INSTALLING AFNI

anc1840 · September 3, 2019, 6:37pm

Hi!

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.

discoraj · September 4, 2019, 1:00am

hi,
It could be a few things.
First try:


brew doctor
brew cleanup
brew update

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.

Let me know how it goes.

Thanks, Justin

anc1840 · September 4, 2019, 1:56pm

[b][i]Thank you very much for your response!

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

PATH=“/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}”
export PATH = [‘’, ‘/Users/anc/Documents’, ‘/Library/Frameworks/Python.framework/Versions/2.7/lib/python27.zip’, ‘/Library/Frameworks/Python.framewo$
export PYTHONPATH=[’', ‘/Users/anc/Documents’, ‘/Library/Frameworks/Python.framework/Versions/2.7/lib/python27.zip’, '/Library/Frameworks/Python.fra$
#PATH=/Applications/Blender/blender.app/Contents/Resources/2.79/python
#export PATH

auto-inserted by @update.afni.binaries :

export PATH=$PATH:/Users/anc/abin

.bashrc:
export DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:/opt/X11/lib/flat_namespace

auto-inserted by @update.afni.binaries :

export PATH=$PATH:/Users/anc/abin

if [ -f $HOME/.afni/help/all_progs.COMP.bash ]
then
. $HOME/.afni/help/all_progs.COMP.bash ]
fi

anc1840 · September 5, 2019, 3:23pm

Hi!!

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!

discoraj · September 6, 2019, 3:51am

Hi,

hmm, a couple of ideas.

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.

Something like this:


mv ~/.bash_profile ~/.bash_profile_afni_backup
touch ~/.bash_profile
mv ~/.bashrc ~/.bashrc_afni_backup
touch ~/.bashrc

Then restart and try the installer.

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.

Thanks, Justin

anc1840 · September 6, 2019, 3:22pm

Thanks a lot, Justin:

I don’t have problems getting in https://github.com/Homebrew/homebrew-core/tree/master/.github in a browser.

When I try


brew install netpbm

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!

discoraj · September 7, 2019, 4:05am

Hi,

Possible certificate problem:

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!)


/usr/bin/ruby -e "$(curl -fsSLk https:// raw.githubusercontent.com/Homebrew/install/master/install)"

The difference from the normal install is the letter “k” after -fsSL that disables the SSL check.

If that works, can you post the output from:


brew config

Thanks, Justin

anc1840 · September 9, 2019, 7:29pm

Thanks again, Justin.

None of the Digicert have expired.

I use bash.
The output of “which curl” is /usr/bin/curl
I tried to manually download homebrew using the letter k after -fsSL as you suggested and I still get the same SSL certificate problem message.

-So it didn’t work. In any case, the output for “brew config” is the following:

HOMEBREW_VERSION: 2.1.11
ORIGIN: https://github.com/Homebrew/brew
HEAD: 37714b5ce1e4909d4d61de2af98343c7012f7cd9
Last commit: 2 weeks ago
Core tap: N/A
HOMEBREW_PREFIX: /usr/local
CPU: quad-core 64-bit sandybridge
Homebrew Ruby: 2.3.7 => /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/bin/ruby
Clang: 8.0 build 800
Git: 2.2.2 => /usr/local/bin/git
Curl: 7.43.0 => /usr/bin/curl
macOS: 10.11.6-x86_64
CLT: 8.2.0.0.1.1480973914
Xcode: N/A
XQuartz: 2.7.11 => /opt/X11

Hopefully this will give you an idea of what else I could try

discoraj · September 10, 2019, 8:16pm

Hi,
We could try a remote support screen share.
Email me at:
rajendrajk@nih.gov
So we can set up a time.