Biber 2.20 error
Closed this issue · 14 comments
On macBook with m1 and Sonoma 14.4 and after todays TeXLive update, which should be 2.20:
voss >biber --version
Can't load '/var/folders/46/kr8jdrld7d324jpscgrlw2fh0000gn/T/par-766f7373/cache-351a9b4d1739a271ecf0be692d0ec1ef0a81d258/inc/lib/auto/XML/LibXML/LibXML.bundle' for module XML::LibXML: dlopen(/var/folders/46/kr8jdrld7d324jpscgrlw2fh0000gn/T/par-766f7373/cache-351a9b4d1739a271ecf0be692d0ec1ef0a81d258/inc/lib/auto/XML/LibXML/LibXML.bundle, 0x0001): Symbol not found: _iconv
Referenced from: <4FABCE36-0023-3D1B-A158-3499EFD82412> /private/var/folders/46/kr8jdrld7d324jpscgrlw2fh0000gn/T/par-766f7373/cache-351a9b4d1739a271ecf0be692d0ec1ef0a81d258/libxml2.2.dylib
Expected in: <E05EA2EB-4F11-36B6-87E5-41C89C1BCC5D> /private/var/folders/46/kr8jdrld7d324jpscgrlw2fh0000gn/T/par-766f7373/cach
Universal binary?
macBook Sonoma with m1 and up-to-date TL24 and universal-darwin bin dir
Looking at it. Can reproduce, something to do with homebrew on M1s doing something strange.
And the same output with the extracted Biber version in subdirectory .../thin/:
voss>thin:$ ./biber --version
Can't load '/var/folders/46/kr8jdrld7d324jpscgrlw2fh0000gn/T/par-766f7373/cache-351a9b4d1739a271ecf0be692d0ec1ef0a81d258/inc/lib/auto/XML/LibXML/LibXML.bundle' for module XML::LibXML: dlopen(/var/folders/46/kr8jdrld7d324jpscgrlw2fh0000gn/T/par-766f7373/cache-351a9b4d1739a271ecf0be692d0ec1ef0a81d258/inc/lib/auto/XML/LibXML/LibXML.bundle, 0x0001): Symbol not found: _iconv
Referenced from: <4FABCE36-0023-3D1B-A158-3499EFD82412> /private/var/folders/46/kr8jdrld7d324jpscgrlw2fh0000gn/T/par-766f7373/cache-351a9b4d1739a271ecf0be692d0ec1ef0a81d258/libxml2.2.dylib
Expected in: <E05EA2EB-4F11-36B6-87E5-41C89C1BCC5D> /private/var/folders/46/kr8jdrld7d324jpscgrlw2fh0000gn/T/par-766f7373/cache-351a9b4d1739a271ecf0be692d0ec1ef0a81d258/libiconv.2.dylib at /loader/HASH(0x14e082700)/DynaLoader.pm line 210.
at /loader/HASH(0x14e0fce90)/PAR/Heavy.pm line 104.
BEGIN failed--compilation aborted at /var/folders/46/kr8jdrld7d324jpscgrlw2fh0000gn/T/par-766f7373/cache-351a9b4d1739a271ecf0be692d0ec1ef0a81d258/inc/lib/XML/LibXML.pm line 156.
Compilation failed in require at /var/folders/46/kr8jdrld7d324jpscgrlw2fh0000gn/T/par-766f7373/cache-351a9b4d1739a271ecf0be692d0ec1ef0a81d258/inc/lib/XML/LibXML/Simple.pm line 21.
BEGIN failed--compilation aborted at /var/folders/46/kr8jdrld7d324jpscgrlw2fh0000gn/T/par-766f7373/cache-351a9b4d1739a271ecf0be692d0ec1ef0a81d258/inc/lib/XML/LibXML/Simple.pm line 21.
Compilation failed in require at /var/folders/46/kr8jdrld7d324jpscgrlw2fh0000gn/T/par-766f7373/cache-351a9b4d1739a271ecf0be692d0ec1ef0a81d258/inc/lib/Biber/LaTeX/Recode.pm line 16.
BEGIN failed--compilation aborted at /var/folders/46/kr8jdrld7d324jpscgrlw2fh0000gn/T/par-766f7373/cache-351a9b4d1739a271ecf0be692d0ec1ef0a81d258/inc/lib/Biber/LaTeX/Recode.pm line 16.
Compilation failed in require at /var/folders/46/kr8jdrld7d324jpscgrlw2fh0000gn/T/par-766f7373/cache-351a9b4d1739a271ecf0be692d0ec1ef0a81d258/inc/lib/Biber/Utils.pm line 19.
BEGIN failed--compilation aborted at /var/folders/46/kr8jdrld7d324jpscgrlw2fh0000gn/T/par-766f7373/cache-351a9b4d1739a271ecf0be692d0ec1ef0a81d258/inc/lib/Biber/Utils.pm line 19.
Compilation failed in require at /var/folders/46/kr8jdrld7d324jpscgrlw2fh0000gn/T/par-766f7373/cache-351a9b4d1739a271ecf0be692d0ec1ef0a81d258/inc/lib/Biber/Internals.pm line 8.
BEGIN failed--compilation aborted at /var/folders/46/kr8jdrld7d324jpscgrlw2fh0000gn/T/par-766f7373/cache-351a9b4d1739a271ecf0be692d0ec1ef0a81d258/inc/lib/Biber/Internals.pm line 8.
Compilation failed in require at /loader/HASH(0x14e0b2868)/parent.pm line 16.
BEGIN failed--compilation aborted at /var/folders/46/kr8jdrld7d324jpscgrlw2fh0000gn/T/par-766f7373/cache-351a9b4d1739a271ecf0be692d0ec1ef0a81d258/inc/lib/Biber.pm line 5.
Compilation failed in require at script/biber-darwin line 17.
BEGIN failed--compilation aborted at script/biber-darwin line 17.
Same issue here (M1 Pro and M2 Pro CPUs).
In the meantime, restoring the previous versions of biber (68188/2.19) and biber.universal-darwin (66402) via the TeX Live Utility helps.
Can you try the corrected version on SF?
https://sourceforge.net/projects/biblatex-biber/files/biblatex-biber/current/binaries/MacOS/biber-darwin_universal.tar.gz/download
Making a long story short (see full message at https://tug.org/pipermail/tex-live/2024-March/050284.html), the problem seems to be a mismatch between libiconv and libxml in the ARM part of biber.
Namely, libiconv.2.dylib links to the Homebrew version of libiconv, /opt/homebrew/opt/libiconv/lib/libiconv.2.dylib, which defines symbols _libiconv*:
% otool -L libiconv.2.dylib
libiconv.2.dylib:
/opt/homebrew/opt/libiconv/lib/libiconv.2.dylib (compatibility version 9.0.0, current version 9.1.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1336.0.0)
% dsymutil -s libiconv.2.dylib | grep -E "iconv"
Symbol table for: 'libiconv.2.dylib' (arm64)
[ 455] 0000207d 1e (PEXT SECT ) 01 0000 000000000001b170 '_libiconv_relocate'
[ 456] 00002090 1e (PEXT SECT ) 01 0000 000000000001b250 '_libiconv_relocate2'
[ 1322] 00000002 0f ( SECT EXT) 0a 0000 0000000000108020 '__libiconv_version'
[ 1323] 00000015 0f ( SECT EXT) 01 0000 00000000000051ac '_iconv_canonicalize'
[ 1324] 00000029 0f ( SECT EXT) 01 0000 00000000000049a4 '_libiconv'
[ 1325] 00000033 0f ( SECT EXT) 01 0000 00000000000049c8 '_libiconv_close'
[ 1326] 00000043 0f ( SECT EXT) 01 0000 0000000000003858 '_libiconv_open'
[ 1327] 00000052 0f ( SECT EXT) 01 0000 00000000000049e0 '_libiconv_open_into'
[ 1328] 00000066 0f ( SECT EXT) 01 0000 000000000001b0b0 '_libiconv_set_relocation_prefix'
[ 1329] 00000086 0f ( SECT EXT) 01 0000 0000000000004df8 '_libiconvctl'
[ 1330] 00000093 0f ( SECT EXT) 01 0000 0000000000004f2c '_libiconvlist'
while libxml2.2.dylib links to the OS version of libiconv, /usr/lib/libiconv.2.dylib, which defines symbols _iconv*:
% otool -L libxml2.2.dylib
libxml2.2.dylib:
/opt/homebrew/opt/libxml2/lib/libxml2.2.dylib (compatibility version 15.0.0, current version 15.6.0)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.12)
/opt/homebrew/opt/icu4c/lib/libicui18n.74.dylib (compatibility version 74.0.0, current version 74.2.0)
/opt/homebrew/opt/icu4c/lib/libicuuc.74.dylib (compatibility version 74.0.0, current version 74.2.0)
/opt/homebrew/opt/icu4c/lib/libicudata.74.dylib (compatibility version 74.0.0, current version 74.2.0)
/usr/lib/libiconv.2.dylib (compatibility version 7.0.0, current version 7.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1345.100.2)
% dsymutil -s libxml2.2.dylib | grep -E "iconv"
[ 2894] 0000884d 01 ( UNDF EXT) 00 0500 0000000000000000 '_iconv'
[ 2895] 00008854 01 ( UNDF EXT) 00 0500 0000000000000000 '_iconv_close'
[ 2896] 00008861 01 ( UNDF EXT) 00 0500 0000000000000000 '_iconv_open'
Can you try the corrected version on SF? https://sourceforge.net/projects/biblatex-biber/files/biblatex-biber/current/binaries/MacOS/biber-darwin_universal.tar.gz/download
This works:
% arch --arm64 biber --version
biber version: 2.20
I see that you've switched to using OS libraries all along:
% otool -L libiconv.2.dylib
libiconv.2.dylib:
/usr/lib/libiconv.2.dylib (compatibility version 7.0.0, current version 7.0.0)
/usr/lib/libcharset.1.dylib (compatibility version 1.0.0, current version 1.0.0, reexport)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1336.80.1)
% otool -L libxml2.2.dylib
libxml2.2.dylib:
/usr/lib/libxml2.2.dylib (compatibility version 10.0.0, current version 10.9.0)
/usr/lib/libicucore.A.dylib (compatibility version 1.0.0, current version 72.1.0)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.12)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1336.80.1)
The new libiconv defines all sorts of iconv symbols, the new libxml defines none.
Can you try the corrected version on SF? https://sourceforge.net/projects/biblatex-biber/files/biblatex-biber/current/binaries/MacOS/biber-darwin_universal.tar.gz/download
Works for me! (I first updated biber to the buggy version via TeX Live Utility, checked again that it did not work, and then replaced /usr/local/texlive/2024/bin/universal-darwin/biber with the extracted binary.)
Thanks a lot for addressing the issue so quickly!
Thanks for confirming. I will send an update to TL tonight. The issue was, as indicated above, lib mismatches. It was unfortunate I had switched to homebrew from macports as the latter has completely self-contained libraries but homebrew tends to use the system libraries a lot more. Also, since MacOS 11, the system libraries in /usr/lib are not physically present but are in a cache which dlopen() knows how to work with but PAR::Packer's linker doesn't and so I have to materialise the cache libs so they can be packed. Coupled with the fact that homebrew doesn't link system-conflicting libs into /opt/homebrew/lib and there was a perfect storm of technical irritations.
Also, since MacOS 11, the system libraries in
/usr/libare not physically present but are in a cache whichdlopen()knows how to work with butPAR::Packer's linker doesn't and so I have to materialise the cache libs so they can be packed.
Thanks for the lightning-fast fix.
I was curious to see how you implemented the above: call dyld-shared-cache-extractor, which builds upon /usr/lib/dsc_extractor.bundle to extract the libraries from their cache
/System/Volumes/Preboot/Cryptexes/OS/System/Library/dyld/dyld_shared_cache_arm64e to /tmp/libraries, then use the latter as in
--link=/tmp/libraries/usr/lib/libiconv.2.dylib \
--link=/tmp/libraries/usr/lib/libxml2.2.dylib \
Impressive!
It's a pain that Apple aren't really considering all the third-party ways of linking/including libs. If you need to access a file rather than use some cache-aware interface, you have to materialise the cache.
Has biber updated on CTAN? I didn’t noticed an update on CTAN. While I can download the latest version on SF, it would be convenient to update it via tlmgr on the server. Thanks for your work!
Has biber updated on CTAN? I didn’t noticed an update on CTAN. While I can download the latest version on SF, it would be convenient to update it via tlmgr on the server. Thanks for your work!
I have just updated biber.universal-darwin to version 70749 from CTAN (more specifically, from https://ftp.rrze.uni-erlangen.de/ctan/systems/texlive/tlnet/) via the TeX Live Utility, and everything is working again. Not all CTAN mirrors seem to have received the updated version yet.