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tried xcode-select --install and it once went through smoothly and then later again gives error saying this package is no longer maintained - or something of that sort.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
Related
I'm on the M1 MacBook.
This is the error when I try to install Homebrew:
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
Homebrew is not (yet) supported on ARM processors!
Rerun the Homebrew installer under Rosetta 2.
If you really know what you are doing and are prepared for a very broken experience you can use another installation option for installing on ARM:
https://docs.brew.sh/Installation
So how do I "Rerun the Homebrew installer under Rosetta 2."?
Got an answer from a developer in the Homebrew github https://github.com/Homebrew/brew/issues/9173
arch -x86_64 /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
Use this to install packages:
arch -x86_64 brew install <package>
If you have not yet installed Rosetta 2 to emulate Intel CPUs on ARM Macs, you will get the error arch: posix_spawnp: /bin/bash: Bad CPU type in executable. Prompt a Rosetta 2 installation with:
softwareupdate --install-rosetta
I have two instances of brew installed, the Intel version that runs using Rosetta2 and which installs to /usr/local/bin and the Arm version that runs natively and installs to /opt/homebrew/bin. Now it is all working, I do not have to start iTerm using Rosetta.
I have these aliases to reach the two versions.
ibrew='arch -x86_64 /usr/local/bin/brew'
mbrew='arch -arm64e /opt/homebrew/bin/brew'
I have the native version in my path first:
path=( /opt/homebrew/bin /opt/homebrew/opt /usr/local/bin /usr/bin /bin /usr/sbin /sbin /Library/Apple/usr/bin )
Now I can try mbrew search and mbrew install. If they work, I am good to go with a native program. For example:
mbrew install ag
If brew fails I try building from source, with verbose output, e.g.
mbrew install -sv rust
Be warned, this takes a while and may still fail.
If it still fails, (and mbrew install -sv go results in a segmentation fault for me) I have two choices. Use ibrew search and ibrew install to get the Intel build instead, or examine the verbose output and look for problem dependencies. In some cases an install -s on the dependencies is enough to get the native brew to work.
I must stress that native brew always prints this warning
Warning: You are running macOS on a arm64 CPU architecture.
We do not provide support for this (yet).
Reinstall Homebrew under Rosetta 2 until we support it.
So proceed at your own discretion.
For completeness, and assuming you have iTerm2, Rosetta2 and the Xcode command line tools installed, I did this to install brew under Rosetta (with credit to all those who have posted on this page before me):
Copy the installed iTerm2.app application to iRosetta2.app
Press command+I to Get Info for iRosetta.app, click Open Using Rosetta2
Run iRosetta2 and use this command from https://brew.sh
Like so
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)
alias ibrew='arch -x86_64 /usr/local/bin/brew' # put this in ~/.zshrc
And I did this to install native brew, taken from other contributors to Stack Overflow and the Homebrew alternative installation site, using iTerm2 without Open Using Rosetta2
mkdir ~/homebrew
curl -L https://github.com/Homebrew/brew/tarball/master | tar xz --strip 1 -C homebrew
sudo mv ~/sudo mv homebrew /opt
mbrew='arch -arm64e /opt/homebrew/bin/brew' # for .zshrc
export PATH="/opt/homebrew/bin:/opt/homebrew/opt:$PATH" # also for .zshrc
Edit
Time has passed and I have changed the architecture to arm64e following Fernando García Redondo observation. Now the warning about Arm architecture not supported has gone and Rust and Go install without problems and without compiling from source. I assume the good people at Homebrew have been working hard over Christmas. Thanks!
Edit Feb 21
The Homebrew team have announced that they support Apple silicon. So I wondered if I could delete my aliases and just use brew to install for Apple silicon. The short answer is no! if you run brew from /usr/local without the arch -x86_64, it complains that /usr/local is reserved as the Intel default prefix and using /opt/homebrew is required. So I will retain my two aliases and try mbrew first and only use ibrew if the native brew fails.
Another option is by going into your applications in Finder, select Terminal and press ⌘+I and check the "Open using Rosetta" option.
Sorry if the formatting is off, first time posting a solution.
The easiest way to run Homebrew is with Rosetta 2.
1. Duplicate Your Favourite Terminal for Rosetta
Find your favourite terminal, right-click to duplicate it, and rename it for easier identification. In this example, I'm using the default Terminal app on Big Sur 11.2.1.
Right-click the Terminal Rosetta and go to Get Info to check the Open using Rosetta option.
2. Install Homebrew
Open the rosetta terminal and run the following command:
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
Running this command will ask you for the password, and then it will provide you with the information of what all it will install and which new directories it will create.
3. Using Homebrew
Once HomeBrew is installed, you can start using it to install your required packages into the M1 Mac.
Run the following command to get brew help:
brew help
To install a package, you can run the following command:
brew install packagename
That’s all about installing and getting started with Homebrew on Apple M1 Macs.
EDIT: Thanks all! Upvote to help other devs! Homebrew 3.0.0 now officially supports Apple Silicon (https://brew.sh/2021/02/05/homebrew-3.0.0/)
After I installed Rosetta, I added an alias so I can use brew install <package> as I would normally.
alias brew='arch -x86_64 brew'
I agree with everyone else in that you need to add the arch -x86_64 in front of the original command so thought to include that alias to help anyone finding this thread in the future
arch -x86_64 /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)" worked on my new M1 Mac
Do below
/usr/sbin/softwareupdate --install-rosetta --agree-to-license
arch -x86_64 /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
alias brew='arch -x86_64 brew'
brew install azure-cli
now try az login. you are good to go
You can change the setting of Terminal to launch it using Rosetta.
Go to your Application/Utilities folder, right click on the Terminal App and check the tick box 'Open using Rosetta'
But to be honest, I have Homebrew installed without Rosetta. Just removed the x86 version yesterday and installed a fresh version without Rosetta.
I did svn --version on command line and it says it is 1.17.10.
I want to uninstall it completely, so I can re-install 1.16.12
How do I do that in OS X?
Thanks
As said Mike Christensen, in order to uninstall it, you just need to delete the binary. Run which svn to know where your binary is installed.
In order to install subversion, you need to:
Download it.
Uncompress it (tar xzf subversion-1.x.y.tar.gz).
Compile it (./configure && make).
Install it (sudo make install).
I’m pretty sure this will install it in /usr/local/bin. So if you want svn to call the subversion you just installed (instead of the one built in XCode), you need to edit your $PATH so that /usr/local/bin is before /usr/bin. On Mac OS X, editing the path is done by editing the file /etc/paths.
Note that steps 3 and 4 requires a compiler and make. The easiest way to get those on Mac OS X is to install XCode.
If you get any error in following Etienne Miret solution so the following
after setp 3
brew install apr
brew install apr-util
/configure --with-apr=/usr/local/Cellar/apr/1.5.2_3/ --with-apr-util=/usr/local/Cellar/apr-util/1.5.4_4 && make
sudo make install
After completion, you can see the new SVN installed here
/usr/local/bin/svn --version
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.
I installed MongoDB via Homebrew (following http://docs.mongodb.org/manual/tutorial/install-mongodb-on-os-x/) but it's not working.
Typing mongod at shell prompt gives me:
-bash: mongod: command not found
Not sure if I need to add something for Homebrew to my PATH env var?
I can see Mongo is installed under /usr/local/Cellar/mongodb – but am assuming I don't need to add everything I install via homebrew to the path? Also, assuming I can run mongod from any directory or am I actually meant to be in install directory?
When I run brew doctor I get:
Warning: You have unlinked kegs in your Cellar
Followed by a list of 3 items which includes MongoDB – but I'm not sure how I'm meant to link them?
Works perfectly
brew update
brew tap mongodb/brew
brew install mongodb-community#4.2
For latest version, check https://docs.mongodb.com/manual/release-notes/
You're getting this error because your 'brew' install failed to create the correct symlinks in /usr/local/bin. As a result, the shell can't find the mongo executables in your $PATH. You can fix this using the following steps:
Check the permissions on /usr/local/bin and make sure that you own that directory and have write permissions on it
$ ls -ld /usr/local/bin
Once you've fixed that, run 'brew link' to fix the symlinks
$ brew link mongodb
If you are on mongodb-community#4.0. You can try to reinstall with brew reinstall mongodb-community#4.0.
Then I get the following hint:
==> Caveats
mongodb-community#4.0 is keg-only, which means it was not symlinked into /usr/local,
because this is an alternate version of another formula.
If you need to have mongodb-community#4.0 first in your PATH run:
echo 'export PATH="/usr/local/opt/mongodb-community#4.0/bin:$PATH"' >> ~/.bash_profile
So you can just copy the echo command and restart your shell!
Copied from a different channel running these commands in the terminal updated the installation/configuration issues as described in OP
brew tap mongodb/brew
brew install mongodb-community
brew services start mongodb-community
I faced the same problem and this solution seemed to work for me. I had previously uninstalled mongodb and reinstalled it through homebrew which gave me a bunch of problems. This solution seemed to work just fine.
brew uninstall --force mongodb
brew cleanup -s mongodb
brew cleanup --prune-prefix
brew install mongodb
It works from the directory since the sh searches the ENV path and then the cwd for a program named mongod. I have been looking around a little and it seems that the default install of MongoDB (I am not a Mac user) does not install a rc or init script for which sh to understand it's running behaviour as stated here:
http://docs.mongodb.org/manual/tutorial/install-mongodb-on-os-x/#using-mongodb-from-homebrew-and-macports
The packages installed with Homebrew and MacPorts contain no control
scripts or interaction with the system’s process manager.
If you have configured Homebrew and MacPorts correctly, including
setting your PATH, the MongoDB applications and utilities will be
accessible from the system shell. Start the mongod process in a
terminal (for testing or development) or using a process management
tool.
So you must actually define (as you said) MongoDBs path, here is an example: https://snipt.net/sido/installing-mongodb-on-os-x/
Edit: the example is not mine. I just stole it from it's user: https://snipt.net/sido/
After I got MacPorts installed and did a 'sudo port -v selfupdate', I try to install meld.
The installation just starts to Fetching all kinds of stuff
gnome-comoon
perl5.8
perl5
pkgconfig
.....
this goes on and on.
Is that normal?
You may want to install it via HomeBrew (already mentioned before):
brew install homebrew/gui/meld
Though you may face stability issues (as I did). So I'd rather recommend to use "Meld for OSX":
Go to https://yousseb.github.io/meld/
Download DMG file you prefer (e.g. "Download latest DMG" https://github.com/yousseb/meld/releases/download/osx-6/meldmerge.dmg)
Install it to your Applications folder
We are basically done, but it is not accessible via command line.
Solution:
Write a small wrapper to run from Terminal:
echo -e '#!/bin/sh
params="$#"
open -W -a Meld --args $params' | sudo tee /usr/local/bin/meld
sudo chmod +x /usr/local/bin/meld
Try (you must use absolute paths though):
meld /home/a.txt /home/b.txt
Or just run Meld from menu.
meld is now available in homebrew. The formula can be found here.
See this answer by cmedeiros on SuperUser for more information on installing and getting it to work. This is much easier than using MacPorts.
Current command with updated formula to install meld with homebrew is:
brew install caskroom/cask/meld
Yes, it is normal to pull in dependencies but it shouldn't take too long. For comparison, installing Meld with Homebrew took about 15 minutes for me.
For reference, my installation of Meld on OS X Mavericks:
Install Xcode from the app store
Install XQuartz from package (Meld will complain if you don't have it)
command line: 'brew install meld'
If you are prompted to install the Xcode command line tools at some point, do so.
Hope this helps.
Unfortunately, the is very normal with MacPorts, and is the reason that people many have switched to homebrew http://github.com/mxcl/homebrew
However, I found this post because homebrew doesn't include Meld. Sigh.
Consider downloading macOS meld version dmg https://github.com/yousseb/meld/releases/
Brew now works brew install --cask meld.
See https://formulae.brew.sh/cask/meld#default
UPDATE Jul-23-2020
Just do :
brew install homebrew/gui/meld
using the updated brew link: brew install caskroom/cask/meld
even after this its not working when I install backup and restore tool by google. I guess its messing up with the python version.