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arb-project / homebrew-arb

Homebrew tap for formulae to build ARB (http://www.arb-home.de) and related software.
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Arb 7 line 94 problem, Mac OS 12.7.4 #31

Open bjmacgreg opened 6 months ago

bjmacgreg commented 6 months ago

Hi,

I am trying to install the production version of Arb, and have been around this circle several times:

bmacgreg@MacPro2 ~ % arb /opt/local/bin/arb: line 94: ARBHOME: unbound variable bmacgreg@MacPro2 ~ % brew unlink arb Unlinking /usr/local/Cellar/arb/7.1-beta_r19270... 1 symlinks removed. bmacgreg@MacPro2 ~ % brew link arb Linking /usr/local/Cellar/arb/7.1-beta_r19270... 1 symlinks created. bmacgreg@MacPro2 ~ % arb /opt/local/bin/arb: line 94: ARBHOME: unbound variable

I did have an older arb version installed, and suspect that could be the problem, but don't know how to fix it. Any suggestions?

Thanks,

Barbara

jgerken commented 6 months ago

Hi Barbara,

that's a very odd error which I have not seen before. I also have multiple ARB versions installed:

brew list --versions arb
arb HEAD-19493 7.1-beta_r19270

But I am already on macOS 14 and do not have access to a Mac with macOS 12 anymore. Was the old version of ARB also installed via Homebrew?

Could you run the following commands and post their output?

brew doctor
brew config
ls -l /opt/local/bin/arb

Maybe we can figure out what's different on your Mac and solve the issue from there.

rwestram commented 6 months ago

Is '/opt/local/bin/arb' ever created by homebrew? Or is that a relict from e.g. a previous MacPorts installation?

bjmacgreg commented 6 months ago

I'll do these one at a time, looks like the results may be long... It was a while ago that Arb was installed here, I'm sorry I don't remember which method I used. Much of what's on this computer was moved over from an older MacPro that was used by several people, so there could be some accumulated issues, although this is the first real problem I've had.

Last login: Tue May 7 08:45:43 on console bmacgreg@MacPro2 ~ % brew doctor Please note that these warnings are just used to help the Homebrew maintainers with debugging if you file an issue. If everything you use Homebrew for is working fine: please don't worry or file an issue; just ignore this. Thanks!

Warning: Some installed formulae are deprecated or disabled. You should find replacements for the following formulae: openssl@1.1 perl@5.18

Warning: Unbrewed dylibs were found in /usr/local/lib. If you didn't put them there on purpose they could cause problems when building Homebrew formulae, and may need to be deleted.

Unexpected dylibs: /usr/local/lib/libtcl8.6.dylib /usr/local/lib/libtk8.6.dylib

Warning: Unbrewed header files were found in /usr/local/include. If you didn't put them there on purpose they could cause problems when building Homebrew formulae, and may need to be deleted.

Unexpected header files: /usr/local/include/fakemysql.h /usr/local/include/fakepq.h /usr/local/include/fakesql.h /usr/local/include/itcl.h /usr/local/include/itcl2TclOO.h /usr/local/include/itclDecls.h /usr/local/include/itclInt.h /usr/local/include/itclIntDecls.h /usr/local/include/itclMigrate2TclCore.h /usr/local/include/itclTclIntStubsFcn.h /usr/local/include/mysqlStubs.h /usr/local/include/odbcStubs.h /usr/local/include/pandaseq-2/pandaseq-algorithm.h /usr/local/include/pandaseq-2/pandaseq-args.h /usr/local/include/pandaseq-2/pandaseq-assembler.h /usr/local/include/pandaseq-2/pandaseq-common.h /usr/local/include/pandaseq-2/pandaseq-iter.h /usr/local/include/pandaseq-2/pandaseq-linebuf.h /usr/local/include/pandaseq-2/pandaseq-log.h /usr/local/include/pandaseq-2/pandaseq-module.h /usr/local/include/pandaseq-2/pandaseq-mux.h /usr/local/include/pandaseq-2/pandaseq-nt.h /usr/local/include/pandaseq-2/pandaseq-plugin.h /usr/local/include/pandaseq-2/pandaseq-seqid.h /usr/local/include/pandaseq-2/pandaseq-set.h /usr/local/include/pandaseq-2/pandaseq-url.h /usr/local/include/pandaseq-2/pandaseq-writer.h /usr/local/include/pandaseq-2/pandaseq.h /usr/local/include/pqStubs.h /usr/local/include/tcl.h /usr/local/include/tclDecls.h /usr/local/include/tclOO.h /usr/local/include/tclOODecls.h /usr/local/include/tclPlatDecls.h /usr/local/include/tclThread.h /usr/local/include/tclTomMath.h /usr/local/include/tclTomMathDecls.h /usr/local/include/tdbc.h /usr/local/include/tdbcDecls.h /usr/local/include/tdbcInt.h /usr/local/include/tk.h /usr/local/include/tkDecls.h /usr/local/include/tkPlatDecls.h

Warning: Unbrewed '.la' files were found in /usr/local/lib. If you didn't put them there on purpose they could cause problems when building Homebrew formulae, and may need to be deleted.

Unexpected '.la' files: /usr/local/lib/libhmsbeagle-cpu-sse.la /usr/local/lib/libhmsbeagle-cpu.la /usr/local/lib/libhmsbeagle-cuda.la /usr/local/lib/libhmsbeagle-jni.la /usr/local/lib/libhmsbeagle.la /usr/local/lib/libpandaseq-url.la /usr/local/lib/libpandaseq.la

Warning: Unbrewed '.pc' files were found in /usr/local/lib/pkgconfig. If you didn't put them there on purpose they could cause problems when building Homebrew formulae, and may need to be deleted.

Unexpected '.pc' files: /usr/local/lib/pkgconfig/pandaseq-2-url.pc /usr/local/lib/pkgconfig/pandaseq-2.pc /usr/local/lib/pkgconfig/tcl.pc /usr/local/lib/pkgconfig/tk.pc

Warning: Unbrewed static libraries were found in /usr/local/lib. If you didn't put them there on purpose they could cause problems when building Homebrew formulae, and may need to be deleted.

Unexpected static libraries: /usr/local/lib/libpandaseq-url.a /usr/local/lib/libpandaseq.a /usr/local/lib/libtclstub8.6.a /usr/local/lib/libtkstub8.6.a

Warning: You have unlinked kegs in your Cellar. Leaving kegs unlinked can lead to build-trouble and cause formulae that depend on those kegs to fail to run properly once built. Run brew link on these: python@3.12 arb@7 python@3.9

Warning: Some installed formulae are not readable: denismm/gv/gv: Unsupported special dependency :x11 bmacgreg@MacPro2 ~ %

bjmacgreg commented 6 months ago

bmacgreg@MacPro2 ~ % brew config HOMEBREW_VERSION: 4.2.20 ORIGIN: https://github.com/Homebrew/brew HEAD: c2ed3327c605c3e738359c9807b8f4cd6fec09eb Last commit: 9 days ago Core tap JSON: 06 May 15:39 UTC Core cask tap JSON: 06 May 15:42 UTC HOMEBREW_PREFIX: /usr/local HOMEBREW_CASK_OPTS: [] HOMEBREW_DISPLAY: /private/tmp/com.apple.launchd.SUPvyxYELA/org.xquartz:0 HOMEBREW_MAKE_JOBS: 16 Homebrew Ruby: 3.1.4 => /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/3.1.4/bin/ruby CPU: 16-core 64-bit ivybridge Clang: 14.0.0 build 1400 Git: 2.37.1 => /Library/Developer/CommandLineTools/usr/bin/git Curl: 8.4.0 => /usr/bin/curl macOS: 12.7.4-x86_64 CLT: 14.2.0.0.1.1668646533 Xcode: 14.2

bjmacgreg commented 6 months ago

And also:

bmacgreg@MacPro2 ~ % ls -l /opt/local/bin/arb -rwxr-xr-x 1 root wheel 4685 Dec 17 2020 /opt/local/bin/arb

jgerken commented 6 months ago

Looks for me like the /opt/local/bin/arb file is a relict from a pre-Homebrew installation. Can you try to rename the file, e.g. 

sudo mv /opt/local/bin/arb /opt/local/bin/arb.old

The arb linked from Homebrew should be /usr/local/bin/arb which should be found after you renamed the old file.

bjmacgreg commented 6 months ago

Okay, that worked! Yay, no more screen sharing. Except one small remaining problem, similar to one with the old version. The first time I start Arb, it will open fine, but then freezes as soon as I open the sequence editor. If I quit out of Terminal and then restart, I can now edit without issues. I don't really care since it works in the end, but maybe eventually it won't? Below is the story of the two latest attempts. (There are also a lot more than 100 sequences in the database, but I guess that number is just a placeholder.)

Last login: Tue May 7 10:01:45 on ttys000 bmacgreg@MacPro2 ~ % sudo mv /opt/local/bin/arb /opt/local/bin/arb.old Password: bmacgreg@MacPro2 ~ % arb Using ARBHOME='/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome' Using properties from /Users/bmacgreg/.arb_prop Please wait while the program ARB is starting ..... Waiting for '/Users/bmacgreg/.arb_tmp/sockets/arb_launcher.11147'.. Tue May 7 11:05:25 CDT 2024 arb server.log created by arb_launcher [arb_launcher[0]: log for ARB_PID='11147'] [arb_launcher[0]: Starting 'arb_ntree'..] Using properties from '/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/lib/arb_default/ntree.arb' Using properties from '/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/lib/arb_default/status.arb' limited resource 3 to 20971520 (was: 8388608 of 67104768) [ Tue May 7 11:05:48 2024 - 0 sec ] start /Loading database [ Tue May 7 11:05:48 2024 - 0 sec ] end \Loading database ARB: Loading 'ntree.arb' ARB: Loading '/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/lib/arb_default/ntree.arb' done

ARB: ARB: Loading '/Users/bmacgreg/Documents/Actin_2023/Actin_2023_realignment.arb' ARB: ARB: no FastLoad File '/Users/bmacgreg/Documents/Actin_2023/Actin_2023_realignment.ARM' found => loading entire DB ARB: ARB: Loading '/Users/bmacgreg/Documents/Actin_2023/Actin_2023_realignment.arb' done

[Action: arb_macro_compatibility.sh &] [ Tue May 7 11:05:49 2024 - 0 sec ] start /Checking consistency [ Tue May 7 11:05:49 2024 - 0 sec ] Formatting alignments [ Tue May 7 11:05:49 2024 - 0 sec ] end \Checking consistency Progress: Loading database ARB: no FastLoad File '/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/demo.ARM' found => loading entire DB ...................................................................... [100.0%] used: 0s [done] Number of species in database: 100 [Action: arb_edit4 -c default_configuration &] Using properties from '/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/lib/arb_default/status.arb' Using properties from '/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/lib/arb_default/edit4.arb' /usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/bin/arb_sina.sh: line 29: sina: command not found Note: SINA (SILVA Aligner) disabled (Reason: Could not execute SINA binary 'arb_sina.sh' (exitstatus was 127)) [ Tue May 7 11:05:57 2024 - 0 sec ] start /EDIT4 startup [ Tue May 7 11:05:57 2024 - 0 sec ] Loading species [ Tue May 7 11:05:57 2024 - 0 sec ] end \EDIT4 startup

*(Quit out of terminal, then restarted)***** Last login: Tue May 7 11:05:06 on ttys000 bmacgreg@MacPro2 ~ % arb Using ARBHOME='/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome' Using properties from /Users/bmacgreg/.arb_prop Please wait while the program ARB is starting ..... Waiting for '/Users/bmacgreg/.arb_tmp/sockets/arb_launcher.11542'.. Tue May 7 11:07:59 CDT 2024 arb server.log created by arb_launcher [arb_launcher[0]: log for ARB_PID='11542'] [arb_launcher[0]: Starting 'arb_ntree'..] Using properties from '/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/lib/arb_default/ntree.arb' Using properties from '/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/lib/arb_default/status.arb' limited resource 3 to 20971520 (was: 8388608 of 67104768) [ Tue May 7 11:08:10 2024 - 0 sec ] start /Loading database [ Tue May 7 11:08:10 2024 - 0 sec ] end \Loading database ARB: Loading 'ntree.arb' ARB: Loading '/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/lib/arb_default/ntree.arb' done

ARB: ARB: Loading '/Users/bmacgreg/Documents/Actin_2023/Actin_2023_realignment.arb' ARB: ARB: no FastLoad File '/Users/bmacgreg/Documents/Actin_2023/Actin_2023_realignment.ARM' found => loading entire DB ARB: ARB: Loading '/Users/bmacgreg/Documents/Actin_2023/Actin_2023_realignment.arb' done

[Action: arb_macro_compatibility.sh &] Progress: Loading database ARB: no FastLoad File '/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/demo.ARM' found => loading entire DB ...................................................................... [100.0%] used: 0s [done] Number of species in database: 100 [ Tue May 7 11:08:10 2024 - 0 sec ] start /Checking consistency [ Tue May 7 11:08:11 2024 - 1 sec ] Formatting alignments [ Tue May 7 11:08:11 2024 - 0 sec ] end \Checking consistency [Action: arb_edit4 -c default_configuration &] Using properties from '/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/lib/arb_default/status.arb' Using properties from '/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/lib/arb_default/edit4.arb' /usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/bin/arb_sina.sh: line 29: sina: command not found Note: SINA (SILVA Aligner) disabled (Reason: Could not execute SINA binary 'arb_sina.sh' (exitstatus was 127)) [ Tue May 7 11:08:26 2024 - 0 sec ] start /EDIT4 startup [ Tue May 7 11:08:27 2024 - 1 sec ] Loading species [ Tue May 7 11:08:27 2024 - 0 sec ] end \EDIT4 startup

jgerken commented 6 months ago

That's a known issue but we don't know why it freezes on first use. Alternatively, you can use one of these two workarounds to not have to start ARB twice.

bjmacgreg commented 6 months ago

Okay, thanks. Looking forward to see what's in this new version.

bjmacgreg commented 6 months ago

Hi,

In case it's any help - here's what I have to do to start Arb, quitting out of Terminal twice until it works the third time. Like I said I can live with it, this is just in case there are any useful clues. The freeze the second time through comes when I try to edit a sequence, not sure if other actions might do the same (not motivated enough to test them all).

Barbara

Last login: Tue May 14 08:26:53 on console bmacgreg@MacPro2 ~ % arb Using ARBHOME='/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome' Using properties from /Users/bmacgreg/.arb_prop Please wait while the program ARB is starting ..... Waiting for '/Users/bmacgreg/.arb_tmp/sockets/arb_launcher.1439'.. Tue May 14 09:25:54 CDT 2024 arb server.log created by arb_launcher [arb_launcher[0]: log for ARB_PID='1439'] [arb_launcher[0]: Starting 'arb_ntree'..] Using properties from '/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/lib/arb_default/ntree.arb' Using properties from '/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/lib/arb_default/status.arb' limited resource 3 to 20971520 (was: 8388608 of 67104768)

Last login: Tue May 14 09:25:48 on ttys000 bmacgreg@MacPro2 ~ % arb Using ARBHOME='/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome' Using properties from /Users/bmacgreg/.arb_prop Please wait while the program ARB is starting ..... Waiting for '/Users/bmacgreg/.arb_tmp/sockets/arb_launcher.1780'.. Tue May 14 09:27:01 CDT 2024 arb server.log created by arb_launcher [arb_launcher[0]: log for ARB_PID='1780'] [arb_launcher[0]: Starting 'arb_ntree'..] Using properties from '/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/lib/arb_default/ntree.arb' Using properties from '/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/lib/arb_default/status.arb' limited resource 3 to 20971520 (was: 8388608 of 67104768) [ Tue May 14 09:27:12 2024 - 0 sec ] start /Loading database [ Tue May 14 09:27:12 2024 - 0 sec ] end \Loading database ARB: Loading 'ntree.arb' ARB: Loading '/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/lib/arb_default/ntree.arb' done

ARB: ARB: Loading '/Users/bmacgreg/Documents/Actin_2024_from_other_computer/Actin_2023_realignment.arb' ARB: ARB: no FastLoad File '/Users/bmacgreg/Documents/Actin_2024_from_other_computer/Actin_2023_realignment.ARM' found => loading entire DB ARB: ARB: Loading '/Users/bmacgreg/Documents/Actin_2024_from_other_computer/Actin_2023_realignment.arb' done

[Action: arb_macro_compatibility.sh &] Progress: Loading database ARB: no FastLoad File '/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/demo.ARM' found => loading entire DB ...................................................................... [100.0%] used: 0s [done] Number of species in database: 100 [ Tue May 14 09:27:12 2024 - 0 sec ] start /Checking consistency [ Tue May 14 09:27:12 2024 - 0 sec ] Formatting alignments [ Tue May 14 09:27:12 2024 - 0 sec ] end \Checking consistency [Action: arb_edit4 -c default_configuration &] Using properties from '/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/lib/arb_default/status.arb' Using properties from '/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/lib/arb_default/edit4.arb' /usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/bin/arb_sina.sh: line 29: sina: command not found Note: SINA (SILVA Aligner) disabled (Reason: Could not execute SINA binary 'arb_sina.sh' (exitstatus was 127)) [ Tue May 14 09:27:20 2024 - 0 sec ] start /EDIT4 startup [ Tue May 14 09:27:20 2024 - 0 sec ] Loading species [ Tue May 14 09:27:20 2024 - 0 sec ] end \EDIT4 startup

Last login: Tue May 14 09:26:57 on ttys000 bmacgreg@MacPro2 ~ % arb Using ARBHOME='/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome' Using properties from /Users/bmacgreg/.arb_prop Please wait while the program ARB is starting ..... Waiting for '/Users/bmacgreg/.arb_tmp/sockets/arb_launcher.1909'.. Tue May 14 09:28:22 CDT 2024 arb server.log created by arb_launcher [arb_launcher[0]: log for ARB_PID='1909'] [arb_launcher[0]: Starting 'arb_ntree'..] Using properties from '/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/lib/arb_default/ntree.arb' Using properties from '/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/lib/arb_default/status.arb' limited resource 3 to 20971520 (was: 8388608 of 67104768) [ Tue May 14 09:28:31 2024 - 0 sec ] start /Loading database [ Tue May 14 09:28:32 2024 - 0 sec ] end \Loading database ARB: Loading 'ntree.arb' ARB: Loading '/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/lib/arb_default/ntree.arb' done

ARB: ARB: Loading '/Users/bmacgreg/Documents/Actin_2024_from_other_computer/Actin_2023_realignment.arb' ARB: ARB: no FastLoad File '/Users/bmacgreg/Documents/Actin_2024_from_other_computer/Actin_2023_realignment.ARM' found => loading entire DB ARB: ARB: Loading '/Users/bmacgreg/Documents/Actin_2024_from_other_computer/Actin_2023_realignment.arb' done

[Action: arb_macro_compatibility.sh &] Progress: Loading database ARB: no FastLoad File '/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/demo.ARM' found => loading entire DB ...................................................................... [100.0%] used: 0s [done] Number of species in database: 100 [ Tue May 14 09:28:32 2024 - 0 sec ] start /Checking consistency [ Tue May 14 09:28:32 2024 - 0 sec ] Formatting alignments [ Tue May 14 09:28:32 2024 - 0 sec ] end \Checking consistency [Action: arb_edit4 -c default_configuration &] Using properties from '/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/lib/arb_default/status.arb' Using properties from '/usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/lib/arb_default/edit4.arb' /usr/local/Cellar/arb/7.1-beta_r19270/ArbHome/bin/arb_sina.sh: line 29: sina: command not found Note: SINA (SILVA Aligner) disabled (Reason: Could not execute SINA binary 'arb_sina.sh' (exitstatus was 127)) [ Tue May 14 09:28:37 2024 - 0 sec ] start /EDIT4 startup [ Tue May 14 09:28:37 2024 - 0 sec ] Loading species [ Tue May 14 09:28:37 2024 - 0 sec ] end \EDIT4 startup