I'm getting recurring errors when using make on Mac OS Mountain Lion v10.8.4.
I tried to install libev, and, after running ./configure, I ran make and got:
libtool: link: gcc -dynamiclib -Wl,-undefined -Wl,dynamic_lookup -o .libs/libev.4.dylib .libs/ev.o .libs/event.o -O3 -install_name /usr/local/lib/libev.4.dylib -compatibility_version 5 -current_version 5.0 -Wl,-single_module
libtool: link: dsymutil .libs/libev.4.dylib || :
libtool: link: (cd ".libs" && rm -f "libev.dylib" && ln -s "libev.4.dylib" "libev.dylib")
libtool: link: ar cru .libs/libev.a ev.o event.o
ranlib: unrecognized option `-q'
ranlib: Try `ranlib --help' for more information.
ar: internal ranlib command failed
make[1]: *** [libev.la] Error 1
make: *** [all] Error 2
I see a pattern because when I run make when trying to install httpd
I get this error:
libtool: link: rm -fr .libs/libev.4.dylib .libs/libev.4.dylib.dSYM .libs/libev.a .libs/libev.dylib
libtool: link: gcc -dynamiclib -Wl,-undefined -Wl,dynamic_lookup -o .libs/libev.4.dylib .libs/ev.o .libs/event.o -O3 -install_name /usr/local/lib/libev.4.dylib -compatibility_version 5 -current_version 5.0 -Wl,-single_module
libtool: link: dsymutil .libs/libev.4.dylib || :
libtool: link: (cd ".libs" && rm -f "libev.dylib" && ln -s "libev.4.dylib" "libev.dylib")
libtool: link: ar cru .libs/libev.a ev.o event.o
ranlib: unrecognized option `-q'
ranlib: Try `ranlib --help' for more information.
ar: internal ranlib command failed
make[1]: *** [libev.la] Error 1
make: *** [all] Error 2
It looks like I have an issue with ranlib but I'm not sure how to fix it.
I saw somewhere that I should reinstall my developer tools, so I did but it hasn't helped.
First the obvious actions: make sure you have the latest libev release, and Xcode is up to date. The configure system seems outdated, as it detects the (my) host system as i386-apple-darwin12.4.0 rather than x86_64-apple-darwin12.4.0. Though it still seemed to build.
If you have the autotools installed, e.g., autoconf-2.69, automake-1.13.3, and libtool-2.4.2 (which is typically installed as glibtool on OS X), you can run the included autoreconf command with: sh autogen.sh to refresh the configure system. It will issue a few warnings that can be ignored.
./configure CC="clang" CFLAGS="-pipe -W -Wall -O2 [-march=core2]"
Xcode -> Preferences -> Downloads -> Components :
check and install "Command Line Tools if you haven't already, which might be enough. If you still have a terminal open through the process, type the rehash command. Possibly you've done all this, but some Mac developers never leave the IDE.
Related
I am trying to build a project using cmake. however when cmake verifies whether I have a working c compiler it fails with the output:
Run Build Command(s):/usr/bin/make -f Makefile cmTC_a842e/fast && /Library/Developer/CommandLineTools/usr/bin/make -f CMakeFiles/cmTC_a842e.dir/build.make CMakeFiles/cmTC_a842e.dir/build
Building C object CMakeFiles/cmTC_a842e.dir/testCCompiler.c.o
/usr/bin/clang -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk -MD -MT CMakeFiles/cmTC_a842e.dir/testCCompiler.c.o -MF CMakeFiles/cmTC_a842e.dir/testCCompiler.c.o.d -o CMakeFiles/cmTC_a842e.dir/testCCompiler.c.o -c /Users/simon/Desktop/Sommer22/DA_Lab/cpp_impl/lab22-p4-streaming/SHJ_producer_consumer/build/CMakeFiles/CMakeTmp/testCCompiler.c
Linking C executable cmTC_a842e
/usr/local/Cellar/cmake/3.24.0/bin/cmake -E cmake_link_script CMakeFiles/cmTC_a842e.dir/link.txt --verbose=1
/usr/bin/clang -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/cmTC_a842e.dir/testCCompiler.c.o -o cmTC_a842e
ld: library not found for -lSystem
indeed, I do not have a libSystem.dylib installed on my Mac.
I am using clang 13 to build it.
deleting CommandLine tools directory and doing Xcode-select --install fixed the problem
I am trying to implement text generator of JAMR. It redirects me to install cdec. I followed this tutorial to install cdec. BUT
I installed gcc-4.8 (I had a better version 5.x but I thought 4.8 is neccessary). So I installed gcc-4.8 using this. And I build Boost using this (in ~/prefix/sw), I used boost_1_58 because it was latest. Everything worked fine.
Coming back to the tutorial, instead of cd ~/prefix/sw I went to cd jamr/tools/cdec where my cdec is present. Did autoreconf -ifv and ./configure --prefix=/home/student/prefix, fine till now (I just had to comment line 216 of containing boost_major_version and wrote boost_major_version="158"). But when I do make after a while I get
libtool: link: g++ -std=gnu++11 -fPIC -g -O3 /usr/lib /usr/lib -o reconstruct_weights reconstruct_weights.o -L/usr/lib libutils.a -ldl -lrt -lboost_program_options -lboost_regex -lboost_serialization -lboost_system -lboost_filesystem -lz -lbz2
/usr/bin/ld: cannot find /usr/lib: File format not recognized
/usr/bin/ld: cannot find /usr/lib: File format not recognized
collect2: error: ld returned 1 exit status
Makefile:836: recipe for target 'reconstruct_weights' failed
make[2]: *** [reconstruct_weights] Error 1
make[2]: Leaving directory '/home/student/ATS/jamr/tools/cdec-2014-10-12/utils'
Makefile:480: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/student/ATS/jamr/tools/cdec-2014-10-12'
Makefile:410: recipe for target 'all' failed
make: *** [all] Error 2
I tried sudo make, simple ./configure and make clean;make. No help. This is make file.
When you are in the cdec folder and you try to execute the commands there according to the instructions, we see that you get the collect2 error: error: ld returned 1 exit status. In the cdec folder, i initially execute the command:
gcc -std=gnu99 -Wall -Werror -g array_product.c -o array_product -I../../ZDK -L../../ZDK -I../../TestLib04 -L../../TestLib04 -ltestlib04 -lzdk -lncurses -lm
After this command, the error is solved and i get to the file and it says:
> First, you need all the build dependencies, and the fastest way to install them all is this command, which installs not only the compiler but the additional boost libraries and Flex that you'll need. sudo apt-get install build-essential libboost-all-dev cmake flex
> Secondly, create a directory and go into it (you said ~/prefix/sw in your comments).
> Thirdly, git clone https://github.com/redpony/cdec.git
> Fourthly, you probably did not read the README page on the GitHub repository which explains what commands to run to make the software build. It lists these as the build steps, after cd-ing into the newly created cdec folder.
I am trying to install OpenMP enabled xgboost on my mac. I installed gcc with no problem:
brew install gcc --without-multilib
then cloned git repository:
git clone --recursive https://github.com/dmlc/xgboost
cd xgboost; cp make/config.mk ./config.mk
but I get an error when I do
make -j4
Here is the error I get. I'd appreciate if you can help fixing this problem:
c++ -std=c++0x -Wall -O3 -msse2 -Wno-unknown-pragmas -funroll-loops -Iinclude -Idmlc-core/include -Irabit/include -fPIC -fopenmp -o xgboost build/cli_main.o build/learner.o build/logging.o build/c_api/c_api.o build/c_api/c_api_error.o build/common/common.o build/data/data.o build/data/simple_csr_source.o build/data/simple_dmatrix.o build/data/sparse_page_dmatrix.o build/data/sparse_page_raw_format.o build/data/sparse_page_source.o build/data/sparse_page_writer.o build/gbm/gblinear.o build/gbm/gbm.o build/gbm/gbtree.o build/metric/elementwise_metric.o build/metric/metric.o build/metric/multiclass_metric.o build/metric/rank_metric.o build/objective/multiclass_obj.o build/objective/objective.o build/objective/rank_obj.o build/objective/regression_obj.o build/tree/tree_model.o build/tree/tree_updater.o build/tree/updater_colmaker.o build/tree/updater_histmaker.o build/tree/updater_prune.o build/tree/updater_refresh.o build/tree/updater_skmaker.o build/tree/updater_sync.o dmlc-core/libdmlc.a rabit/lib/librabit.a -pthread -lm -fopenmp
c++ -std=c++0x -Wall -O3 -msse2 -Wno-unknown-pragmas -funroll-loops -Iinclude -Idmlc-core/include -Irabit/include -fPIC -fopenmp -shared -o lib/libxgboost.so build/learner.o build/logging.o build/c_api/c_api.o build/c_api/c_api_error.o build/common/common.o build/data/data.o build/data/simple_csr_source.o build/data/simple_dmatrix.o build/data/sparse_page_dmatrix.o build/data/sparse_page_raw_format.o build/data/sparse_page_source.o build/data/sparse_page_writer.o build/gbm/gblinear.o build/gbm/gbm.o build/gbm/gbtree.o build/metric/elementwise_metric.o build/metric/metric.o build/metric/multiclass_metric.o build/metric/rank_metric.o build/objective/multiclass_obj.o build/objective/objective.o build/objective/rank_obj.o build/objective/regression_obj.o build/tree/tree_model.o build/tree/tree_updater.o build/tree/updater_colmaker.o build/tree/updater_histmaker.o build/tree/updater_prune.o build/tree/updater_refresh.o build/tree/updater_skmaker.o build/tree/updater_sync.o dmlc-core/libdmlc.a rabit/lib/librabit.a -pthread -lm -fopenmp
clangclang: : warningwarning: : argument unused during compilation: '-pthread'argument unused during compilation: '-pthread'
ld: library not found for -lgomp
ld: library not found for -lgomp
clang: error: clanglinker command failed with exit code 1 (use -v to see invocation):
error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [lib/libxgboost.so] Error 1
make: *** Waiting for unfinished jobs....
make: *** [xgboost] Error 1
I have the same issue and solved it by:
brew install clang-omp
export CC=clang-omp
export CXX=clang-omp++
git clone --recursive https://github.com/dmlc/xgboost
cd xgboost; cp make/config.mk ./config.mk; make -j4
cd python-package
sudo python setup.py install
If you used pip to install xgboost before, then delete the previous installed xgboost from your project. Then use
pip install xgboost
to install it again.
A new versions of OSX has a Clang as a default c\c++ compiler. Therefore your c++ command refers to clang++.
You should define a CC\CXX environmental variables for your make command like this CC=gcc CXX=g++ make -j
Also you can build an OpenMP for clang OpenMPrt and customise your shell environment (I didn't try this by own)
(I have no mac at this moment to check this solution; just linux)
Update
The error happens at line 8962 of libtool, which performs a lot of commands inside a loop. The content of the problematic command is
arm-xilinx-linux-gnueabi-gcc -shared -fPIC -DPIC genl/.libs/ctrl.o genl/.libs/family.o genl/.libs/genl.o genl/.libs/mngt.o -Wl,-rpath -Wl,/usr/arm-linux-gnueabi/lib -L/usr/arm-linux-gnueabi/lib -lnl-3 -lpthread -lm -O2 -Wl,--version-script=../libnl.sym -Wl,-soname -Wl,libnl-genl-3.so.200 -o .libs/libnl-genl-3.so.200.19.0
If I manually run it, it says
error: genl/.libs/ctrl.o: No such file or directory
the .o s are there, but the problem is that make install is under sudo, but sudo is a different environment and it doesn't recognize the paths. So solution is:
sudo -s
source /opt/pkg/......./settings.sh
source command is required by Xilinx Petalinux for the paths. Now make install will work
Original
I am following the beyond logic example to cross compile the iw tool. The first step is the libnl. I am using CentOS to crossc compile libnl, so I have to run source /opt/pkg/.../settings.sh to setup the arm-xilinx-linux-gnueabi-gcc paths. I then used ./configure --host=arm-xilinx-linux-gnueabi --prefix=/usr/arm-xilinx-linux-gnueabi
The make is running fine. But make install failed with following errors:
libtool: install: (cd /xxx/libnl-3.2.24/lib; /bin/sh /home/xxx/libnl-3.2.24/libtool --silent --tag CC --mode=relink arm-xilinx-linux-gnueabi-gcc -g -O2 -version-info 219:0:19 -Wl,--version-script=../libnl.sym -o libnl-genl-3.la -rpath /usr/arm-xilinx-linux-gnueabi/lib genl/ctrl.lo genl/family.lo genl/genl.lo genl/mngt.lo libnl-3.la -lpthread -lm )
/xxx/libnl-3.2.24/libtool: line 8962:
arm-xilinx-linux-gnueabi-gcc: command not found
libtool: install: error: relink `libnl-genl-3.la' with the above command before installing it
make[3]: *** [install-libLTLIBRARIES] Error 1
make[3]: Leaving directory `/xxx/libnl-3.2.24/lib'
make[2]: *** [install-am] Error 2
make[2]: Leaving directory `/xxx/libnl-3.2.24/lib'
make[1]: *** [install] Error 2
make[1]: Leaving directory `/xxx/libnl-3.2.24/lib'
make: *** [install-recursive] Error 1
so since make is successful using arm-xilinx-linux-gnueabi-gcc, why make install is complaining it can't find it?
Problem is with following statement
./configure --host=arm-xilinx-linux-gnueabi --prefix=/usr/arm-xilinx-linux-gnueabi
arm-xilinx-linux-gnueabi is not installed at /usr thats why getting arm-xilinx-linux-gnueabi-gcc: command not founderror.
Install arm toolchain and then follow procedure mentioned in beyond logic example
This is a follow-up to the question at Element-Wise Matrix Multiplication in Rcpp
I have been getting a number of different kinds of errors with RcppArmadillo since upgrading to Mavericks. I have Xcode 5.0.2 and Command Line Tools installed. Also, gfortran from Homebrew. But I keep encountering the error below --
> cppFunction("arma::mat schur(arma::mat& a, arma::mat& b)
{ return(a % b); }", depends="RcppArmadillo")
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [sourceCpp_18474.so] Error 1
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include - I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include" -fPIC "-mtune=native -g -O2 -Wall -pedantic -Wconversion" -c fileaf992bfb8f84.cpp -o fileaf992bfb8f84.o clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o sourceCpp_18474.so fileaf992bfb8f84.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -lgfortran /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
Error in sourceCpp(code = code, env = env, rebuild = rebuild, showOutput = showOutput, :
Error 1 occurred building shared library.
WARNING: The tools required to build C++ code for R were not found.
Please install Command Line Tools for XCode (or equivalent).
# Contents of Makevars
$ cat ~/.R/Makevars
CC=clang
CXX=clang++
CXXFLAGS="-mtune=native -g -O2 -Wall -pedantic -Wconversion"
FLIBS=-lgfortran
Commenting FLIBS=-lgfortran does not help and results in even more error messages --
> cppFunction("arma::mat schur(arma::mat& a, arma::mat& b) { return(a % b); }", depends="RcppArmadillo")
ld: warning: directory not found for option '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64'
ld: warning: directory not found for option '-L/usr/local/lib/x86_64'
ld: warning: directory not found for option '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [sourceCpp_50381.so] Error 1
Thanks in advance.
Update
Following suggestions from response from Kevin and Dirk below, I re-installed Rcpp, RcppArmadillo and inline from source and updated FLIBS to point to the actual directory. This solved the issue.
# Update FLIBS in ~/.R/Makevars
FLIBS=-L/usr/local/Cellar/gfortran/4.8.2/gfortran
#Re-Install from source
install.packages(c("Rcpp","RcppArmadillo","inline"),type="source")
#Restart R
EDIT: If you're a Homebrew user, you now instead need to use brew install gcc (gfortran is no longer provided separate of gcc), and you can then follow the instructions here to get set up.
You have to symlink the libraries to /usr/local/lib manually:
ln -s /usr/local/Cellar/gfortran/4.8.2/gfortran/lib/libgfortran.* /usr/local/lib/
I thought brew link gfortran would handle this, but apparently it only symlinks the gfortran program and not the actual libraries. So, unfortunately, you have to do it yourself.
(Replace 4.8.2 with whichever version of gfortran you're using from homebrew.)
Alternatively, if you want to keep from modifying /usr/local/lib, you can use
FLIBS=-L/usr/local/Cellar/gfortran/4.8.2/gfortran
in your ~/.R/Makevars file instead, so R knows where to find the gfortran libraries.
I can only suggest you study the numerous threads on the r-sig-mac list, the different answers here on SO as well as the posts on the rcpp-devel list.
As your error comes from the failed Fortran linking, maybe also review the standard page by Simon U. as well as the tools page it points too. AFAIK you should use the (older) gfortran 4.2.* from that page with R -- but then I am not an OS X user.
Edit in late 2016: We now have more detailed instructions in section 2.16 of the Rcpp FAQ.