bib file not found even though known to kpse

[AndrewSwann]

Running biber 2.18 on a mac, installed via macports texlive distribution, bib files that can be found by kpsewhich in the shell are not longer found by biber. This was previously working for me a few days ago.

Running with --trace, I get

[0] Config.pm:306> INFO - This is Biber 2.18
[0] Config.pm:309> INFO - Logfile is 'a.blg'
[80] biber-darwin:340> INFO - === Wed Jun 29, 2022, 08:39:55
[97] Biber.pm:418> INFO - Reading 'a.bcf'
[196] Biber.pm:978> INFO - Found 1 citekeys in bib section 0
[196] Biber.pm:981> DEBUG - The citekeys for section 0 are: test
[323] biber-darwin:426> TRACE - 
....
[335] Biber.pm:4401> INFO - Processing section 0
[335] Biber.pm:4515> DEBUG - Looking for directly cited keys: test
[347] Biber.pm:4592> INFO - Looking for bibtex file 'x.bib' for section 0
[347] Utils.pm:410> ERROR - Cannot find 'x.bib'!
[347] Biber.pm:135> INFO - ERRORS: 1

Looking at the source of Utils.pm suggests that kpsewhich was never tried, otherwise the report should have included messages such as Looking for file '$sourcepath' via kpsewhich etc. I have tried removing the biber cache and running again, but this does not change the result.

[herbs]

On Jul 4, 2022, at 5:35 AM, plk @.***> wrote:

Looks like this might be an issue with an older version of PAR::Packer as I can fix the issue by upgrading this on MacOS 10.12. I will be upgrading the MacOS build servers and pushing new versions soon.

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Howdy,

Now that I have the updated biblatex I ran biber on my test file. Running

biber MyBiblatexTest

failed to find tugboat.bib. However,

/Library/TeX/texbin/biber MyBiblatexTest

or

/usr/local/texlive/2022/bin/universal-darwin/biber MyBiblatexTest

ran fine. This is true whether the cache was already present or needed to be re-created.

Just an added data point though a bit late.

Good Luck,

Herb Schulz @.***

[amunn]

Late to the party here, but I'm having the same problem (regularly installed MacTeX) MacOS 12.4 (Monterey). biber 2.18.

[herbs]

On Jul 4, 2022, at 1:13 PM, Alan Munn @.***> wrote:

Late to the party here, but I'm having the same problem (regularly installed MacTeX) MacOS 12.4 (Monterey). biber 2.18.

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Howdy,

Just to be clear. Can we assume you are on an Intel system? It seems that the arm64 code runs. I've got one of each, so...

Good Luck,

Herb Schulz @.***

[amunn]

On Jul 4, 2022, at 1:13 PM, Alan Munn @.***> wrote: Late to the party here, but I'm having the same problem (regularly installed MacTeX) MacOS 12.4 (Monterey). biber 2.18. Howdy, Just to be clear. Can we assume you are on an Intel system? It seems that the arm64 code runs. I've got one of each, so

Yes, Intel system. Using the full path works, but not the filename alone.

[plk]

It's a problem with the module used to package the binary I believe. I am in the process of getting a new release out with a fix but my main build server is having a few issues I have to deal with first, hopefully this evening.

[plk]

After coincidental and irritating server issues, I have rebuilt the binaries for 2.18 and before I push then to CTAN/TL, they are on SF:

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

Can you get the universal binary from here and try it with non-absolute paths?

[herbs]

On Jul 6, 2022, at 6:34 AM, plk @.***> wrote:

After coincidental and irritating server issues, I have rebuilt the binaries for 2.18 and before I push then to CTAN/TL, they are on SF:

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

Can you get the universal binary from here and try it with non-absolute paths?

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Howdy,

Sigh... Unfortunately, after running pdflatex on BibTestBiber.tex which is on the Desktop on my Intel system, I get

% biber BibTestBiber zsh: killed biber BibTestBiber

so it refuses to run. As before, it runs fine on my ARM system.

Good Luck,

Herb Schulz @.***

[plk]

@herbs - Did you do the usual unblocking routine via System Preferences? That isn't notarized and so will need to be manually authorized until it's in TL.

[herbs]

On Jul 6, 2022, at 7:11 AM, plk @.***> wrote:

@herbs - Did you do the usual unblocking routine via System Preferences? That isn't notarized and so will need to be manually authorized until it's in TL.

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Howdy,

I didn't but now I did and it runs fine under Intel.

For others, I first put biber on the Desktop. I then ran

~/Desktop/biber --version

which give rise to a dialog box about not being able to check the programmer. Going into the Security & Privacy' pane ofSystem Preferences' I can manually give my approval to run biber. I then run biber using

~/Desktop/biber --version

again and I get a another dialog box that lets me Open biber whcih then runs fine. I finally move, NOT COPY, biber to it's standard location using

sudo mv ~/Desktop/biber /usr/local/texlive/2022/bin/universal-darwin

run

biber --version

so it's found along the path and all is fine. Finally, I change the owner and group to the standard for those executables with

chown root:wheel /usr/local/texlive/2022/bin/universal-darwin/biber

and it now works fine. You can't copy to the final location because the copy won't be approved to run.

Good Luck,

Herb Schulz @.***

[amunn]

Thanks, this binary works fine for me (Intel Mac).

[plk]

CTAN publishing will be done today and you should see 2.18-1 for MacOS in TL.

[herbs]

On Jul 6, 2022, at 11:44 AM, plk @.***> wrote:

CTAN publishing will be done today and you should see 2.18-1 for MacOS in TL.

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Howdy,

Thanks for your patience and working on this so quickly.

Good Luck,

Herb Schulz @.***

[herbs]

On Jul 6, 2022, at 11:44 AM, plk @.***> wrote:

CTAN publishing will be done today and you should see 2.18-1 for MacOS in TL.

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Howdy,

The update came through today. No problems. Running

% biber --version

returns

biber version: 2.18

so no change there. Certainly not a problem.

Thanks again.

Good Luck,

Herb Schulz @.***

[plk]

Good, at least we know what the problem was and that it's fixed.

[AndrewSwann]

Dear Philip,

Many thanks for sorting this out. The latest update works well. Sorry, for not responding earlier but I have been offline.

Best wishes

Andrew

-- Andrew Swann | Professor of Mathematics | Tel +45 871 55767 | @.**@.> | https://users-math.au.dk/swann/ | Department of Mathematics, Aarhus University, Ny Munkegade 118, Bldg 1530, DK-8000 Aarhus C, Denmark | Dept +45 871 50000

From: plk @.> Date: Friday, 8 July 2022 at 14:03 To: plk/biber @.> Cc: Andrew Francis Swann @.>, Mention @.> Subject: Re: [plk/biber] bib file not found even though known to kpse (Issue #416)

Good, at least we know what the problem was and that it's fixed.

— Reply to this email directly, view it on GitHubhttps://github.com/plk/biber/issues/416#issuecomment-1178910271, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACDDEFJT4RGCVUGEYMKLPBDVTAKJ7ANCNFSM52ET6D3A. You are receiving this because you were mentioned.Message ID: @.***>

[herbs]

On Jun 30, 2022, at 8:46 AM, Herbert Schulz @.***> wrote:

On Jun 30, 2022, at 8:09 AM, plk @.***> wrote:

Can you try the following and see what happens?

cp /usr/local/texlive/2022/bin/universal-darwin/biber ~/Desktop/biber codesign --remove-signature ~/Desktop/biber ~/Desktop/biber --tool biblatex-examples.bib

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Howdy,

I had to approve the running of an unsigned app in the `Security & Privacy' tab of System Preferences. Even after approving it zsh killed the run.

Good Luck,

Herb Schulz @.***

Howdy,

Ignore that! I was running on the wrong system.

If I copy biber to the Desktop and run it without removing the signature I first get

Approving the running of it anyway in the `Security & Privacy' tab of System Preferences. I can then run it \emph{and it runs fine}.

Similarly running the test app needs approval and then it runs fine with the expected output:

PATH=/Users/herbs/opt/anaconda3/bin:/Users/herbs/opt/anaconda2/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/Applications/Little Snitch.app/Contents/Components:/opt/X11/bin:/Library/Apple/usr/bin /Library/TeX/texbin/kpsewhich

Good Luck,

Herb Schulz @.***

[herbs]

On Dec 17, 2022, at 9:00 AM, Leon Moonen @.***> wrote:

Hi again, I have just updated my mac to Ventura and updated MacTeX as well, and it looks we have a regression in MacTeX/TeXLive: ➤ biber --version biber version: 2.18

➤ biber --tool biblatex-examples.bib INFO - This is Biber 2.18 running in TOOL mode INFO - Logfile is 'biblatex-examples.bib.blg' INFO - Looking for bibtex file 'biblatex-examples.bib' ERROR - Cannot find 'biblatex-examples.bib'! INFO - ERRORS: 1

➤ kpsewhich biblatex-examples.bib /usr/local/texlive/2022/texmf-dist/bibtex/bib/biblatex/biblatex/biblatex-examples.bib

➤ tlmgr info biber package: biber category: Package shortdesc: A BibTeX replacement for users of BibLaTeX longdesc: Biber is a BibTeX replacement for users of BibLaTeX. Biber supports full UTF-8, can (re)-encode input and output, supports highly configurable sorting, dynamic bibliography sets and many other features. The CTAN distribution offers a compressed tar archive of the sources, etc., together with "binary" distributions for a variety of platforms. Note: on SourceForge biber is formally named "biblatex-biber", to distinguish it from an earlier (now apparently moribund) project called "biber". installed: Yes revision: 64367 sizes: src: 1217k, doc: 269k, bin: 98113k relocatable: No cat-version: 2.18 cat-license: artistic2 cat-topics: biblio cat-related: bibtex crosstex biblatex cat-contact-home: http://biblatex-biber.sourceforge.net/ cat-contact-bugs: https://github.com/plk/biber/issues cat-contact-repository: https://github.com/plk/biber collection: collection-bibtexextra

➤ tlmgr restore --dry-run biber tlmgr restore: dry run, no changes will be made Available backups for biber: 63965 (2022-12-08 00:23)

At this point, I downloaded https://sourceforge.net/projects/biblatex-biber/files/biblatex-biber/current/binaries/MacOS/biber-darwin_universal.tar.gz/download, ensured that the downloaded executable can be executed (w. xattr), and all works as expected: ➤ xattr -d com.apple.quarantine ~/Downloads/biber

➤ ~/Downloads/biber --version biber version: 2.18

➤ ~/Downloads/biber --tool biblatex-examples.bib INFO - This is Biber 2.18 running in TOOL mode INFO - Logfile is 'biblatex-examples.bib.blg' INFO - Looking for bibtex file 'biblatex-examples.bib' INFO - LaTeX decoding ... INFO - Found BibTeX data source '/usr/local/texlive/2022/texmf-dist/bibtex/bib/biblatex/biblatex/biblatex-examples.bib' INFO - Overriding locale 'en_US' defaults 'variable = shifted' with 'variable = non-ignorable' INFO - Overriding locale 'en_US' defaults 'normalization = NFD' with 'normalization = prenormalized' INFO - Sorting list 'tool/global//global/global' of type 'entry' with template 'tool' and locale 'en_US' INFO - No sort tailoring available for locale 'en_US' INFO - Writing 'biblatex-examples_bibertool.bib' with encoding 'UTF-8' INFO - Output to biblatex-examples_bibertool.bib

I'll just overwrite the TeXLive version with that binary, but I guess more people will run into this... cheers, Leon — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

Howdy,

Hmmm... Did you do a full update after installing TeX Live 2022 with MacTeX? I'm using a fully updated TeX Live 2022 and don't see that problem.

Good Luck,

Herb Schulz @.***

[leonmoonen]

yeah, it looks like I somehow ended with a mix of old and new versions of biber, and the path changed to prefer an old one...