biber removes texlive-bibtex-extra

Bug #1565842 reported by Muelli
This bug report is a duplicate of:  Bug #1589644: [SRU] biber 2.4 to xenial. Edit Remove
386
This bug affects 76 people
Affects Status Importance Assigned to Milestone
biber (Ubuntu)
Medium
Unassigned

Bug Description

It seems you can either install either texlive-bibtex-extra or biber but not both. However, both packages are required in order to use biber for bibliography management when compiling a LaTeX document.

sudo apt-get install texlive-bibtex-extra biber
Reading package lists... Done
Building dependency tree
Reading state information... Done
texlive-bibtex-extra is already the newest version (2015.20160320-1).
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies.
 texlive-bibtex-extra : Breaks: biber (< 2.4) but 2.3-1 is to be installed
E: Unable to correct problems, you have held broken packages.

ProblemType: Bug
DistroRelease: Ubuntu 16.04
Package: biber (not installed)
ProcVersionSignature: Ubuntu 4.4.0-16.32-generic 4.4.6
Uname: Linux 4.4.0-16-generic x86_64
ApportVersion: 2.20.1-0ubuntu1
Architecture: amd64
CurrentDesktop: GNOME
Date: Mon Apr 4 17:07:58 2016
InstallationDate: Installed on 2015-12-02 (124 days ago)
InstallationMedia: Ubuntu-GNOME 16.04 LTS "Xenial Xerus" - Alpha amd64 (20151027)
SourcePackage: biber
UpgradeStatus: No upgrade log present (probably fresh install)

Revision history for this message
Muelli (ubuntu-bugs-auftrags-killer) wrote :
Revision history for this message
Launchpad Janitor (janitor) wrote :

Status changed to 'Confirmed' because the bug affects multiple users.

Changed in biber (Ubuntu):
status: New → Confirmed
Changed in biber (Ubuntu):
importance: Undecided → Medium
Revision history for this message
Reiner Jung (prefec2) wrote :

I have investigated this a little bit and removed biber 2.3-1 which allows to upgrade texlive-bibtex-extra. Subsequently I have installed biber 2.4 from the original biber web page http://biblatex-biber.sourceforge.net/
Unfortunately, in this combination the biber output is not compilable with pdflatex. Biber 2.3 refuses to process the biblatex files.

Revision history for this message
Kjell L. (lkjell) wrote :

 Tried biber 2.4 and it works had to remoeve the tmp files *.bbl and *.bcf first compiled with lualatex

description: updated
Revision history for this message
mo (deez) wrote :

For me to use biber in my tex document, I require both the biber binary and the "biblatex.sty" file from the "texlive-bibtex-extra". The shouldn't be exclusive of each other and in previous versions of Ubuntu that wasn't the case.

Workaround:
1) # apt-get install texlive-bibtex-extra
2) Download biber (biber-linux_x86_64.tar.gz) from http://biblatex-biber.sourceforge.net/
3) # tar xzf biber-linux_x86_64.tar.gz
4) # cp biber /usr/local/bin

Revision history for this message
Michael Kiermaier (michael-kiermaier) wrote :

Yes, the fix would simply be to provide the biber package in version 2.4 in Xenial. Hope that this will be done soon.

description: updated
Revision history for this message
Tamas Papp (tkpapp) wrote :

As a workaround, you can install the latest biber from Debian:
https://packages.debian.org/sid/all/biber/download

Revision history for this message
Markus (microsome) wrote :

Importantly, remove the files *.bbl and *.bcf files form the folder containing the tex file(s).

Revision history for this message
Sebastian Gabriel (gabriel-grissu) wrote :

Installing the Debian biber package would remove texlive-bibtex-extra as well.

Revision history for this message
Rodrigo G (rodrigog83) wrote :

A workaround is to install biber 2.4 package from yakkerty: http://packages.ubuntu.com/yakkety/biber
dpkg -i biber_2.4-1_all.deb
and then install dependencies using
sudo apt -f install

Works flawlessly.

Revision history for this message
Titus von der Malsburg (malsburg) wrote :

I can confirm that Rodrigo's workaround solves the problem. Can we please have a fix in Xenial? This will affect a lot of users I'm afraid. Thank you.

MatthiasE (matthiaa)
Changed in biber (Ubuntu):
assignee: nobody → MatthiasE (matthiaa)
assignee: MatthiasE (matthiaa) → nobody
Revision history for this message
Robert Bredereck (rbredereck) wrote :

Unfortunately, Rodrigo's workaround does not work anymore. (yakkerty's biber is too new now)

Can we please have a fix?

Revision history for this message
Christopher Barrington-Leigh (cpbl) wrote :

From this link, I chose my platform and downloaded the tgz file

https://sourceforge.net/projects/biblatex-biber/files/biblatex-biber/2.4/binaries/

ie, just clicked on the link below to get the 64 bit Linux version:

https://sourceforge.net/projects/biblatex-biber/files/biblatex-biber/2.4/binaries/Linux/biber-linux_x86_64.tar.gz/download

To "install" this, simply unpack it and copy the single file, biber, to your path. You could put it locally in your LaTeX source folder, or in your own bin path, or (using sudo) in /usr/bin/.

This older version seems compatible with 16.04's biblatex, and I can compile my file.

Revision history for this message
Muelli (ubuntu-bugs-auftrags-killer) wrote :
Revision history for this message
Christianus Pistorius (carbeck) wrote :

The link to biber 2.4 Muelli posted doesn't work for me (404); the link to Debian's package database reveals that they've also updated to 2.5.

Revision history for this message
Rodrigo G (rodrigog83) wrote :

Now that the packages have been updated to 2.5, another workaround is downloading biber 2.4 from this ppa: https://launchpad.net/~jonathonf/+archive/ubuntu/biber (direct link to deb: http://ppa.launchpad.net/jonathonf/biber/ubuntu/pool/main/b/biber/biber_2.4-1~ubuntu14.04.1york3_all.deb )

Same as before:

sudo dpkg -i biber_2.4-1~ubuntu14.04.1york3_all.deb
sudo apt -f install

(no need to add the ppa)

Revision history for this message
Robert Bredereck (rbredereck) wrote :

Does Ubuntu have package maintainers like Debian has? If yes, could the package maintainer please upgrade biber to 2.4? (Just take a copy from yakkety development.)

Revision history for this message
Ales Cepek (ales-cepek) wrote : Re: [Bug 1565842] Re: biber removes texlive-bibtex-extra

I do not know much about Ubuntu. I switched to Ubuntu from Debian few years
ago just to have the same system as our students (we used to have Linux in
our curricula). And as I experience some queer minor problems with Ubuntu
16.04, the more and more I am considering return home to Debian ;-) ... but
definitely not before current semester is closed.
Ales

cepek@biggy:~/work$ dpkg -l biber
Desired=Unknown/Install/Remove/Purge/Hold
|
Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
||/ Name Version Architecture Description
+++-==============-============-============-======================
rc biber 2.3-1 all Much-augmented BibTeX
replacement
cepek@biggy:~/work$
cepek@biggy:~/work$ which biber
/usr/local/bin/biber
cepek@biggy:~/work$ biber --version
biber version: 2.4

On 6 June 2016 at 10:42, Robert Bredereck <email address hidden> wrote:

> Does Ubuntu have package maintainers like Debian has? If yes, could the
> package maintainer please upgrade biber to 2.4? (Just take a copy from
> yakkety development.)
>
> --
> You received this bug notification because you are subscribed to the bug
> report.
> https://bugs.launchpad.net/bugs/1565842
>
> Title:
> biber removes texlive-bibtex-extra
>
> Status in biber package in Ubuntu:
> Confirmed
>
> Bug description:
> It seems you can either install either texlive-bibtex-extra or biber
> but not both. However, both packages are required in order to use
> biber for bibliography management when compiling a LaTeX document.
>
> sudo apt-get install texlive-bibtex-extra biber
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> texlive-bibtex-extra is already the newest version (2015.20160320-1).
> Some packages could not be installed. This may mean that you have
> requested an impossible situation or if you are using the unstable
> distribution that some required packages have not yet been created
> or been moved out of Incoming.
> The following information may help to resolve the situation:
>
> The following packages have unmet dependencies.
> texlive-bibtex-extra : Breaks: biber (< 2.4) but 2.3-1 is to be
> installed
> E: Unable to correct problems, you have held broken packages.
>
> ProblemType: Bug
> DistroRelease: Ubuntu 16.04
> Package: biber (not installed)
> ProcVersionSignature: Ubuntu 4.4.0-16.32-generic 4.4.6
> Uname: Linux 4.4.0-16-generic x86_64
> ApportVersion: 2.20.1-0ubuntu1
> Architecture: amd64
> CurrentDesktop: GNOME
> Date: Mon Apr 4 17:07:58 2016
> InstallationDate: Installed on 2015-12-02 (124 days ago)
> InstallationMedia: Ubuntu-GNOME 16.04 LTS "Xenial Xerus" - Alpha amd64
> (20151027)
> SourcePackage: biber
> UpgradeStatus: No upgrade log present (probably fresh install)
>
> To manage notifications about this bug go to:
> https://bugs.launchpad.net/ubuntu/+source/biber/+bug/1565842/+subscriptions
>

Revision history for this message
Rodrigo G (rodrigog83) wrote :

Found a mirror with the original biber 2.4 package from Debian:

http://ftp.gnome.org/mirror/cdimage/snapshot/Debian/pool/main/b/biber/biber_2.4-1_all.deb

In case it gets deleted, I upload a copy.

Revision history for this message
Michael Kiermaier (michael-kiermaier) wrote :

@Robert Bredereck:
I completely agree. The problem affects many people, and the fix is almost trivial. But sadly we don't even know if anyone in the position of applying it is listening at all.

Revision history for this message
Nick Andrik (andrikos) wrote :

Can someone check the 2.5-1 version from yakkety which can be found in yakkety in the following link?
http://packages.ubuntu.com/yakkety/all/biber/download

If this is confirmed to work, then we can update this bug to request a backport of this version from yakkety to xenial.

If the proper fix is using biber 2.4, I can prepare a version for xenial, and after we check that it works, we will request a backport.

Thanks in advance for your feedback,
Nick

Revision history for this message
Rodrigo G (rodrigog83) wrote :

Hello Nick, it doesn't work with 2.5-1 version (requires texlive 2016).

$ sudo dpkg -i biber_2.5-1_all.deb
dpkg: regarding biber_2.5-1_all.deb containing biber:
 biber breaks texlive-bibtex-extra (<< 2016)
  texlive-bibtex-extra (version 2015.20160320-1) is present and installed.

dpkg: error processing archive biber_2.5-1_all.deb (--install):
 installing biber would break texlive-bibtex-extra, and
 deconfiguration is not permitted (--auto-deconfigure might help)
Errors were encountered while processing:
 biber_2.5-1_all.deb

So I think creating a biber 2.4 package for xenial is the way to go.

Thanks!
Rodrigo

Revision history for this message
Nick Andrik (andrikos) wrote :

OK, give me half an hour and I'll see what I can do :)

Revision history for this message
Nick Andrik (andrikos) wrote :

A version 2.4-1 of the package is prepared in my PPA:
https://launchpad.net/~andrikos/+archive/ubuntu/ppa/+packages?field.name_filter=&field.status_filter=published&field.series_filter=xenial

Please check it, and let me know if this resolves the problem for xenial.

Revision history for this message
Frédéric Meynadier (frederic-meynadier-b) wrote :

Thanks @andrikos !

Just to confirm what @rodrigog83 says:

While investigating this matter, I built a fresh VM with Debian testing (stretch) just to test : biber 2.5-1 works well in it... but with

texlive-bibtex-extra 2016.20160520-1

whereas xenial has
texlive-bibtex-extra 2015.20160320-1
(with biblatex.sty version 3.3 in it : technically, this has been issued in 2016, but in the 2015 texlive distribution).

So, I really think biber 2.4 is the way to go... as long as xenial sticks to texlive 2015 (which, I suppose, is the plan ?).

Revision history for this message
Frédéric Meynadier (frederic-meynadier-b) wrote :

@andrikos, comment #24 : Works for me, thank you very much !

Revision history for this message
Rodrigo G (rodrigog83) wrote :

@andrikos, #24: Works like a charm.

Revision history for this message
Nick Andrik (andrikos) wrote :

FYI, Bug: #1589644 is filed for requesting the backport
https://bugs.launchpad.net/xenial-backports/+bug/1589644

Let's hope that it will be accepted soon.

Kind regards,
Nick

Revision history for this message
Robert Bredereck (rbredereck) wrote :

@andrikos: Thanks for taking care of this.

Revision history for this message
Michael Kiermaier (michael-kiermaier) wrote :

@andrikos: Thank you!

Nick Andrik (andrikos)
Changed in biber (Ubuntu):
status: Confirmed → Fix Committed
Revision history for this message
Nick Andrik (andrikos) wrote :

Hello everybody,

This bug is now addressed in the backport request ( Bug 1589644 ) which has been accepted in xenial-proposed.
For this reason, this bug has been marked a duplicate of the other one.

In order for the new package to make it to xenial-updates, we need to perform some testing, similar to what we did with the version from my PPA.

May I kindly request that you move to the aforementioned bug, and follow the instructions posted there?
I'm copying them here for your convenience, please add any comments you have directly to the other bug report.

Thanks a lot in advance,
Nick

---- latest request from Bug 1589644 : https://bugs.launchpad.net/bugs/1589644 ----

Hello Nick, or anyone else affected,

Accepted biber into xenial-proposed. The package will build now and be available at https://launchpad.net/ubuntu/+source/biber/2.4-1ubuntu1.16.04.1 in a few hours, and then in the -proposed repository.

Please help us by testing this new package. See https://wiki.ubuntu.com/Testing/EnableProposed for documentation how to enable and use -proposed. Your feedback will aid us getting this update out to other Ubuntu users.

If this package fixes the bug for you, please add a comment to this bug, mentioning the version of the package you tested, and change the tag from verification-needed to verification-done. If it does not fix the bug for you, please add a comment stating that, and change the tag to verification-failed. In either case, details of your testing will help us make a better decision.

Further information regarding the verification process can be found at https://wiki.ubuntu.com/QATeam/PerformingSRUVerification . Thank you in advance!

Revision history for this message
Richard Bruce Baxter (richardbrucebaxter) wrote :

@andrikos: Thanks - the updated package appears to work.

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