I'm having an issue running KING on Mac OS X . It has to do with a dyld link error, I think. Does anybody have any suggestions on how to fix this error?
Thanks in advance.
> ./king -b ./ex/ex.bed
Returns:
dyld: Symbol not found: __ZdaPvm
Referenced from: /Users/gaelgarcia/Downloads/./king (which was built for Mac OS X 10.13)
Expected in: /usr/local/lib/libstdc++.6.dylib
in /Users/gaelgarcia/./king
Abort trap: 6
I had similar issues trying to use the provided precompiled Mac version. I was able to get a running version built from source running the following in the unzipped source directory:
clang++ -L /opt/local/lib/libomp/ -lm -lz -O2 -fopenmp -o king *.cpp
having first installed libomp in the above directory. I use Macports, so I did this with
port install libomp
For Homebrew users, the recommendation seems to be to simply install llvm, which now includes openmp support directly.
EDIT: Having installed llvm via Homebrew (brew install llvm), the command that got KING properly built and running on my Mac OS 10.12 was:
/usr/local/Cellar/llvm/6.0.0/bin/clang++ -I /usr/local/Cellar/llvm/6.0.0/include -L /usr/local/Cellar/llvm/6.0.0/lib -O2 -fopenmp -lm -lz -o king *.cpp
Running the newly built executable with the example .bed file provided:
> ./king -b ../ex/ex.bed
KING 2.1.3 - (c) 2010-2018 Wei-Min Chen
The following parameters are in effect:
Binary File : ../ex/ex.bed (-bname)
For anyone like me looking for an answer years later, I managed to solve this problem by installing gcc with Homebrew.
brew install gcc
which includes libgfortran. Probably unnecessary, since I had dyld installed in Anaconda, but I found it was the easiest way to get King working on my mac.
Edit: I also had to set my DYLD_LIBRARY_PATH in my bash profile, as well, by going
nano ~/.bash_profile
and adding
export DYLD_LIBRARY_PATH=/opt/local/lib/libgcc/
or wherever the dynamic library libgcc_s.1.dylib is when you search for it on your computer.
Related
I am getting a strange error when trying to compile a simple fortran-90 file using gfortran. I am working on a macOS mojave system. I have gfortran 8.2.0 installed and I checked to be sure of this by doing the following:
Input: gfortran --version
Output: GNU Fortran (GCC) 8.2.0
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.
There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE.
Which indicates that gfortran installed correctly and I also confirmed this by typing simply: gfortran, into the terminal, which returns:
gfortran: fatal error: no input files
compilation terminated.
However, when I try to compile my file like so:
gfortran hello.f90 -o hello.x
I get an error which reads:
ld: library not found for -lSystem
collect2: error: ld returned 1 exit status
I've tried compiling in different ways and I also tried setting the LD_LIBRARY_PATH in .bash_profile as described by https://gcc.gnu.org/wiki/GFortranBinaries32Linux but I still get the same error. The gfortran directory has the pathname: /usr/local/gfortran, however another gfortran which is not a directory can be found in /usr/local/bin
Typing:
which gfortran
Outputs:
/usr/local/bin/gfortran
And a long list search of this directory:
Input: ls -l /usr/local/bin/gfortran
Output: lrwxr-xr-x 1 root wheel 32 15 May 14:07
/usr/local/bin/gfortran -> /usr/local/gfortran/bin/gfortran
How can I fix this where everything seems to be correctly installed?
Any help would be greatly appreciated!
On macOS Big Sur v11.1:
Relevant SO post: https://apple.stackexchange.com/questions/408999/gfortran-compiler-error-on-mac-os-big-sur
The fix is to add the stdlib to your $LIBRARY_PATH. For some reason or another it isn't in your standard $PATH anymore on 11.1.
export LIBRARY_PATH="$LIBRARY_PATH:/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib"
(or add it to login file and restart terminal).
I added this to my ~/.profile:
export SDKROOT=$(xcrun --sdk macosx --show-sdk-path)
export LIBRARY_PATH="$LIBRARY_PATH:$SDKROOT/usr/lib"
And it works.
I'll also chime in (19 Dec 2020) that I just updated from MacOS Mojave to Catalina and suddenly got this error.
It resolved itself with
brew reinstall gcc
brew reinstall gfortran
Update: I tried what was suggested and installed the gfortran build from the gcc package using homebrew which gave me a newer version of gfortran and my problem was fixed!
I had the same problem, but installing gfortran build from the gcc package using homebrew did not help. Instead, I installed the whole gcc using homebrew:
brew install gcc
and that solved the problem.
For those using MacPorts.
# Installed `gcc8` and `gcc_select`
sudo port install gcc_select gcc8
# then to create "gfortran" softlink to "gfortran-mp-8"
sudo port select --set gcc gcc8
# and added to my .profile
export LIBRARY_PATH="$LIBRARY_PATH:/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib"
I did ls -l /Library/Developer/CommandLineTools/SDKs/ and found that Xcode had installed one SDK for Catalina and one for Big Sur. I changed the soft link for MacOSX.sdk to point to the Catalina version.
Just placed this line at the end of .zshrc:
export LIBRARY_PATH="$LIBRARY_PATH:/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib"
and ran my Fortran code again to compile – success! The issue with -lSystem has been solved in my macOS system.
I had this problem, and I'd tried lots of thing to solve the problem, but only using these "both" commands solved it:
brew reinstall gcc
brew reinstall gfortran
I recently had this
ld: library not found for -lSystem
problem after upgrading Mac OS from v10 to v11 (Big Sur). I am using Xcode 12.3 and I used brew install gcc to install gfortran 10.2.0. I still saw the error after trying brew reinstall gcc. I was able to solve the problem using:
brew install gfortran
but I do not know why this works.
I am getting a strange error when trying to compile a simple fortran-90 file using gfortran. I am working on a macOS mojave system. I have gfortran 8.2.0 installed and I checked to be sure of this by doing the following:
Input: gfortran --version
Output: GNU Fortran (GCC) 8.2.0
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.
There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE.
Which indicates that gfortran installed correctly and I also confirmed this by typing simply: gfortran, into the terminal, which returns:
gfortran: fatal error: no input files
compilation terminated.
However, when I try to compile my file like so:
gfortran hello.f90 -o hello.x
I get an error which reads:
ld: library not found for -lSystem
collect2: error: ld returned 1 exit status
I've tried compiling in different ways and I also tried setting the LD_LIBRARY_PATH in .bash_profile as described by https://gcc.gnu.org/wiki/GFortranBinaries32Linux but I still get the same error. The gfortran directory has the pathname: /usr/local/gfortran, however another gfortran which is not a directory can be found in /usr/local/bin
Typing:
which gfortran
Outputs:
/usr/local/bin/gfortran
And a long list search of this directory:
Input: ls -l /usr/local/bin/gfortran
Output: lrwxr-xr-x 1 root wheel 32 15 May 14:07
/usr/local/bin/gfortran -> /usr/local/gfortran/bin/gfortran
How can I fix this where everything seems to be correctly installed?
Any help would be greatly appreciated!
On macOS Big Sur v11.1:
Relevant SO post: https://apple.stackexchange.com/questions/408999/gfortran-compiler-error-on-mac-os-big-sur
The fix is to add the stdlib to your $LIBRARY_PATH. For some reason or another it isn't in your standard $PATH anymore on 11.1.
export LIBRARY_PATH="$LIBRARY_PATH:/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib"
(or add it to login file and restart terminal).
I added this to my ~/.profile:
export SDKROOT=$(xcrun --sdk macosx --show-sdk-path)
export LIBRARY_PATH="$LIBRARY_PATH:$SDKROOT/usr/lib"
And it works.
I'll also chime in (19 Dec 2020) that I just updated from MacOS Mojave to Catalina and suddenly got this error.
It resolved itself with
brew reinstall gcc
brew reinstall gfortran
Update: I tried what was suggested and installed the gfortran build from the gcc package using homebrew which gave me a newer version of gfortran and my problem was fixed!
I had the same problem, but installing gfortran build from the gcc package using homebrew did not help. Instead, I installed the whole gcc using homebrew:
brew install gcc
and that solved the problem.
For those using MacPorts.
# Installed `gcc8` and `gcc_select`
sudo port install gcc_select gcc8
# then to create "gfortran" softlink to "gfortran-mp-8"
sudo port select --set gcc gcc8
# and added to my .profile
export LIBRARY_PATH="$LIBRARY_PATH:/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib"
I did ls -l /Library/Developer/CommandLineTools/SDKs/ and found that Xcode had installed one SDK for Catalina and one for Big Sur. I changed the soft link for MacOSX.sdk to point to the Catalina version.
Just placed this line at the end of .zshrc:
export LIBRARY_PATH="$LIBRARY_PATH:/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib"
and ran my Fortran code again to compile – success! The issue with -lSystem has been solved in my macOS system.
I had this problem, and I'd tried lots of thing to solve the problem, but only using these "both" commands solved it:
brew reinstall gcc
brew reinstall gfortran
I recently had this
ld: library not found for -lSystem
problem after upgrading Mac OS from v10 to v11 (Big Sur). I am using Xcode 12.3 and I used brew install gcc to install gfortran 10.2.0. I still saw the error after trying brew reinstall gcc. I was able to solve the problem using:
brew install gfortran
but I do not know why this works.
I am getting a strange error when trying to compile a simple fortran-90 file using gfortran. I am working on a macOS mojave system. I have gfortran 8.2.0 installed and I checked to be sure of this by doing the following:
Input: gfortran --version
Output: GNU Fortran (GCC) 8.2.0
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.
There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE.
Which indicates that gfortran installed correctly and I also confirmed this by typing simply: gfortran, into the terminal, which returns:
gfortran: fatal error: no input files
compilation terminated.
However, when I try to compile my file like so:
gfortran hello.f90 -o hello.x
I get an error which reads:
ld: library not found for -lSystem
collect2: error: ld returned 1 exit status
I've tried compiling in different ways and I also tried setting the LD_LIBRARY_PATH in .bash_profile as described by https://gcc.gnu.org/wiki/GFortranBinaries32Linux but I still get the same error. The gfortran directory has the pathname: /usr/local/gfortran, however another gfortran which is not a directory can be found in /usr/local/bin
Typing:
which gfortran
Outputs:
/usr/local/bin/gfortran
And a long list search of this directory:
Input: ls -l /usr/local/bin/gfortran
Output: lrwxr-xr-x 1 root wheel 32 15 May 14:07
/usr/local/bin/gfortran -> /usr/local/gfortran/bin/gfortran
How can I fix this where everything seems to be correctly installed?
Any help would be greatly appreciated!
On macOS Big Sur v11.1:
Relevant SO post: https://apple.stackexchange.com/questions/408999/gfortran-compiler-error-on-mac-os-big-sur
The fix is to add the stdlib to your $LIBRARY_PATH. For some reason or another it isn't in your standard $PATH anymore on 11.1.
export LIBRARY_PATH="$LIBRARY_PATH:/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib"
(or add it to login file and restart terminal).
I added this to my ~/.profile:
export SDKROOT=$(xcrun --sdk macosx --show-sdk-path)
export LIBRARY_PATH="$LIBRARY_PATH:$SDKROOT/usr/lib"
And it works.
I'll also chime in (19 Dec 2020) that I just updated from MacOS Mojave to Catalina and suddenly got this error.
It resolved itself with
brew reinstall gcc
brew reinstall gfortran
Update: I tried what was suggested and installed the gfortran build from the gcc package using homebrew which gave me a newer version of gfortran and my problem was fixed!
I had the same problem, but installing gfortran build from the gcc package using homebrew did not help. Instead, I installed the whole gcc using homebrew:
brew install gcc
and that solved the problem.
For those using MacPorts.
# Installed `gcc8` and `gcc_select`
sudo port install gcc_select gcc8
# then to create "gfortran" softlink to "gfortran-mp-8"
sudo port select --set gcc gcc8
# and added to my .profile
export LIBRARY_PATH="$LIBRARY_PATH:/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib"
I did ls -l /Library/Developer/CommandLineTools/SDKs/ and found that Xcode had installed one SDK for Catalina and one for Big Sur. I changed the soft link for MacOSX.sdk to point to the Catalina version.
Just placed this line at the end of .zshrc:
export LIBRARY_PATH="$LIBRARY_PATH:/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib"
and ran my Fortran code again to compile – success! The issue with -lSystem has been solved in my macOS system.
I had this problem, and I'd tried lots of thing to solve the problem, but only using these "both" commands solved it:
brew reinstall gcc
brew reinstall gfortran
I recently had this
ld: library not found for -lSystem
problem after upgrading Mac OS from v10 to v11 (Big Sur). I am using Xcode 12.3 and I used brew install gcc to install gfortran 10.2.0. I still saw the error after trying brew reinstall gcc. I was able to solve the problem using:
brew install gfortran
but I do not know why this works.
I'm having trouble building MySQLdb on Mac OSX Mountain Lion. After upgrading to OSX Mountain Lion from OSX Lion, I have downloaded and installed Xcode 4.4 also. Then, I went to Preference > Downloads of the Xcode and installed Command Line Tools.
I've downloaded MySQL-python ver. 1.2.3 from http://sourceforge.net/projects/mysql-python/
When I run
python setup.py build
I get below message:
running build
running build_py
copying MySQLdb/release.py -> build/lib.macosx-10.6-intel-2.7/MySQLdb
running build_ext
building '_mysql' extension
gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -g -O2 -DNDEBUG -g -O3 -Dversion_info=(1,2,3,'final',0) -D__version__=1.2.3 -I/usr/local/mysql/include -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c _mysql.c -o build/temp.macosx-10.6-intel-2.7/_mysql.o -Os -g -fno-common -fno-strict-aliasing -arch x86_64
unable to execute gcc-4.2: No such file or directory
error: command 'gcc-4.2' failed with exit status 1
However, the gcc exists. When I run
gcc
I get
i686-apple-darwin11-llvm-gcc-4.2: no input files
Below is a similar question that I have found but its solution, which is exactly what I have done already, doesn't work for me.
How to install MySQLdb on Mountain Lion
I've had a similar problem while working with Ruby On Rails 3.2.7.
I too had upgraded the system to Mountain Lion, installed Xcode 4.4.1 and downloaded the Command Line Tools.
On the command line I got an error message saying it was impossible to find the file: /usr/bin/gcc-4.2 (I can't paste the precise output right now, I'm sorry).
I did have a /usr/bin/gcc and its version was i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1
I solved the problem by symlinking the file in the same directory and giving it the name the Ruby script was looking for:
sudo ln -s /usr/bin/gcc /usr/bin/gcc-4.2
After that, everything worked fine.
Use the following command to make make (or similiar) use the correct gcc:
export CC=/usr/bin/gcc
I ran into this. For me it was because I installed python from a DMG installer at http://python.org . Those are built against the wrong gcc. I fixed it by compiling python from source using Homebrew: Link
brew install python
That links against the correct gcc
(In my specific case I was using an older Python which is why I had used a DMG installer. I discovered that homebrew also has formulas for older versions)
I detoured this problem by using ActivePython.
There's specific installation instruction for MySQLdb here.
Since this is the first time I've used ActivePython I'm not sure if this' a robust solution for this problem. Therefore, I will leave this question open until I make sure this works.
I just upgraded from Snow Leopard to Lion, and an old python c-extension that I had to update didn't want to compile properly. I don't really know what to do here. Anyone who could help me out so it compiles ok? It compiled just fine back in Snow Leopard.
Home:folder Me$ python setup.py build
running build
running build_ext
building 'ccookies' extension
gcc -fno-strict-aliasing -fno-common -dynamic -arch ppc -arch i386 -g -O2 -DNDEBUG -g -O3 -I/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c ccookies.c -o build/temp.macosx-10.3-fat-2.7/ccookies.o
llvm-gcc-4.2: error trying to exec '/Developer/usr/bin//../llvm-gcc-4.2/bin/powerpc-apple-darwin11-llvm-gcc-4.2': execvp: No such file or directory
In file included from /usr/include/architecture/i386/math.h:630,
from /usr/include/math.h:28,
from /Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/pyport.h:312,
from /Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/Python.h:58,
from ccookies.c:5:
/usr/include/AvailabilityMacros.h:109:14: warning: #warning Building for Intel with Mac OS X Deployment Target < 10.4 is invalid.
lipo: can't figure out the architecture type of: /var/folders/_t/yg4wppss5fv6dkmh89_6ykm40000gn/T//cc3Cgr3v.out
error: command 'gcc' failed with exit status 255
You appear to be using a 32-bit Python 2.7, possibly installed from python.org. Because of changes in Xcode 4 (dropping of support for the 10.4u SDK and gcc-4.0) it is not practical to build C extension modules with that Python on 10.7 Lion. Either use the Apple-supplied Python 2.7 (/usr/bin/python2.7) or install the python.org 64-bit/32-bit installer for 2.7.2 instead of the 32-bit-only one.
I was trying to install pynauty on my Mac OS X 10.7 and I got this problem. For some reasons, Ned Deily's answer didn't help me. I just want to provide one more way to solve this problem in case someone come to this page and is in the same situation as I am. The way I solved this prolem is:
Before running "python setup.py build", run:
export ARCHFLAGS="-arch x86_64"
On travis, I was getting this error. I've been using osx_image: osx10.11 since forever, but it suddenly stopped working, with this error, in last ~few weeks. Changing to osx_image: xcode7.3 fixed the error for me.