9.1/host-x86_64-unknown-linux-gnu/gcc/cc1: error while loading shared libraries: libmpc.so.2: cannot open shared object file: No such file or directory
configure:3392: $? = 1
configure:3580: checking for suffix of object files
configure:3602: /root/tar/gcc-4.9.1/host-x86_64-unknown-linux-gnu/gcc/xgcc -B/root/tar/gcc-4.9.1/host-x86_64-unknown-linux-gnu/gcc/ -B/usr/local/x86_64-unknown-linux-gnu/bin/ -B/usr/local/x86_64-unknown-linux-gnu/lib/ -isystem /usr/local/x86_64-unknown-linux-gnu/include -isystem /usr/local/x86_64-unknown-linux-gnu/sys-include -c -g -O2 conftest.c >&5
/root/tar/gcc-4.9.1/host-x86_64-unknown-linux-gnu/gcc/cc1: error while loading shared libraries: libmpc.so.2: cannot open shared object file: No such file or directory
configure:3606: $? = 1
configure: failed program was:
But obviously I have libmpc.so.2 in /usr/local/lib. What's wrong??
It looks like the problem is due to the fact that the default path /usr/local/lib is not included in the $LD_LIBRARY_PATH environment variable. Sorry for this stupid question...
Related
I am trying to compile some software that contains a compile.sh shell script. When I run the script, the software fails to compile due to what it reports as a broken C compiler.
I have tried reinstalling C compilers, both within and outside of conda, to no avail.
Below, please find the output of running the compile shell script
(base) userA#server:~/SPAdes-3.13.0-dev$ ./spades_compile.sh
-- The C compiler identification is GNU 7.3.0
-- The CXX compiler identification is GNU 7.3.0
-- Check for working C compiler: /home/userA/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-- Check for working C compiler: /home/userA/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -- broken
CMake Error at /home/userA/anaconda3/share/cmake-3.14/Modules/CMakeTestCCompiler.cmake:60 (message):
The C compiler
"/home/userA/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc"
is not able to compile a simple test program.
It fails with the following output:
Change Dir: /home/userA/SPAdes-3.13.0-dev/build_spades/CMakeFiles/CMakeTmp
Run Build Command(s):/usr/bin/make cmTC_708f4/fast
/usr/bin/make -f CMakeFiles/cmTC_708f4.dir/build.make CMakeFiles/cmTC_708f4.dir/build
make[1]: Entering directory '/home/userA/SPAdes-3.13.0-dev/build_spades/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_708f4.dir/testCCompiler.c.o
/home/userA/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -o CMakeFiles/cmTC_708f4.dir/testCCompiler.c.o -c /home/userA/SPAdes-3.13.0-dev/build_spades/CMakeFiles/CMakeTmp/testCCompiler.c
Linking C executable cmTC_708f4
/home/userA/anaconda3/bin/cmake -E cmake_link_script CMakeFiles/cmTC_708f4.dir/link.txt --verbose=1
/home/userA/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -rdynamic CMakeFiles/cmTC_708f4.dir/testCCompiler.c.o -o cmTC_708f4
/home/userA/anaconda3/bin/x86_64-conda_cos6-linux-gnu-ld: cannot find crtbeginS.o: No such file or directory
/home/userA/anaconda3/bin/x86_64-conda_cos6-linux-gnu-ld: cannot find -lgcc
/home/userA/anaconda3/bin/x86_64-conda_cos6-linux-gnu-ld: cannot find -lgcc
collect2: error: ld returned 1 exit status
CMakeFiles/cmTC_708f4.dir/build.make:86: recipe for target 'cmTC_708f4' failed
make[1]: *** [cmTC_708f4] Error 1
make[1]: Leaving directory '/home/userA/SPAdes-3.13.0-dev/build_spades/CMakeFiles/CMakeTmp'
Makefile:121: recipe for target 'cmTC_708f4/fast' failed
make: *** [cmTC_708f4/fast] Error 2
CMake will not be able to correctly generate this project.
Expected result: properly compiled software
Actual result: report of a broken C compiler
Ok, I'm having trouble building gcc-4.9.2 on Apple's new OS X Yosemite. I'm not sure if I need to be building a gnu-gcc compiler on OS X, as most other software has compiled fine, apart from tesseract-3.0.1 and some of my own wxWidgets applications. Are there certain programs/code features that clang can't compile?
My build steps are as follows:
cd build-gcc
../gcc-4.9.1/configure --program-prefix="gnu-" --prefix="/usr/local/gcc-4.9.1" --with-gmp="/usr/local" --with-mpfr="/usr/local" --with-mpc="/usr/local" CC=clang CXX=clang++
make
My build path and gcc source paths do not contain any whitespace, and I have installed GMP, MPFR and MPC in /usr/local.
My build outputs are:
clang++ -g -DIN_GCC -fno-exceptions -fno-rtti -fasynchronous-unwind-tables -W -Wall -Wno-narrowing -Wwrite-strings -Wcast-qual -Wno-format -Wmissing-format-attribute -pedantic -Wno-long-long -Wno-variadic-macros -Wno-overlength-strings -fno-common -DHAVE_CONFIG_H -Wl,-no_pie -o cc1 c/c-lang.o c-family/stub-objc.o attribs.o c/c-errors.o c/c-decl.o c/c-typeck.o c/c-convert.o c/c-aux-info.o c/c-objc-common.o c/c-parser.o c/c-array-notation.o c-family/c-common.o c-family/c-cppbuiltin.o c-family/c-dump.o c-family/c-format.o c-family/c-gimplify.o c-family/c-lex.o c-family/c-omp.o c-family/c-opts.o c-family/c-pch.o c-family/c-ppoutput.o c-family/c-pragma.o c-family/c-pretty-print.o c-family/c-semantics.o c-family/c-ada-spec.o c-family/c-cilkplus.o c-family/array-notation-common.o c-family/cilk.o c-family/c-ubsan.o i386-c.o darwin-c.o \
cc1-checksum.o libbackend.a main.o tree-browser.o libcommon-target.a libcommon.a ../libcpp/libcpp.a ../libdecnumber/libdecnumber.a libcommon.a ../libcpp/libcpp.a ./../intl/libintl.a -liconv ../libbacktrace/.libs/libbacktrace.a ../libiberty/libiberty.a ../libdecnumber/libdecnumber.a -L/usr/local/lib -L/usr/local/lib -L/usr/local/lib -lmpc -lmpfr -lgmp -L../zlib -lz
ld: warning: ld: warning: ld: warning: ignoring file libbackend.a, file was built for archive which is not the architecture being linked (x86_64): libbackend.aignoring file libcommon-target.a, file was built for archive which is not the architecture being linked (x86_64): libcommon-target.aignoring file ../libdecnumber/libdecnumber.a, file was built for archive which is not the architecture being linked (x86_64): ../libdecnumber/libdecnumber.a
ld: warning: ignoring file ../zlib/libz.a, file was built for archive which is not the architecture being linked (x86_64): ../zlib/libz.a
Undefined symbols for architecture x86_64:
... (Lots of symbols)
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[3]: *** [cc1] Error 1
make[2]: *** [all-stage1-gcc] Error 2
make[1]: *** [stage1-bubble] Error 2
make: *** [all] Error 2
Configure outputs the build type as: x86_64-apple-darwin14.0.0, so I don't understand why this is happening.
Thank You in advance for any help.
Turns out that I had a broken ranlib in /usr/local/bin - maybe GNU Binutils don't work on OS X? All I needed to do to fix the problem was to:
sudo mv /usr/local/bin/ranlib /usr/local/ranlib_old
and then make, and now I have a working GCC!
I've problem with gbarcode gem which has dependency gnu-barcode c application.
When trying to say gem install gbarcode it says:
Building native extensions. This could take a while...
ERROR: Error installing gbarcode-linux:
ERROR: Failed to build gem native extension.
/home/user/.rvm/rubies/ruby-1.8.7-p357/bin/ruby extconf.rb
checking for main() in -lbarcode... yes
creating Makefile
make
gcc -I. -I. -I/home/user/.rvm/rubies/ruby-1.8.7-p357/lib/ruby/1.8/x86_64-linux -I. -fPIC -g -O2 -fPIC -c barcode_wrap.c
gcc -shared -o gbarcode.so barcode_wrap.o -L. -L/home/user/.rvm/rubies/ruby-1.8.7-p357/lib -Wl,-R/home/user/.rvm/rubies/ruby-1.8.7-p357/lib -L. -rdynamic -Wl,-export-dynamic -Wl,-R -Wl,/home/user/.rvm/rubies/ruby-1.8.7-p357/lib -L/home/user/.rvm/rubies/ruby-1.8.7-p357/lib -lruby -lbarcode -lrt -ldl -lcrypt -lm -lc
/usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/4.6/../../../../lib/libbarcode.a(library.o): relocation R_X86_64_32 against `encodings' can not be used when making a shared object; recompile with -fPIC
/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../../lib/libbarcode.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make: *** [gbarcode.so] Error 1
I've tried to install gnu-barcode application from ubuntu software center, apt-get and directly from source http://www.gnu.org/software/barcode/ and the response is always the same.
How should I install gnu barcode so that it's working with the gem.
And yes this project is quite heavy dependent on that gem so replacing it would be really painful to all parties.
I am having trouble installing pyipopt on ubuntu 12.04. During linking, I receive the error:
/usr/bin/ld: cannot find -lcoinhsl
Even though I know that this library is installed and the .so and .la files are available in /home/mostafa/MyBuilds/CoinIpopt/build/lib/
does anyone have a solution for this?
below is the complete return of running setup.py build:
root#ubuntu:~/MyBuilds/pyipopt# sudo python setup.py build
running build
running build_ext
building 'pyipopt' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/home/mostafa/MyBuilds/CoinIpopt/build/include/coin/ -I/usr/include/python2.7 -c src/callback.c -o build/temp.linux-x86_64-2.7/src/callback.o
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/home/mostafa/MyBuilds/CoinIpopt/build/include/coin/ -I/usr/include/python2.7 -c src/pyipopt.c -o build/temp.linux-x86_64-2.7/src/pyipopt.o
src/pyipopt.c: In function ‘set_intermediate_callback’:
src/pyipopt.c:452:15: warning: variable ‘myowndata’ set but not used [-Wunused-but-set-variable]
gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relrobuild/temp.linux-x86_64-2.7/src/callback.o build/temp.linux-x86_64-2.7/src/pyipopt.o -L/home/mostafa/MyBuilds/CoinIpopt/build/lib/ -lipopt -lblas -lcoinhsl -lcoinmetis -llapack -ldl -lm -o build/lib.linux-x86_64-2.7/pyipopt.so -Wl,--rpath -Wl,/home/mostafa/MyBuilds/CoinIpopt/build/lib/
/usr/bin/ld: cannot find -lcoinhsl
collect2: ld returned 1 exit status
error: command 'gcc' failed with exit status 1
-Ldir
Add directory dir to the list of directories to be searched for -l.
You may install your coinhsl library in one of your standard libraries directories and run 'ldconfig` before doing your ppyipopt install
I had a similar problem with another library and the reason why it didn't found it, was that I didn't run the make install (after running ./configure and make) for that library. The make install may require root privileges (in this case use: sudo make install). After running the make install you should have the so files in the correct folder, i.e. here /usr/local/lib and not in the folder mentioned by you.
you can add the Path to coinhsl lib to LD_LIBRARY_PATH variable. May be that will help.
export LD_LIBRARY_PATH=/xx/yy/zz:$LD_LIBRARY_PATH
where /xx/yy/zz represent the path to coinhsl lib.
I'm trying to install gcc 4.6.2 with ppl and cloog in 64 bit ubuntu 10.10. I get the following error when I do make.
make[3]: Entering directory `/home/praveen/gcc-4.6.2/host-x86_64-unknown-linux-gnu/gcc'
/home/praveen/gcc-4.6.2/host-x86_64-unknown-linux-gnu/prev-gcc/xgcc -B/home/praveen/gcc-4.6.2/host-x86_64-unknown-linux-gnu/prev-gcc/ -B/usr/local/x86_64-unknown-linux-gnu/bin/ -B/usr/local/x86_64-unknown-linux-gnu/bin/ -B/usr/local/x86_64-unknown-linux-gnu/lib/ -isystem /usr/local/x86_64-unknown-linux-gnu/include -isystem /usr/local/x86_64-unknown-linux-gnu/sys-include -g -O2 -gtoggle -DIN_GCC -W -Wall -Wwrite-strings -Wcast-qual -Wstrict-prototypes -Wmissing-prototypes -Wmissing-format-attribute -pedantic -Wno-long-long -Wno-variadic-macros -Wno-overlength-strings -Wold-style-definition -Wc++-compat -DHAVE_CONFIG_H -static-libstdc++ -static-libgcc -o cc1 c-lang.o c-family/stub-objc.o attribs.o c-errors.o c-decl.o c-typeck.o c-convert.o c-aux-info.o c-objc-common.o c-parser.o tree-mudflap.o c-family/c-common.o c-family/c-cppbuiltin.o c-family/c-dump.o c-family/c-format.o c-family/c-gimplify.o c-family/c-lex.o c-family/c-omp.o c-family/c-opts.o c-family/c-pch.o c-family/c-ppoutput.o c-family/c-pragma.o c-family/c-pretty-print.o c-family/c-semantics.o c-family/c-ada-spec.o i386-c.o \
cc1-checksum.o main.o libbackend.a ../libcpp/libcpp.a ../libdecnumber/libdecnumber.a ../libcpp/libcpp.a ../libiberty/libiberty.a ../libdecnumber/libdecnumber.a -lcloog -lppl_c -lppl -lpwl -lgmpxx -lmpc -lmpfr -lgmp -rdynamic -ldl -L../zlib -lz
libbackend.a(graphite-ppl.o): In function `ppl_powerset_is_empty':
graphite-ppl.c:(.text+0xd5d): undefined reference to `ppl_new_PIP_Problem_from_constraints'
graphite-ppl.c:(.text+0xd66): undefined reference to `ppl_PIP_Problem_is_satisfiable'
graphite-ppl.c:(.text+0xd71): undefined reference to `ppl_delete_PIP_Problem'
collect2: ld returned 1 exit status
make[3]: *** [cc1] Error 1
make[3]: Leaving directory `/home/praveen/gcc-4.6.2/host-x86_64-unknown-linux-gnu/gcc'
make[2]: *** [all-stage2-gcc] Error 2
make[2]: Leaving directory `/home/praveen/gcc-4.6.2'
make[1]: *** [stage2-bubble] Error 2
make[1]: Leaving directory `/home/praveen/gcc-4.6.2'
make: *** [all] Error 2
Can some one help me out on this ?
I faced the same problem a while ago on my gentoo installation. The workarround was to build gcc without graphite option then to rebuild ppl and cloog-ppl libraries with a new version of gcc. Only after that gcc was successfully built with graphite.
The problem, I believe, is that the ppl library libppl_c.so.4 is reported by make to be non-existent during the linking process -- even if the library has been installed to the standard /usr/local/lib directory successfully. Try reconfiguring with the flag --with-ppl-lib. I also included the flag --with-ppl-include and the corresponding cloog flags too (just to pre-empt any possible corresponding problems with cloog) because I didn't want to have to keep recompiling to discover exactly which flags I needed, so I played it cautiously and included all of these; maybe you also need them too, but probably not. Whilst you should be able to just use the flag --with-ppl, that will not work.
# I installed ppl and cloog to the standard subdirectories of /usr/local
# but you can amend the flag inputs as necessary
tar xjf gcc-x.tar.bz2
mkdir build && cd build
../gcc-x/configure --with-ppl-lib=/usr/local/lib \
--with-ppl-include=/usr/local/include \
--with-cloog-lib=/usr/local/lib \
--with-cloog-include=/usr/local/include
Again, the issue is probably that the non-existence of the --with-ppl-lib flag is setting some internal configure variable incorrectly rather than there being a general linking issue with the library.