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sjbonner / mark-on-mac

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Install issues on Macbook M1 #7

Open kevtolan opened 3 weeks ago

kevtolan commented 3 weeks ago

Hello,

I'm having an issue installing mark-on-mac on my Macbook M1 (Sonoma 14.5).

I had originally tried downloading MARK for RMark on Mac following this guide, but it wasn't working for my system.

When I follow the Intel Mac directions, I get the expected error for an M1. 

> (base) ktol@KTolVCE ~ % which mark
> /opt/homebrew/bin/mark
> (base) ktol@KTolVCE ~ % mark
> /opt/homebrew/bin/mark: line 2: /usr/local/bin/mark.64.OSX: No such file or directory

When I follow the Apple Silicon directions, it's unable to bypass permission restrictions. I do notice that, despite running brew uninstall mark-on-mac, when I try to install it again it tells me sjbonner/tap/mark-on-mac 10.1.2 is already installed and up-to-date.

(base) ktol@KTolVCE ~ % brew uninstall mark-on-mac
Uninstalling /opt/homebrew/Cellar/mark-on-mac/10.1.2... (6 files, 4.3MB)
(base) ktol@KTolVCE ~ % softwareupdate --install-rosetta
I have read and agree to the terms of the software license agreement. A list of Apple SLAs may be found here: https://www.apple.com/legal/sla/
Type A and press return to agree: A
2024-10-29 17:06:30.166 softwareupdate[69568:2330107] Package Authoring Error: 062-01890: Package reference com.apple.pkg.RosettaUpdateAuto is missing installKBytes attribute
Install of Rosetta 2 finished successfully
(base) ktol@KTolVCE ~ % arch --x86_64 /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
==> Checking for `sudo` access (which may request your password)...
Password:
==> This script will install:
/usr/local/bin/brew
/usr/local/share/doc/homebrew
/usr/local/share/man/man1/brew.1
/usr/local/share/zsh/site-functions/_brew
/usr/local/etc/bash_completion.d/brew
/usr/local/Homebrew

Press RETURN/ENTER to continue or any other key to abort:
==> /usr/bin/sudo /usr/sbin/chown -R ktol:admin /usr/local/Homebrew
==> Downloading and installing Homebrew...
==> Updating Homebrew...
==> Installation successful!

==> Homebrew has enabled anonymous aggregate formulae and cask analytics.
Read the analytics documentation (and how to opt-out) here:
  https://docs.brew.sh/Analytics
No analytics data has been sent yet (nor will any be during this install run).

==> Homebrew is run entirely by unpaid volunteers. Please consider donating:
  https://github.com/Homebrew/brew#donations

==> Next steps:
- Run these commands in your terminal to add Homebrew to your PATH:
    echo >> /Users/kevintolan/.zprofile
    echo 'eval "$(/usr/local/bin/brew shellenv)"' >> /Users/kevintolan/.zprofile
    eval "$(/usr/local/bin/brew shellenv)"
- Run brew help to get started
- Further documentation:
    https://docs.brew.sh

(base) ktol@KTolVCE ~ % echo "alias beer='arch --x86_64 /usr/local/Homebrew/bin/brew'" >> ~/.zsh_aliases
(base) ktol@KTolVCE ~ % source ~/.zsh_aliases
(base) ktol@KTolVCE ~ % beer install gcc
beer tap sjbonner/tap
beer install mark-on-mac
Warning: gcc 14.2.0_1 is already installed, it's just not linked.
To link this version, run:
  brew link gcc
Warning: sjbonner/tap/mark-on-mac 10.1.2 is already installed and up-to-date.
To reinstall 10.1.2, run:
  brew reinstall mark-on-mac
(base) ktol@KTolVCE ~ % mark
zsh: permission denied: mark

I saw this closed issue and tried to follow the code given, but it didn't return anything:

(base) ktol@KTolVCE ~ % ls -l "$( which mark )"

ls: mark not found: No such file or directory

The commenter referred to deleting everything "mark" related from their system. I tried deleting mark from /usr/local/bin and rerunning the instructions, it's not even identifying mark anymore 

(base) ktol@KTolVCE ~ % mark
zsh: command not found: mark
(base) ktol@KTolVCE ~ % which mark
mark not found

I was hoping that others might have insight into my issue, and that I've supplied the proper background information to begin diagnosing my problem. Please let me know if there are other details that you need!

Best,

Kevin

sjbonner commented 3 weeks ago

Hey @kevtolan,

It seems like you may have tried a few things, but I'll see what I can do. I think that one of the confusions may be between brew and beer. You mentioned that homebrew reported that mark was still installed even after running brew uninstall. That will install the Mac silicon version, but not the rosetta version.

I'd suggest you start by trying to uninstall both versions: brew uninstall mark-on-mac beer uninstall mark-on-mac Then try installing with rosetta beer install mark-on-mac Finally, it seems there is a problem with permissions as noted at the end of [https://oliviergimenez.github.io/popdyn-workshop/tutorials/rmark-mac.html]. I'm not sure why and I haven't heard this from other people. However, the poster suggested simply changing the permissions to make the binary executable sudo chmod 755 /usr/local/bin/mark You may need to us the ls command to find the right path.

Let me know if that works!

kevtolan commented 3 weeks ago

Hi @sjbonner, Thanks for the reply. I tried that, reinstalled, and it's now throwing an error:

(base) ktol@ip0af53556 ~ % beer uninstall mark-on-mac
Uninstalling /usr/local/Cellar/mark-on-mac/10.1.2... (6 files, 4.3MB)
(base) ktol@ip0af53556 ~ % brew uninstall mark-on-mac
Error: No such keg: /opt/homebrew/Cellar/mark-on-mac
(base) ktol@ip0af53556 ~ % softwareupdate --install-rosetta
I have read and agree to the terms of the software license agreement. A list of Apple SLAs may be found here: https://www.apple.com/legal/sla/
Type A and press return to agree: A
2024-10-30 09:13:13.926 softwareupdate[80102:2674874] Package Authoring Error: 062-01890: Package reference com.apple.pkg.RosettaUpdateAuto is missing installKBytes attribute
Install of Rosetta 2 finished successfully
(base) ktol@ip0af53556 ~ % arch --x86_64 /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
==> Checking for `sudo` access (which may request your password)...
Password:
==> This script will install:
/usr/local/bin/brew
/usr/local/share/doc/homebrew
/usr/local/share/man/man1/brew.1
/usr/local/share/zsh/site-functions/_brew
/usr/local/etc/bash_completion.d/brew
/usr/local/Homebrew

Press RETURN/ENTER to continue or any other key to abort:
==> /usr/bin/sudo /usr/sbin/chown -R ktol:admin /usr/local/Homebrew
==> Downloading and installing Homebrew...
remote: Enumerating objects: 41, done.
remote: Counting objects: 100% (37/37), done.
remote: Compressing objects: 100% (24/24), done.
remote: Total 41 (delta 15), reused 33 (delta 13), pack-reused 4 (from 1)
==> Updating Homebrew...
==> Installation successful!

==> Homebrew has enabled anonymous aggregate formulae and cask analytics.
Read the analytics documentation (and how to opt-out) here:
  https://docs.brew.sh/Analytics
No analytics data has been sent yet (nor will any be during this install run).

==> Homebrew is run entirely by unpaid volunteers. Please consider donating:
  https://github.com/Homebrew/brew#donations

==> Next steps:
- Run these commands in your terminal to add Homebrew to your PATH:
    echo >> /Users/kevintolan/.zprofile
    echo 'eval "$(/usr/local/bin/brew shellenv)"' >> /Users/kevintolan/.zprofile
    eval "$(/usr/local/bin/brew shellenv)"
- Run brew help to get started
- Further documentation:
    https://docs.brew.sh

(base) ktol@ip0af53556 ~ % echo "alias beer='arch --x86_64 /usr/local/Homebrew/bin/brew'" >> ~/.zsh_aliases
(base) ktol@ip0af53556 ~ % source ~/.zsh_aliases
(base) ktol@ip0af53556 ~ % beer install gcc

Warning: gcc 14.2.0_1 is already installed, it's just not linked.
To link this version, run:
  brew link gcc
(base) ktol@ip0af53556 ~ % beer tap sjbonner/tap

(base) ktol@ip0af53556 ~ % beer install mark-on-mac

==> Fetching sjbonner/tap/mark-on-mac
==> Downloading https://github.com/sjbonner/mark-on-mac/archive/refs/tags/v10.1.
Already downloaded: /Users/kevintolan/Library/Caches/Homebrew/downloads/ebe2790f5944f5ad061c0988a10ba8ed40bc7dbecfdeca052ad7558b5a855605--mark-on-mac-10.1.2.tar.gz
==> Installing mark-on-mac from sjbonner/tap
🍺  /usr/local/Cellar/mark-on-mac/10.1.2: 6 files, 4.3MB, built in 1 second
==> Running `brew cleanup mark-on-mac`...
Disable this behaviour by setting HOMEBREW_NO_INSTALL_CLEANUP.
Hide these hints with HOMEBREW_NO_ENV_HINTS (see `man brew`).
(base) ktol@ip0af53556 ~ % which mark
/usr/local/bin/mark
(base) ktol@ip0af53556 ~ % mark

Program received signal SIGILL: Illegal instruction.

Backtrace for this error:
#0  0x1052f9d6e
#1  0x1052f8f1d
#2  0x7ff80b5e6fdc
#3  0x104f9367b
#4  0x10536a58e
/usr/local/bin/mark: line 2: 81932 Illegal instruction: 4  DYLD_LIBRARY_PATH=/usr/local/lib/gcc/current/ /usr/local/bin/mark.64.OSX $@
kevtolan commented 3 weeks ago

I manually deleted the mark files and reinstalled. It reinstalled two files in /usr/local/bin: "mark" and "mark.64.OSX", but I'm still getting the same error:

(base) ktol@KTolVCE ~ % which mark
/usr/local/bin/mark
(base) ktol@KTolVCE ~ % mark

Program received signal SIGILL: Illegal instruction.

Backtrace for this error:
#0  0x10240ed6e
#1  0x10240df1d
#2  0x7ff80b5e6fdc
#3  0x1020a867b
#4  0x10247f58e
/usr/local/bin/mark: line 2:  7073 Illegal instruction: 4  DYLD_LIBRARY_PATH=/usr/local/lib/gcc/current/ /usr/local/bin/mark.64.OSX $@