I used brew install GDL. The install was completed, but once I try to use GDL, it says " command not found: gdl".
I used "which gdl", but still can't be located. I tried reinstalling GDL via brew, but same error.
I tried changing the directory to the folder where brew installed GDL, but no luck either.
I looked through my other compilers and those are saved into bin, while GDL is not (if that's relevant at this point).
Anything will help!
If the intention was to install GNU Data Language, please try installing gnudatalanguage from homebrew-science: https://github.com/brewsci/homebrew-science/blob/master/Formula/gnudatalanguage.rb
I am trying to install ROOT (cern.root.ch). When I run ./configure , I get a message that libX11 is missing and must be installed.
I did some research and found that I need to install
) XQuartz (I already have the latest version.)
) Command line tools in Xcode.
I tried installing Command Line Tools from apple's developer website. The installation goes through smoothly but how do I know whether it has been installed? I still get libX11 missing error with root's configure command.
I also tried xcode-select --install and it once went through smoothly and then later again gives error saying this package is no longer maintained - or something of that sort.
I understand I may have multiple installations... But I am still facing the problem of not having libX11 and not being able to install ROOT.
Thanks,
Hershal.
This link and the one referenced in it suggests you use homebrew (brew) to install it
$ ruby <(curl -fsS https://raw.github.com/mxcl/homebrew/go)
$ brew doctor
Remember to add the Homebrew directory to your PATH by adding the directory (found with brew --prefix) to your .bashrc, .zshrc or whatever shell file you’re using (.bashrc is the OS X default). We’ll also add the XQuartz binaries to the PATH in case anything needs them in the future.
export PATH=/usr/local/bin:/opt/X11/bin:$PATH
Start a new Terminal session to pick up the changes.
Now that Homebrew is installed, we can use it to install the required dependencies. Each may take some time as Homebrew generally compiles from source.
$ brew install gfortran # Fortran compiler
$ brew install python # Python interpreter
$ brew install pcre # Regular Expressions library
$ brew install fftw # Fast Fourier Transforms
$ brew install cmake # Cross-platform make
install root
$ brew tap homebrew/science
$ brew install --with-cocoa root
You don't say whether you have installed XCode as well as the commandline tools but I think you will need it
I'm completely new to Homebrew and Anaconda installation and I hope someone could help me out with the warning after executing brew doctor. I'm running on Snow Leopard 10.6.8. The warning is as follows:
Warning: "config" scripts exist outside your system or Homebrew directories.
`./configure` scripts often look for *-config scripts to determine if
software packages are installed, and what additional flags to use when
compiling and linking.
Having additional scripts in your path can confuse software installed via
Homebrew if the config script overrides a system or Homebrew provided
script of the same name. We found the following "config" scripts:
/Users/user.name/anaconda/bin/freetype-config
/Users/user.name/anaconda/bin/libpng-config
/Users/user.name/anaconda/bin/libpng15-config
/Users/user.name/anaconda/bin/llvm-config
/Users/user.name/anaconda/bin/python-config
/Users/user.name/anaconda/bin/python2-config
/Users/user.name/anaconda/bin/python2.7-config
/Users/user.name/anaconda/bin/xml2-config
/Users/user.name/anaconda/bin/xslt-config
I executed brew --config and the following shows the configuration (hope it helps w/ the issue):
HOMEBREW_VERSION: 0.9.4
ORIGIN: (none)
HEAD: (none)
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CELLAR: /usr/local/Cellar
CPU: dual-core 64-bit penryn
OS X: 10.6.8-i386
Xcode: 3.2.6
GCC-4.0: build 5494
GCC-4.2: build 5666
LLVM-GCC: build 2335
Clang: 1.7 build 77
X11: 2.7.4 => /opt/X11
System Ruby: 1.8.7-358
Perl: /usr/bin/perl
Python: /Users/user.name/anaconda/bin/python
Ruby: /usr/bin/ruby => /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
Really appreciate your help. Thank you.
tl;dr: you can't really fix this but you can probably ignore it
Those scripts ending in -config provide information for other packages that want to link to them during installation. Let's take libpng for example. If brew (or anything really) compiles a package that depends on libpng it might execute libpng-config to find out some details about the library.
The problem is that brew brings its own version of libpng so if both are installed brew might pick up the wrong libpng-config when installing additional software.
You can do one of four things now:
Ignore the warning if you're confident that the stuff you install with homebrew will not conflict with the stuff that comes with anaconda.
Edit your ~/.bash_profile and remove anaconda from the PATH. If you do this you will have to specify the full path every time you want to run anaconda python.
Move those anaconda config files aside (out of your PATH, e.g. into a config subdirectory). This will likely prevent additional software from linking to anaconda components but should be ok if you intend to keep anaconda isolated.
Remove anaconda completely (just delete the folder) and install brew's version of python. This will also give you pip which should make it easy to reinstall most of the other packages that come with anaconda.
i.e.
brew install python
Then to install e.g. numpy, simply:
pip install numpy
(To make brew's python your default add export PATH="/usr/local/bin:$PATH" to your ~/.bash_profile)
I believe I've found a reasonably safe way to deal with this (if you are using the fish shell).
Install Anaconda but don't add to PATH
Add a symlink to the conda binary somewhere on your PATH (in my case ~/bin)
mkdir ~/bin
cd ~/bin; ln -s ~/anaconda3/bin/conda .
Add section like follows to ~/.config/fish
set -gx PATH $PATH ~/bin
source ~/anaconda3/etc/fish/conf.d/conda.fish
Note that this activate's the conda shell configuration for fish -- use conda activate some-env to switch into an anaconda environment rather than the bash-style source activate some-env. brew doctor should show that this issue no longer exists.
This setup lets you use the conda command to switch into conda-managed environments without worrying about leaky interactions between homebrew-managed python/dependency environments.
The one thing to remember is to avoid running homebrew when a conda environment is active as your path will be set for the conda environmnent and unsafe for homebrew usage.
Ran "brew doctor" and got some errors. I managed to fix the path issue by following the advice at this link: How to modify PATH for Homebrew?.
However, completely lost with what to do with the following error:
Warning: "config" scripts exist outside your system or Homebrew directories.
`./configure` scripts often look for *-config scripts to determine if
software packages are installed, and what additional flags to use when
compiling and linking.
Having additional scripts in your path can confuse software installed via
Homebrew if the config script overrides a system or Homebrew provided
script of the same name. We found the following "config" scripts:
/opt/sm/pkg/active/bin/curl-config
/opt/sm/pkg/active/bin/ncurses5-config
/opt/sm/pkg/active/bin/ncursesw5-config
/opt/sm/pkg/active/bin/pkg-config
/opt/sm/pkg/active/bin/xml2-config
/opt/sm/pkg/active/bin/xslt-config
Noob. Running OSX. Appreciate any assistance from wiser Jedis...
If you see this message it means you have packages installed without using homebrew.
If these packages are only installed outside homebrew their config scripts should not interfere with homebrew and you don't have to worry.
There might be a problem if you have, for example curl, installed in homebrew and in another packages manager or manually.
If you need these softwares you should remove them and reinstall them in homebrew otherwise you can leave them in /opt or uninstall them.
I am having trouble getting MacPorts to function properly. I just installed OSX Lion 10.7.3 I downloaded and installed MacPorts first, and then after reading the requirements, I downloaded Xcode4.3 from the App Store, and then installed it. I launched Xcode and it looks to be operational and functional. However when I attempted to port with MacPorts, it gave me this error message(excerpt):
Warning: xcodebuild exists but failed to execute
Warning: Xcode does not appear to be installed; most ports will likely fail to build.
I followed the advice from:
How do i install additional packages for Xcode on OSX Lion to allow MacPorts to work
and installed command_line_tools_for_xcode from the Preferences within Xcode. I closed Xcode, and again got the errors:
$ sudo port install libsocketsPassword:
Warning: xcodebuild exists but failed to execute
Warning: Xcode does not appear to be installed; most ports will likely fail to build.
---> Computing dependencies for libsockets
---> Dependencies to be installed: openssl zlib
---> Extracting zlib
Error: Couldn't determine your Xcode version (from '/usr/bin/xcodebuild -version').
Error:
Error: If you have not installed Xcode, install it now; see:
Error: http://guide.macports.org/chunked/installing.xcode.html
Error:
Error: Target org.macports.extract returned: unable to find Xcode
Error: Failed to install zlib
Log for zlib is at: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_archivers_zlib/zlib/main.log
Error: The following dependencies were not installed: openssl zlib
Error: Status 1 encountered during processing.
I am uncertain where to go next with this. How do i trouble shoot my Xcode and MacPort interface?
In theory this should work if you have Xcode4.3 installed (in /Applications):
$ sudo xcode-select -switch /Applications/Xcode.app/Contents/Developer/
(And you've installed the optional command line tools)
Everything will start working fine after installation of "Command Line Tools for Xcode" package.
You can get it from here: https://developer.apple.com/downloads/index.action#
Please see the MacPorts migration instructions for Xcode 4.3.
The instructions are pretty involved. You need to run xcode-select to set a new tools path, update developer_dir in macports.conf (as described by Henk Poley), re-install MacPorts (ouch), and finally uninstall and re-install all of your ports (double ouch).
Edit: libpvx still wouldn't install after the above. Two extra steps were required:
sudo ln -s /Developer /
sudo ln -s /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs /SDKs
YMMV if you have different ports installed!
Also in /opt/local/etc/macports/macports.conf change the line with developer_dir to point to / instead of /Developer.
After
sudo xcode-select -switch /Applications/Xcode.app
I also had to run
sudo xcodebuild -license
and accept the licence
Here is a solution that has worked for me:
Install Command Line Tools for Xcode
Xcode -> Preferences -> Downloads
Help MacPorts find the right Xcode folder
sudo /usr/bin/xcode-select -switch /Applications/Xcode.app
Create symbolic links for clang compilers as they now live elsewhere
sudo ln -s `which clang` /Applications/Xcode.app/Contents/Developer/usr/bin/
sudo ln -s `which clang++` /Applications/Xcode.app/Contents/Developer/usr/bin/
Try using trunk, there's no release supporting Xcode 4.3 yet.
Setting the developer path in /opt/local/etc/macports.conf works for me,
developer_dir /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain
since most of the compilers are stored there now instead of /usr/bin under Developer.
None of this works for me. Wait for macports to release a new version that officially supports XCode 4.3+
sudo mv /usr/bin/xcodebuild /usr/bin/xcodebuild.old
sudo ln -s /Applications/Xcode.app/Contents/Developer/usr/bin/xcodebuild /usr/bin/xcodebuild
Starting with Xcode 4.3, the command-line build tools are not installed by default. Launch Xcode, open the Preferences, and go to the Downloads tab. From there you should have an option to install the command-line tools.
You can also download them from the web here: https://developer.apple.com/downloads/index.action
Disclaimer: I haven't installed Xcode 4.3 yet. I have only read about it on the web.
As of 27/2/2012, the official suggestion from MacPorts seems to be to not use XCode 4.3 and instead use 4.1 through 4.2.1, which can be downloaded from Apple.
There is a bug ticket which might be useful to follow the evolution of this.
Incidentally, and as reported in my comment #11 in that bug report, I am able to build ports without warnings by using the 2 most sane-looking suggestions found in this question: sudo /usr/bin/xcode-select -switch /Applications/Xcode.app/Contents/Developer and changing developer_dir in /opt/local/etc/macports/macports.conf to /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain
I have macports installed without admin/root privileges, so I was unable to test the xcode-select answers. However, I observed that Pall Melsted's answer worked, but not initially. What I found out was that I had not accepted the Xcode 4.5 license agreement!
If you have just installed Xcode for the purposes of macports, and you haven't accepted the Xcode license yet, you might get the error presented by the original post. When I checked my Xcode version using /usr/bin/xcodebuild -version, I was given the prompt to read and accept the license. After doing so, and after having made the changes suggested by Pall to the macports.conf developer_dir, it all works now.
As alternative: you can make downgrade of Xcode to 4.2.1 version. DMG of Xcode 4.2.1 placed here: https://developer.apple.com/downloads/index.action
After this MacPorts became works fine for me.
This is fixed in MacPorts 2.0.4.
To upgrade:
Download MacPorts 2.0.4 from the install site or run sudo port selfupdate.
Run the MacPorts migration described here to reinstall all ports. This is painful but required to get back to a working state.
You should definitely run sudo xcode-select -switch /Applications/Xcode.app like everyone here says, that'll fix many problems, but certainly not all.
Afaik, all the remaining problems exist within the configuration information for various packages. You might simply reinstall MacPorts as described in the migration instructions, but I found another solution.
You should begin finding all effected port files using commands like grep /Developer/ ..., after executing sudo bash and cd /opt/local naturally.
You should identify all effected ports by using port provides ..., which I piped through sed and sort | uniq. You could simply reinstall all these ports using either port -n upgrade --force ... or separate port uninstall ... and port install ... commands.
I recommend using one large port -n upgrade --force ... command to avoid duplicate rebuilds of dependencies, using the separate uninstall and install commands afterwards.
There are of course various ports for which /Developer exists only inside text config files, meaning you can fix them manually with sed -i -e 's/\/Developer//g' ..., but you cannot do so with binaries obviously.
I'm afraid you must at minimum rebuild all your Python and Perl installations, making this upgrade an ideal time to clean out packages that depend upon older versions, ala python26 and perl5.8.
There are several technically effected ports I decided against rebuilding like fuse4x-kext, who contained /Developer inside Library/Extensions/fuse4x.kext/Contents/MacOS/fuse4x but hasn't prevented sshfs from working correctly.
I had initially installed xcode 3.2.2, after which I installed 4.3. When I ran the xcode-select, I still got the same error about no xcode project in /Applications. I then dug into the /usr/bin/xcodebuild script and found out that this was working correctly, and another instance of xcodebuild (the one installed with xcode 4.3, not the one in /usr/bin) was being run and returning the error:
xcodebuild: error: The directory /Applications does not contain an Xcode project.
It seems the /usr/bin/xcode-select does not work for xcode 4.3, (it's compiled so you can't really see why it's not working). Strings doesn't give any clues. Good thing osx has strace.. oh wait.
Anyways, the best I could do was modify /opt/local/etc/macports.conf
and uncomment the line containing the path to the xcode installation. That seems to fix my problem for the most part.