gnames / gnparser

GNparser normalises scientific names and extracts their semantic elements.
MIT License
39 stars 5 forks source link

“gnparser” cannot be opened because the developer cannot be verified. #236

Closed jar398 closed 1 year ago

jar398 commented 1 year ago

the README says: "To use GNparser as a command line tool under Windows, Mac or Linux, download the latest release, uncompress it, and copy gnparser binary somewhere in your PATH."

So I did as directed, tried to run from the shell, and got this error message in a popup:

“gnparser” cannot be opened because the developer cannot be verified.

Since MacOS isn't mentioned in the installation section of the README, my guess is that you can't support it on the Mac any more, so the mention of "Mac" at the top no longer applies. My recommendation is to remove 'Mac' from the README. But of course if there is a solution that would be great!

dimus commented 1 year ago

Thanks for letting me know @jar398, this is very strange, I will try to reproduce the problem on Windows. Mac is supported, and it is pretty much the same procedure as for Linux: https://github.com/gnames/gnparser#linux-or-os-x

Homebrew is enother way to install it on Mac: https://github.com/gnames/gnparser#install-with-homebrew

dimus commented 1 year ago

I added 'Mac' to docs with https://github.com/gnames/gnparser/commit/80acf2cb8ce46dd3779d4f487cbcabf69fd8c185 for clarity

jar398 commented 1 year ago

Yeah, I was referring to the quickstart instructions at the top of the readme.

But I did find out how to get the prebuilt mac executable to go. In the security panel in system preferences select accept from other developers. Then try to open; it will fail. Then look in the security panel again and there will be a question asking whether you want to run gnparser in spite of it being unidentified developer. Say yes. Then try again.

I'm running 10.15.7. Of course things will change in the future...

jar398 commented 1 year ago

This is all about the gradually tightening MacOS security model. They seem to be moving in the direction of allowing only App Store applications even on laptops. I doubt you'll learn anything by checking behavior on Windows.

dimus commented 1 year ago

ah, I see, I understood now that it was a Mac 10.15.7 security problem. That is very unfortunate. I wonder if the homebrew method is still working without doing system preferences modification.

dimus commented 1 year ago

Does this sound right, @jar398?

https://github.com/gnames/gnparser/commit/79c2dc180828e4c632a7160640a0ebd708dca2c8

jar398 commented 1 year ago

Yes, that will do. I'll see if brew installation still works in the next week, sorta busy right now.

jar398 commented 1 year ago

FYI here's what I get from brew installation, which almost works:

bash-3.2$ brew tap gnames/gn
==> Tapping gnames/gn
Cloning into '/usr/local/Homebrew/Library/Taps/gnames/homebrew-gn'...
remote: Enumerating objects: 436, done.        
remote: Counting objects: 100% (49/49), done.        
remote: Compressing objects: 100% (32/32), done.        
remote: Total 436 (delta 20), reused 44 (delta 17), pack-reused 387        
Receiving objects: 100% (436/436), 41.57 KiB | 228.00 KiB/s, done.
Resolving deltas: 100% (183/183), done.
Tapped 6 formulae (18 files, 61.5KB).
bash-3.2$ brew install gnparser
==> Downloading https://ghcr.io/v2/homebrew/core/go/manifests/1.19.2
############################################################################################# 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/go/blobs/sha256:042e0203094cd3727f3e0b12052d4a02478
==> Downloading from https://pkg-containers.githubusercontent.com/ghcr1/blobs/sha256:042e0203094cd37
############################################################################################# 100.0%
==> Downloading https://github.com/gnames/gnparser/archive/v1.6.8.tar.gz
==> Downloading from https://codeload.github.com/gnames/gnparser/tar.gz/refs/tags/v1.6.8
##O=#  #                                                                                           
==> Installing gnparser from gnames/gn
Error: Your Xcode (10.3) is too outdated.
Please update to Xcode 12.4 (or delete it).
Xcode can be updated from the App Store.

I am currently undecided what to do about xcode, delete or upgrade (or nothing - I can run gnparser on my linux machine just fine so don't really need it on the mac, but it would be nice)

jar398 commented 1 year ago

I'm sorry but my mac is too old for the required Xcode update (because it in turn requires an operating system upgrade), so I won't be able to do this test. I've been able to use brew to install other things, so I think it's a good gamble that it will also work for gnparse. I can ask a friend to test the installation via brew but no promises.

dimus commented 1 year ago

Looks like people do not have problem installing gn apps with brew. Closing this ticket.