Update Zotero 5 standalone client

[nico202]

@ttuegel hi, I'm tagging you since no mantainer is explicitly set, and I saw you did some PR on this.
Do you think upgrading to zotero 5 is doable?
Thanks, Nicolò

[nico202]

on arch linux [1], they simply download the binary. Maybe is possible to manually build it, however

The build instructions are here [2], but I don't know if they are updated
[1] https://aur.archlinux.org/cgit/aur.git/tree/PKGBUILD?h=zotero
[2] https://www.zotero.org/support/dev/client_coding/building_the_standalone_client

[ttuegel]

I'm tagging you since no mantainer is explicitly set, and I saw you did some PR on this.

I used to be the maintainer for this package, but I haven't used Zotero in several years.

As far as updating, it would be advisable to repackage the standalone client using buildFHSUserEnv.

[nico202]

Fixed in the commit by @timor.
Thanks!

[nico202]

I'm reopening this since opening external programs fails with

relocation error: /usr/lib/libc.so.6: symbol __tunable_get_val, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time reference

as in:

/nix/store/mrw4x303zmfxcngggr1vnx38dn20b0i4-bash-4.4-p12/bin/bash: relocation error: /usr/lib/libc.so.6: symbol __tunable_get_val, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time reference
/nix/store/07q5ay5psyi96lidy3i58lprc0s3mi6p-firefox-unwrapped-51.0.1/lib/firefox-51.0.1/firefox: relocation error: /usr/lib/libc.so.6: symbol __tunable_get_val, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time reference
/nix/store/07q5ay5psyi96lidy3i58lprc0s3mi6p-firefox-unwrapped-51.0.1/lib/firefox-51.0.1/firefox: relocation error: /usr/lib/libc.so.6: symbol __tunable_get_val, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time reference

[jluttine]

Do you know if this supports Zotero extensions/plugins like Zotfile? I suppose they'd need to be packaged for nix and then somehow made available for Zotero. Would be nice to have Zotfile.

[nico202]

I installed betterbibtex and zotfile and they do work indeed

[timor]

@nico202 Can you provide instructions to reproduce the error?

[nico202]

@timor I just opened zotero5 (it automatically used my zotero 4-firefox plugin directory), double click on a pdf file, open with: /home/USERNAME/.nix-profile/bin/okular
or right click: open folder -> with /home/USERNAME/.nix-profile/bin/pcmanfm

[timor]

@nico202 Hmm, sorry. I use evince instead of okular, and opening files works for me. I would try to change it to okular for testing, but I don't know how to make it ask again for the path...

edit How do you set your plugin directory?

[nico202]

@timor the same happens for me when zotero tries to open firefox when opening links from zotero, too. Firefox and zotero are added to the profile with nix-env -f ./nixpkgs/ -i {zotero,firefox} using the master checkout.

zotero --help does not show the help, and zotero -P does not open the profile manager, so I don't know how to try a clean profile.

Also, I don't know how to set the plugin directory. I think it's using the firefox one (my library was inside zotero-firefox before having to move to standalone).

[timor]

@nico202 Maybe this has to do with your library location then? I have had my library separate, and my standalone installation does not seem to have picked up my plugins.

I think that standalone zotero should actually be working without knowing anything about your day-to-day firefox. As far as I understand, they basically ship their own version of the firefox internals with zotero. Maybe it is some kind of conflict between these two?

[nico202]

I think so. But I don't know how to let it forget about my old profile.

The bin is the right one: ls -lah $(which zotero) -> /nix/store/sp6ixxhsly25jaycwcx5rxfy4af5ykbh-zotero-5.0.25/bin/zotero

Renamed the the library dir (inside firefox) and rename ~/.zotero.

/nix/store/07q5ay5psyi96lidy3i58lprc0s3mi6p-firefox-unwrapped-51.0.1/lib/firefox-51.0.1/firefox: relocation error: /usr/lib/libc.so.6: symbol __tunable_get_val, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time reference

I don't even know why it is calling firefox 51.

However, extensions get installed correctly (tried with https://github.com/retorquere/zotero-better-bibtex) (got installed under ~/.zotero/zotero/profile.dir/extensions/extension.xpi)

[timor]

@nico202 Can you try the following:

1. run less $(which zotero) and note the location of the zotero-fhs-env script location
2. run that script without any arguments to enter the chroot
3. start firefox from there manually (e.g. /run/current-system/bin/firefox or the path to your custom profile)

[nico202]

@timor zotero-fhs-env-chrootenv:username@machine:~$ /home/username/.nix-profile/bin/firefox -> works

[timor]

@nico202 Ok, no idea then. Could you create a new user and see if it works then? I think we don't know yet whether this is related to your profile or the zotero installation.

[jluttine]

I'm unable to open PDFs with Okular from Zotero. I get the following error:

This application failed to start because it could not find or load the Qt platform plugin "xcb" in "".

Reinstalling the application may fix this problem.

When opening the PDF and choosing an app for opening the file, I choose /run/current-system/sw/bin/okular (because which okular points there). Any ideas? I guess it could be fixed by installing Okular to my home directory with nix-env but I wouldn't want to do that.

[timor]

@jluttine
This may be related to #30977. For me, the only way to get okular working correctly (independently from zotero) right now is having it installed via nix-env into my personal profile, btw.

[jluttine]

Ok. Okular works for me outside of zotero, but I have it installed in system packages.

[plumps]

There seems to be an issue with the zotero and a missing libX11-xcb.so.1 atm:

/nix/store/7jwflsnyg92p8x31h9dxpyl4xx70vhak-zotero-fhs-env/bin/zotero-fhs-env /nix/store/pn5gywigh5fcm4pjlmzc19ky5qfxfdw0-zotero-5.0.35.1-pkg/bin/zotero
XPCOMGlueLoad error for file /nix/store/pn5gywigh5fcm4pjlmzc19ky5qfxfdw0-zotero-5.0.35.1-pkg/data/libxul.so:
libX11-xcb.so.1: cannot open shared object file: No such file or directory
Couldn't load XPCOM.

[schmittlauch]

#48814 seems to be the specific issue about not being able to open content in Zotero using external programs.
So I suggest closing this issue in favor of the more specific one.

[NickHu]

I found a fix for running okular from zotero (both installed system-wide) here #48814; zotero is now up to date so this issue should probably be closed

[schmittlauch]

@ttuegel This can be closed