I’ve been trying to install AFNI using the afni_macOS_install_BETA_V2.app but I’m having problems installing netpbm. Please, help! I’ve tried everything I could possibly try.
I have MacOS El Capitan 10.11.6.
It could be a problem with a certificate, but I have no idea how to solve it.
I also tried to install netpbm not using homebrew, but it doesn’t seem to work fine.
Here are the messages I get at the end of the afni installation:
Cloning into ‘/usr/local/Homebrew/Library/Taps/homebrew/homebrew-core’…
fatal: unable to access ‘https://github.com/Homebrew/homebrew-core/’: SSL certificate problem: Untrusted root certificate
Error: Failure while executing; git clone https://github.com/Homebrew/homebrew-core /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core --depth=1 exited with 128.
Error: Failure while executing; /usr/local/bin/brew tap homebrew/core exited with 1.
==> Tapping homebrew/core
Cloning into ‘/usr/local/Homebrew/Library/Taps/homebrew/homebrew-core’…
fatal: unable to access ‘https://github.com/Homebrew/homebrew-core/’: SSL certificate problem: Untrusted root certificate
Error: Failure while executing; git clone https://github.com/Homebrew/homebrew-core /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core --depth=1 exited with 128.
Error: Failure while executing; /usr/local/bin/brew tap homebrew/core exited with 1.
Then restart the computer and try the installer again.
If that doesn’t help, can you look at your .bash_profile or .bashrc and see if there is anything strange in there.
Like a change in your path that you don’t expect or a configuration program running.
If you have anaconda or conda in your path, it may also cause a problem.
brew doctor gives me the following messages:[/i][/b]
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 which 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:
/Library/Frameworks/Python.framework/Versions/2.7/bin/python-config
/Library/Frameworks/Python.framework/Versions/2.7/bin/python2-config
/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7-config
==> Tapping homebrew/core
Cloning into ‘/usr/local/Homebrew/Library/Taps/homebrew/homebrew-core’…
fatal: unable to access ‘https://github.com/Homebrew/homebrew-core/’: SSL certificate problem: Untrusted root certificate
Error: Failure while executing; git clone https://github.com/Homebrew/homebrew-core /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core --depth=1 exited with 128.
Error: Failure while executing; /usr/local/bin/brew tap homebrew/core exited with 1.
brew cleanup also gives me the same SSL certificate problem message.
And with brew update I get the following plus the same SSL certificate problem message:
fatal: unable to access ‘https://github.com/Homebrew/brew/’: Could not resolve host: github.com
Error: Fetching /usr/local/Homebrew failed!
==> Homebrew has enabled anonymous aggregate formulae and cask analytics.
Read the analytics documentation (and how to opt-out) here: https://docs.brew.sh/Analytics
I am running something right now, but I’ll restart my computer as soon as that work finishes and will try the installer again (although I’m afraid that things haven’t changed). In the meantime, I’ve taken a look at the two bash RC files in my home directory and I’m copying down here what’s in there because I’m not sure if there’s anything unexpected. Maybe you can tell me if you see something strange there. Thanks!!!
.bash_profile:
Setting PATH for Python 2.7
The orginal version is saved in .bash_profile.pysave
Just an update… I restarted my computer after my message yesterday and tried the AFNI installer again. Still the same error messages
Any help would be greatly appreciated!
What happens when you go to https://github.com/Homebrew/homebrew-core in a browser?
If there is a problem, it could be your organization’s firewall or a DNS problem. (I doubt it…)
If it is the case that it is a problem connecting and if the machine is a laptop, try installing from another network.
If you can connect to github, what happens when you just run?"
brew install netpbm
Can you post the output of this command?
brew config
For the .bash_profile, how much of that did you put there manually?
Having ‘/Users/anc/Documents’ in your path may cause some problems.
And it seems like the python version that is added in the .bash_profile is the default macOS version.
So it should not need to be there.
Try saving the .bash_profile and .bashrc with different names, restarting (or quit the terminal and log out and back in), then run the installer again.
To see if the problem is being caused by some configuration issue with your current setup, you could try creating a new user account on your machine.
Then run the installer and if it works, we need to fix something in your original account’s setup.
I get the SSL certificate error message:
==> Tapping homebrew/core
Cloning into ‘/usr/local/Homebrew/Library/Taps/homebrew/homebrew-core’…
fatal: unable to access ‘https://github.com/Homebrew/homebrew-core/’: SSL certificate problem: Untrusted root certificate
Error: Failure while executing; git clone https://github.com/Homebrew/homebrew-core /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core --depth=1 exited with 128.
Error: Failure while executing; /usr/local/bin/brew tap homebrew/core exited with 1.
I don’t remember exactly what but I added something manually in the .bash files. I just saved .bash_profile and .bashrc with different names, followed all the steps you told me, restarted my laptop and tried to install AFNI again and got the following message:
Installing Homebrew packages
Cloning into ‘/usr/local/Homebrew/Library/Taps/homebrew/homebrew-core’…
fatal: unable to access ‘https://github.com/Homebrew/homebrew-core/’: SSL certificate problem: Untrusted root certificate
Error: Failure while executing; git clone https://github.com/Homebrew/homebrew-core /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core --depth=1 exited with 128.
Error: Failure while executing; /usr/local/bin/brew tap homebrew/core exited with 1.
==> Tapping homebrew/core
Cloning into ‘/usr/local/Homebrew/Library/Taps/homebrew/homebrew-core’…
fatal: unable to access ‘https://github.com/Homebrew/homebrew-core/’: SSL certificate problem: Untrusted root certificate
Error: Failure while executing; git clone https://github.com/Homebrew/homebrew-core /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core --depth=1 exited with 128.
Error: Failure while executing; /usr/local/bin/brew tap homebrew/core exited with 1.
Something bad happened. Try again…
I also tried to install AFNI using a new user account in my laptop and unfortunately I got the same error message.
Is it possible that my system is too old for this homebrew to be install? or I wonder if I could manually add this “untrusted” keychain or certificate.
I’m clueless. Any suggestions are very welcome!
Open “Keychain Access” in Applications → Utilities
Search for “DigiCert”
From the “View” menu select “Show Expired Certificates” (All of my DigiCert certificates expire sometime in the 2030’s)
If there is an expired one, delete it (right click and choose delete), restart and try the install again.
Doubtful possibilities:
Which shell are you using?
echo $0
Is it possible your computer is using a different curl?
What is the output of:
which curl
Brute force:
Let’s try manually installing homebrew without checking for an SSL certificate.
Run this code in your terminal:
(I had to add a space " " after https:// so the message board does not convert it into a link. Remove that space when you enter it into the terminal!)
Hi,
We could try a remote support screen share.
Email me at: rajendrajk@nih.gov
So we can set up a time.
The
National Institute of Mental Health (NIMH) is part of the National Institutes of
Health (NIH), a component of the U.S. Department of Health and Human
Services.