ARB Error when installing on MacOS 15.3.1

[elikbehar]

Hello all,

I've been attempting to download ARB on my Mac using the latest update (Sequoia 15.3.1) with an M2 chip, using Homebrew. I was following the instructions on the ARB website, and ran across this error message:

Warning: Calling gsub!(before, after, false) is deprecated! Use gsub!(before, after, audit_result: false) instead.

Also:

make[1]: *** [all] Error 2
---------------------------------------- [excerpt of obvious errors below; full log in build.log]
mkptypes.cxx;17;10; fatal error; 'cstddef' file not found
clang++; error; no such file or directory; 'mkptypes.o'
/private/tmp/arb-20250223-13162-ntjvjo/INCLUDE/arbtools.h;19;10; fatal error; 'new' file not found
./arb_core.h;16;10; fatal error; 'cstdio' file not found
./BufferedFileReader.h;18;10; fatal error; 'cstdio' file not found
./BufferedFileReader.h;18;10; fatal error; 'cstdio' file not found
./arb_core.h;16;10; fatal error; 'cstdio' file not found
./arb_diff.h;17;10; fatal error; 'cstdlib' file not found
./arb_core.h;16;10; fatal error; 'cstdio' file not found
./arb_core.h;16;10; fatal error; 'cstdio' file not found
./arb_mem.h;16;10; fatal error; 'cstdlib' file not found
./arb_core.h;16;10; fatal error; 'cstdio' file not found
make: *** [ALL] Error 1

Does anyone know why this is, and how to fix it? Thank you so much!

[jgerken]

Sorry, for the late response. I have fixed the warnings now.

Please install the latest development version. Currently, the latest production version is not compatible to recent macOS versions.

brew install --HEAD arb-project/arb/arb

I installed this version on an M3 MacBook running Sequoia 15.3.2, so I don't expect any problems with your setup.

[elikbehar]

Thank you for responding. I tried using the installation command provided by you, and am now receiving this message:

make[1]: *** [all] Error 2
---------------------------------------- [excerpt of obvious errors below; full log in build.log]
mkptypes.cxx;17;10; fatal error; 'cstddef' file not found
clang++; error; no such file or directory; 'mkptypes.o'
./arb_core.h;16;10; fatal error; 'cstdio' file not found
/private/tmp/arb-20250409-55511-xdlkux/INCLUDE/arbtools.h;19;10; fatal error; 'new' file not found
./BufferedFileReader.h;18;10; fatal error; 'cstdio' file not found
./BufferedFileReader.h;18;10; fatal error; 'cstdio' file not found
./arb_core.h;16;10; fatal error; 'cstdio' file not found
./arb_diff.h;17;10; fatal error; 'cstdlib' file not found
./arb_core.h;16;10; fatal error; 'cstdio' file not found
./arb_core.h;16;10; fatal error; 'cstdio' file not found
./arb_mem.h;16;10; fatal error; 'cstdlib' file not found
./arb_core.h;16;10; fatal error; 'cstdio' file not found
make: *** [ALL] Error 1

What is going on here, and how can I fix it? Thanks again!

[jgerken]

I now get an error when building ARB on macOS 15.5. But it seems to be a different one from yours. Can you please attach the following file to the ticket: ~/Library/Logs/Homebrew/arb/01.make

[callabush]

Hi! I am getting the same error when I try to build/brew ARB on macOS 15.5.

[jgerken]

That's a very weird error indicating an issue with the C/C++ compiler. At some point the C++ version was set incorrectly maybe that caused the issue. Can you please try again if the error persists?

[labrat789]

Hi, I'm running OSX 15.7.3 on an intel macbook pro, and have been trying to reinstall ARB after something blew up my previous installation (happened after I installed hhsuite). Tried to start with a fresh install after removing suspected offending builds, I now get the same error as above with or without the '--HEAD' flag. Any new developments here? I've uploaded the log file if that helps.

Thanks!

01.make.log

UPDATE: When I tried just using 'brew install arb@7', I get this error:

jones@Mykopat002178 ~ % brew install arb@7
==> Fetching downloads for: arb@7
✔︎ Formula arb@7 (7.0.1) Verified 25.8MB/ 25.8MB
==> Installing arb@7 from arb-project/arb
==> Patching
==> make all ARB_64=1 OPENGL=1 MACH=DARWIN DARWIN=1 LINUX=0 DEBIAN=0 REDHAT=0 DEBUG=0 TRACESYM=1
Last 15 lines from /Users/jones/Library/Logs/Homebrew/arb@7/01.make.log:
BASE='dnaml' PREFIX='HELP_GEN'
BASE='clustalw' PREFIX='HELP_GEN'
./genhelp.sh HELP_GEN/phylip.help "phylip" arb_help.head HELP_DOC_GEN/phylip.doc
./genhelp.sh HELP_GEN/phyml.help "phyml" arb_help.head HELP_DOC_GEN/phyml.doc
./genhelp.sh HELP_GEN/proml.help "proml" arb_help.head HELP_DOC_GEN/proml.doc
./genhelp.sh HELP_GEN/protpars.help "protpars" arb_help.head HELP_DOC_GEN/protpars.doc
./genhelptree.sh HELP_GEN/readseq.help "readseq" arb_help.head ../READSEQ/Readme ../READSEQ/Formats ../READSEQ/Readseq.help
./genhelptree.sh HELP_GEN/phylip_distance.help "phylip_distance" arb_help.head ./HELP_DOC_GEN/fitch.doc ./HELP_DOC_GEN/kitsch.doc ./HELP_DOC_GEN/neighbor.doc ./HELP_DOC_GEN/dnadist.doc ./HELP_DOC_GEN/protdist.doc
(echo " [ generated from ../../GDE/TREEPUZZLE/doc/manual.html ]"; echo ""; lynx -dump -nolist -display_charset=iso-8859-1 ../GDE/TREEPUZZLE/doc/manual.html) | /private/tmp/arbA7-20260213-56622-1klhlq/arbsrc_18910/SH/arb_sed -e 's/?/(C)/' -e 's/^\s\s*__*$//' > HELP_DOC_GEN/treepuzzle.doc
BASE='readseq' PREFIX='HELP_GEN'
BASE='phylip_distance' PREFIX='HELP_GEN'
./genhelp.sh HELP_GEN/treepuzzle.help "treepuzzle" arb_help.head HELP_DOC_GEN/treepuzzle.doc
[33:13.953032000] ------------------------------------------------ Make GDEHELP [done]
make[1]: *** [arb] Error 2
make: *** [all] Error 2

If reporting this issue please do so at (not Homebrew/* repositories):
https://github.com/arb-project/homebrew-arb/issues