I installed matrix2png on my Mac and had used it without problem before last week when I installed another image manipulating tool "circos". Circos requires me to install a different version of libpng, and I did. After that, I am no longer able to run matrix2png, which gives me the following error. I think the old ligpnb is not linked any more. Does anyone know how to fix this error? - appreciate your help.
dyld: Library not loaded: /usr/local/lib/libpng15.15.dylib
Referenced from: /usr/local/bin/matrix2png
Reason: image not found
Those step solve my problem:
brew versions libpng
You will see some versions of libpng, but unfortunately not 1.5.15, so next you should install 1.5.18.
git checkout 7bec702 Library/Formula/libpng.rb
brew install libpng
You'll will find version 1.5.18 and some another versions.
ln -s /usr/local/Cellar/libpng/1.5.18/lib/libpng15.15.dylib /usr/local/lib/libpng15.15.dylib`
See https://github.com/Homebrew/homebrew-php/issues/1055
Some more info on installing certain versions of brew formulas can be found at https://coderwall.com/p/lqphzg.
Your new version of libpng has probably changed the name of its dyld files. This often happens with upgrades (especially following a major release). To verify this, open up the terminal and type:
ls /usr/local/lib/libpng*
What do you see?
From your error message we know that matrix2png is looking for libpng15 but if you've upgraded when instaling circos then you may now have libpng16 on your system. Consequently matrix2png won't be able to find the files that it's looking for and will be unhappy.
Fixing it this time:
Try re-installing matrix2png and see whether it notices the dependency issues and fixes it for you. You don't really want to downgrade libpng nor do you want to have two versions of it on your system, so having an up-to-date version of matrix2png would be good.
It looks like matrix2png comes from C source code, so you'll want to rebuild it. Download the source code or and then open a terminal. Navigate to the folder with the source code and run configure and then make. Configure will generate a Makefile for your system, and then make will use that file to generate a new binary. I've tested this on my Mac (with libpng16), and found that matrix2png built without any errors.
Suggested future approach:
To prevent future linking problems, you may want to use a package manager like homebrew or macports. In case you're using (or want to use) homebrew, it has circos and lib2png (but not matrix2png, sorry!). Once brew is installed, type the following into the terminal:
brew install libpng
And it should detect linking issues / version conflicts and guide you through fixing them. Brew places all of it's files in a 'cellar' location in /usr/local/Cellar and then symbolically links them into your system.
In case you're already using brew, try brew doctor and follow the instructions to resolve problems.
My experience (I've been dealing with a lot of version conflicts in the past few weeks) is that package managers make life much easier. Occasionally I've had to remove and reinstall packages to fix version issues, but in general brew keeps things neat and working.
Related
I want to install YouCompleteMe, on Mac OSX, early 2015.
I have installed it under guidance of Mac OSX part. However, I got one warning:
NoExtraConfDetected: No .ycm_extra_conf.py file detected.
Then I read the full installation guide, and know that I should Download the latest version of libclang. However, there are so many source code on the official webpage of LLVM, and I don't know what to install (figure below).
So, could you please tell me, which one I should install?
Thanks!
If you go to http://llvm.org/releases/download.html#3.8.0 you can see Pre-Build binaries for MacOsX that's what you need to download and extract. Once you extract this. You will need to source it's location using the path variable.
Now, You can also install clang using brew from the terminal.
brew install --with-clang llvm
I recently installed Octave using the binary installer found on this site: http://wiki.octave.org/Octave_for_MacOS_X
I then tried to install the control package using 'pkg install -forge control' but it gave me the error 'pkg: error running `make' for the control package.'. I have gone through most of the threads regarding this error but with no success.
I then tried to use MacPorts to install the control package, I followed the instructions on the wiki page above with some help from this thread: Installing general package in octave has error. I believe I succeeded installing the packages because I can see them in the folder tree for Octave and MacPorts says it is installed when using the console.
The problem is that when i run some code in Octave it cannot build as it doesn't know that I have installed any additional packages. Using 'pkg list' in Octave it says that no additional packages installed. I feel like I need to link the two together but I don't know how?
I'll happily explain more if I need to and I hope you can help me out.
Many Thanks,
Sam.
You cannot "link the two together" (assuming you mean the binary version of octave and the MacPorts version).
If you have packages installed via MacPorts for the MacPorts version of octave, then they will only be available from the the MacPorts version of octave, so make sure you are running that.
Otherwise, figure out how to install the package with the octave binary version. It seems you require a build environment for this, but installing the command line tools (which you must have done for MacPorts to work) might have already solved this problem.
It seems to be a problem with gfortan compiler built-in with Octave. To solve this you should install an external fortran compiler.
Try this:
Install Xcode and command line tools for Xcode
Download and install a fortran compiler for MacOS, for example: http://coudert.name/software/gfortran-6.1-ElCapitan.dmg
Change the fortran compiler path in your octave, to this if you installed the compiler that I suggested in point number 2 you only must to open Octave and type: setenv('F77', '/usr/local/gfortran/bin/gfortran').
And Enjoy Octave for MacOS
Octave with control package 3.0.0 on MacOS
You haven't provided enough information for a precise diagnostic, but I had the same error message (and a few more), and re-installing octave from source solved it; see this link for more info, but essentially you can do it by running brew reinstall --build-from-source octave.
I have been trying to install bakefile(v0.2.9) in mac osx 10.11. Whenever I try to install bakefile using the dmg file I get The installation failed.The installer could not install the software because there was no software found to install error.
I even tried building it from the source code(v1.2.5.1 from github). I built it using the sudo make command.However sudo make install command throws No rule to make target install.
Is there any other way to install bakefile in macosx 10.11?
Edit :
Finally I managed to install the bakefile 0.2.9 in osx 10.11. I can't use the latest version as it does not supports the bakefile we have been using in our projects.
Though the installation is successful,I get the segmentation fault 11 when I try to build the bakefiles(.bkl). Some of the forums suggested that the problem could be associated with python 2.7. I followed all the steps needed to resolve the issue. But none of them helped.
I have been using python 2.7.11. How can I avoid this segmentation fault?
I advice against using the legacy 0.2.9 version.
I even tried building it from the source code(v1.2.5.1 from github).
You didn’t, that’s the problem — you tried to build a very different version, 0.2.9 != 1.2.5.1. The relation between these two branches is explained at http://bakefile.org — they are incompatible and different.
If you want to build 0.2.9 from sources, you need to download and build 0.2.9.
If you want to use the 1.x version, you can download packaged “binary” version, as explained at https://github.com/vslavik/bakefile
P.S. You don’t need to, and shouldn’t, use sudo when installing somewhere you typically have access to, such as /usr/local on OS X.
I was trying to get wxHaskell installed on my mac (Osx Mavericks). I fixed the issue with gcc, and I used brew to install wxmac (version 3.0). The issue that keeps coming up is that the hackage cabal searches for looks for wx 2.9, while I have 3.0. It says that it can't find:
Warning: No config found to match: /usr/local/bin/wx-config --version=2.9 --version-full
in /usr/local/Cellar/wxmac/3.0.0.0/lib/wx/config
If you require this configuration, please install the desired
library build. If this is part of an automated configuration
test and no other errors occur, you may safely ignore it.
You may use wx-config --list to see all configs available in
the default prefix.
I can't find any way to install a different version of wx through brew. Does anyone have a fix?
Thanks!
I want the latest version of openmpi. I like to use macports because it is easy to install, uninstall, and upgrade software. I have installed the latest mpi via building from source, but no one seems to be able to get it to build properly with macports. There is always a build error. There are tickets (and you can see the logs at ), but they seem to be collecting dust and it seems strange that no one had found a solution.
I have tried uninstalling the built in version (I know, openmpi says not to do that--but it works fine if I reinstall it--even in a different directory), but I still the same build errors. I also tried with different gcc.
Does anyone know what is so difficult about getting openmpi via macports?
sudo port install openmpi
worked for me