As a requirement for chef-client, I am trying to install yajl-ruby on OpenSUSE 12.1. So far, it is returning the following message:
linux:~ # gem install yajl-ruby
Building native extensions. This could take a while...
ERROR: Error installing yajl-ruby:
ERROR: Failed to build gem native extension.
/usr/bin/ruby extconf.rb
creating Makefile
make
gcc -I. -I/usr/lib64/ruby/1.8/x86_64-linux -I/usr/lib64/ruby/1.8/x86_64-linux -I. -fPIC -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -g -fno-strict-aliasing -fPIC -Wall -funroll-loops -c yajl.c
gcc -I. -I/usr/lib64/ruby/1.8/x86_64-linux -I/usr/lib64/ruby/1.8/x86_64-linux -I. -fPIC -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -g -fno-strict-aliasing -fPIC -Wall -funroll-loops -c yajl_alloc.c
gcc -I. -I/usr/lib64/ruby/1.8/x86_64-linux -I/usr/lib64/ruby/1.8/x86_64-linux -I. -fPIC -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -g -fno-strict-aliasing -fPIC -Wall -funroll-loops -c yajl_buf.c
gcc -I. -I/usr/lib64/ruby/1.8/x86_64-linux -I/usr/lib64/ruby/1.8/x86_64-linux -I. -fPIC -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -g -fno-strict-aliasing -fPIC -Wall -funroll-loops -c yajl_encode.c
yajl_encode.c: In function ‘hexToDigit’:
yajl_encode.c:201:1: internal compiler error: Aborted
Please submit a full bug report,
with preprocessed source if appropriate.
See <http://bugs.opensuse.org/> for instructions.
make: *** [yajl_encode.o] Error 1
Gem files will remain installed in /usr/lib64/ruby/gems/1.8/gems/yajl-ruby-1.1.0 for inspection.
Results logged to /usr/lib64/ruby/gems/1.8/gems/yajl-ruby-1.1.0/ext/yajl/gem_make.out
The appropriate packages are installed:
zypper install ruby ruby-devel ruby-ri ruby-rdoc ruby-shadow gcc gcc-c++ automake autoconf make curl dmidecode
It may be an issue with the compiler or there may be an issue specific on OpenSUSE. So far, I am not sure which path to take.
gcc clearly recommends you to send bug report to OpenSuse with full preprocessed source (-E option instead of "-c" and add a redirect to file). This may be because opensuse gcc might have some modifications. You should check instructions on bugs.opensuse.org and send a bug report to OpenSuse. If the bug is in basic gcc too, opensuse bugzilla people will forward it upstream or will ask you to do this
To avoid an "internal compiler error" without sending bugs you can try to change build options. Usually "internal compiler error" means that something goes wrong in complex process of optimizations, so you can just change this process (order of optimization stages and which are enabled). Easiest is to change level of optimization (e.g. replace -O2 with -O1 or -O0) or add something like -Osize.
Related
I'm trying to use f2py on a MAC M2. My programs all run successfully on an Intel MAC. The first part of the process to produce C code from my Fortran source which seems to work but I get the following error when the C compilation attempts and fails
clang-14clang-14: : error: error: the clang compiler does not support '-march=core2'the clang compiler does not support '-march=core2'
Followed by this long string
error: Command "x86_64-apple-darwin13.4.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/condaTest/include -arch arm64 -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/condaTest/include -arch arm64 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /opt/homebrew/Caskroom/miniforge/base/include -D_FORTIFY_SOURCE=2 -isystem /opt/homebrew/Caskroom/miniforge/base/include -ftrapping-math -DNPY_DISABLE_OPTIMIZATION=1 -I/var/folders/np/393cjs953159dbj23mgqmlqr0000gn/T/tmpf0_vcv2d/src.macosx-11.0-arm64-3.9 -I/opt/homebrew/Caskroom/miniforge/base/envs/condaTest/lib/python3.9/site-packages/numpy/core/include -I/opt/homebrew/Caskroom/miniforge/base/envs/condaTest/include/python3.9 -c /var/folders/np/393cjs953159dbj23mgqmlqr0000gn/T/tmpf0_vcv2d/src.macosx-11.0-arm64-3.9/fib3module.c -o /var/folders/np/393cjs953159dbj23mgqmlqr0000gn/T/tmpf0_vcv2d/var/folders/np/393cjs953159dbj23mgqmlqr0000gn/T/tmpf0_vcv2d/src.macosx-11.0-arm64-3.9/fib3module.o -MMD -MF /var/folders/np/393cjs953159dbj23mgqmlqr0000gn/T/tmpf0_vcv2d/var/folders/np/393cjs953159dbj23mgqmlqr0000gn/T/tmpf0_vcv2d/src.macosx-11.0-arm64-3.9/fib3module.o.d" failed with exit status 1
I would be very grateful for any help with this.
I am not sure how much the
link helps. I have to see the list of these messages upon opening the terminal. It came with installing clang for the sake of pystan I believe.
I would very much like to denoise the following, but I've not got a good clue. Appreciate any input, thanks.
INFO: activate_clang_osx-64.sh made the following environmental changes:
+AR=//anaconda/bin/x86_64-apple-darwin13.4.0-ar
+AS=//anaconda/bin/x86_64-apple-darwin13.4.0-as
+CC=x86_64-apple-darwin13.4.0-clang
+CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe
+CHECKSYMS=//anaconda/bin/x86_64-apple-darwin13.4.0-checksyms
+CLANG=//anaconda/bin/x86_64-apple-darwin13.4.0-clang
+CODESIGN_ALLOCATE=//anaconda/bin/x86_64-apple-darwin13.4.0-codesign_allocate
+CONDA_BUILD_SYSROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk
+CPPFLAGS=-D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9
+DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra
+HOST=x86_64-apple-darwin13.4.0
+INDR=//anaconda/bin/x86_64-apple-darwin13.4.0-indr
+INSTALL_NAME_TOOL=//anaconda/bin/x86_64-apple-darwin13.4.0-install_name_tool
+LD=//anaconda/bin/x86_64-apple-darwin13.4.0-ld
+LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs
+LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs
+LIBTOOL=//anaconda/bin/x86_64-apple-darwin13.4.0-libtool
+LIPO=//anaconda/bin/x86_64-apple-darwin13.4.0-lipo
+NM=//anaconda/bin/x86_64-apple-darwin13.4.0-nm
+NMEDIT=//anaconda/bin/x86_64-apple-darwin13.4.0-nmedit
+OTOOL=//anaconda/bin/x86_64-apple-darwin13.4.0-otool
+PAGESTUFF=//anaconda/bin/x86_64-apple-darwin13.4.0-pagestuff
+RANLIB=//anaconda/bin/x86_64-apple-darwin13.4.0-ranlib
+REDO_PREBINDING=//anaconda/bin/x86_64-apple-darwin13.4.0-redo_prebinding
+SEGEDIT=//anaconda/bin/x86_64-apple-darwin13.4.0-segedit
+SEG_ADDR_TABLE=//anaconda/bin/x86_64-apple-darwin13.4.0-seg_addr_table
+SEG_HACK=//anaconda/bin/x86_64-apple-darwin13.4.0-seg_hack
+SIZE=//anaconda/bin/x86_64-apple-darwin13.4.0-size
+STRINGS=//anaconda/bin/x86_64-apple-darwin13.4.0-strings
+STRIP=//anaconda/bin/x86_64-apple-darwin13.4.0-strip
+_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0
INFO: activate_clangxx_osx-64.sh made the following environmental changes:
+CLANGXX=//anaconda/bin/x86_64-apple-darwin13.4.0-clang++
+CXX=x86_64-apple-darwin13.4.0-clang++
+CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0
+DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 -Og -g -Wall -Wextra
I actually fixed this by the link, but it remains murky which of the versions btw clangxx_osx-64-4.0.1-h22b1bf0_8 vs. clangxx_osx-64-4.0.1-h22b1bf0_11 caused it. It seemed more likely that the recent version should be the reason for it, but I actually got lucky by commenting out the lines that were similarly mentioned in the link from the older version..
I am trying to install mitproxy on my EC2 linux instance using pip:
sudo pip install mitmproxy
I have python2.7 installed, and now 2 instances of libffi
$ rpm -qa | grep libff
libffi-3.0.13-11.4.amzn1.x86_64
libffi-devel-3.0.13-11.4.amzn1.x86_64
but each time I try to run the install command I get the following error message:
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/usr/include/python2.7 -c build/temp.linux-x86_64-2.7/_openssl.c -o build/temp.linux-x86_64-2.7/build/temp.linux-x86_64-2.7/_openssl.o
build/temp.linux-x86_64-2.7/_openssl.c:423:30: fatal error: openssl/opensslv.h: No such file or directory
#include <openssl/opensslv.h>
^
compilation terminated.
error: command 'gcc' failed with exit status 1
Any thoughts where I'm going wrong?
Just solved the problem with following solution:
wget source code gzip package from https://www.openssl.org/source/
config&&make&&make install
Good luck!
I am trying to install Platypus and have gotten the following error message:
building 'htslibWrapper' extension
x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/python2.7 -c htslibWrapper.c -o build/temp.linux-x86_64-2.7/htslibWrapper.o -msse2 -msse3 -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC
htslibWrapper.c:243:25: fatal error: htslib/bgzf.h: No such file or directory
#include "htslib/bgzf.h"
^
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
I am new to Bioinformatics and cannot seem to find a working solution online.
Sometimes the bioinformatics applications don't describe thier dependencies all that well. See this link for a possible solution
Install htslib from http://www.htslib.org/download/ and copy c headers to Platypus root folder:
cp -r htslib-x.x.x/htslib platypus_folder/
Build again
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.