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arb-project / homebrew-arb

Homebrew tap for formulae to build ARB (http://www.arb-home.de) and related software.
MIT License
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make[1]: *** [arb] Error 2, error when installing ARB on MacOS 15.0.1 #33

Open CyrielleDeb opened 2 days ago

CyrielleDeb commented 2 days ago

Hello,

I have been trying to install ARB on a MacOS Sequoia 15.0.1. After updating the Command Line Tools and Xcode, it finally seemed to be installing ARB, then I got this strange issue :

==> 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/clairedastorg/Library/Logs/Homebrew/arb@7/01.make: clang++ -O3 -arch x86_64 -Wno-error=implicit-function-declaration -pipe -fmessage-length=0 -fshow-column -funit-at-a-time -fPIC -fno-common -fstrict-aliasing -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DDARWIN -Wwrite-strings -Wunused -Wno-aggregate-return -DIN_ARB_EDIT4 -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute -Wctor-dtor-privacy -Wmissing-noreturn -Winit-self -Wstrict-aliasing -Wextra -Weffc++ -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int -Wno-gnu-static-float-init -c -o ED4_root.o ED4_root.cxx -I. -I/private/tmp/arbA7-20241022-54506-yh9dov/arbsrc_18910/INCLUDE -I/include -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/usr/local/Cellar/pcre2/10.44/include -I/usr/local/Cellar/glib/2.82.2/include/glib-2.0 -I/usr/local/Cellar/glib/2.82.2/lib/glib-2.0/include -I/usr/local/opt/gettext/include 2>&1 | /private/tmp/arbA7-20241022-54506-yh9dov/arbsrc_18910/SOURCE_TOOLS/postcompile.pl --compiler=16.0.0 ED4_root.cxx clang++ -O3 -arch x86_64 -Wno-error=implicit-function-declaration -pipe -fmessage-length=0 -fshow-column -funit-at-a-time -fPIC -fno-common -fstrict-aliasing -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DDARWIN -Wwrite-strings -Wunused -Wno-aggregate-return -DIN_ARB_EDIT4 -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute -Wctor-dtor-privacy -Wmissing-noreturn -Winit-self -Wstrict-aliasing -Wextra -Weffc++ -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int -Wno-gnu-static-float-init -c -o ED4_search.o ED4_search.cxx -I. -I/private/tmp/arbA7-20241022-54506-yh9dov/arbsrc_18910/INCLUDE -I/include -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/usr/local/Cellar/pcre2/10.44/include -I/usr/local/Cellar/glib/2.82.2/include/glib-2.0 -I/usr/local/Cellar/glib/2.82.2/lib/glib-2.0/include -I/usr/local/opt/gettext/include 2>&1 | /private/tmp/arbA7-20241022-54506-yh9dov/arbsrc_18910/SOURCE_TOOLS/postcompile.pl --compiler=16.0.0 ED4_search.cxx clang++ -O3 -arch x86_64 -Wno-error=implicit-function-declaration -pipe -fmessage-length=0 -fshow-column -funit-at-a-time -fPIC -fno-common -fstrict-aliasing -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DDARWIN -Wwrite-strings -Wunused -Wno-aggregate-return -DIN_ARB_EDIT4 -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute -Wctor-dtor-privacy -Wmissing-noreturn -Winit-self -Wstrict-aliasing -Wextra -Weffc++ -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int -Wno-gnu-static-float-init -c -o ED4_seq_colors.o ED4_seq_colors.cxx -I. -I/private/tmp/arbA7-20241022-54506-yh9dov/arbsrc_18910/INCLUDE -I/include -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/usr/local/Cellar/pcre2/10.44/include -I/usr/local/Cellar/glib/2.82.2/include/glib-2.0 -I/usr/local/Cellar/glib/2.82.2/lib/glib-2.0/include -I/usr/local/opt/gettext/include 2>&1 | /private/tmp/arbA7-20241022-54506-yh9dov/arbsrc_18910/SOURCE_TOOLS/postcompile.pl --compiler=16.0.0 ED4_seq_colors.cxx clang++ -O3 -arch x86_64 -Wno-error=implicit-function-declaration -pipe -fmessage-length=0 -fshow-column -funit-at-a-time -fPIC -fno-common -fstrict-aliasing -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DDARWIN -Wwrite-strings -Wunused -Wno-aggregate-return -DIN_ARB_EDIT4 -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute -Wctor-dtor-privacy -Wmissing-noreturn -Winit-self -Wstrict-aliasing -Wextra -Weffc++ -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int -Wno-gnu-static-float-init -c -o ED4_terminal.o ED4_terminal.cxx -I. -I/private/tmp/arbA7-20241022-54506-yh9dov/arbsrc_18910/INCLUDE -I/include -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/usr/local/Cellar/pcre2/10.44/include -I/usr/local/Cellar/glib/2.82.2/include/glib-2.0 -I/usr/local/Cellar/glib/2.82.2/lib/glib-2.0/include -I/usr/local/opt/gettext/include 2>&1 | /private/tmp/arbA7-20241022-54506-yh9dov/arbsrc_18910/SOURCE_TOOLS/postcompile.pl --compiler=16.0.0 ED4_terminal.cxx clang++ -O3 -arch x86_64 -Wno-error=implicit-function-declaration -pipe -fmessage-length=0 -fshow-column -funit-at-a-time -fPIC -fno-common -fstrict-aliasing -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DDARWIN -Wwrite-strings -Wunused -Wno-aggregate-return -DIN_ARB_EDIT4 -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute -Wctor-dtor-privacy -Wmissing-noreturn -Winit-self -Wstrict-aliasing -Wextra -Weffc++ -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int -Wno-gnu-static-float-init -c -o ED4_text_terminals.o ED4_text_terminals.cxx -I. -I/private/tmp/arbA7-20241022-54506-yh9dov/arbsrc_18910/INCLUDE -I/include -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/usr/local/Cellar/pcre2/10.44/include -I/usr/local/Cellar/glib/2.82.2/include/glib-2.0 -I/usr/local/Cellar/glib/2.82.2/lib/glib-2.0/include -I/usr/local/opt/gettext/include 2>&1 | /private/tmp/arbA7-20241022-54506-yh9dov/arbsrc_18910/SOURCE_TOOLS/postcompile.pl --compiler=16.0.0 ED4_text_terminals.cxx clang++ -O3 -arch x86_64 -Wno-error=implicit-function-declaration -pipe -fmessage-length=0 -fshow-column -funit-at-a-time -fPIC -fno-common -fstrict-aliasing -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DDARWIN -Wwrite-strings -Wunused -Wno-aggregate-return -DIN_ARB_EDIT4 -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute -Wctor-dtor-privacy -Wmissing-noreturn -Winit-self -Wstrict-aliasing -Wextra -Weffc++ -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int -Wno-gnu-static-float-init -c -o ED4_tools.o ED4_tools.cxx -I. -I/private/tmp/arbA7-20241022-54506-yh9dov/arbsrc_18910/INCLUDE -I/include -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/usr/local/Cellar/pcre2/10.44/include -I/usr/local/Cellar/glib/2.82.2/include/glib-2.0 -I/usr/local/Cellar/glib/2.82.2/lib/glib-2.0/include -I/usr/local/opt/gettext/include 2>&1 | /private/tmp/arbA7-20241022-54506-yh9dov/arbsrc_18910/SOURCE_TOOLS/postcompile.pl --compiler=16.0.0 ED4_tools.cxx clang++ -O3 -arch x86_64 -Wno-error=implicit-function-declaration -pipe -fmessage-length=0 -fshow-column -funit-at-a-time -fPIC -fno-common -fstrict-aliasing -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DDARWIN -Wwrite-strings -Wunused -Wno-aggregate-return -DIN_ARB_EDIT4 -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute -Wctor-dtor-privacy -Wmissing-noreturn -Winit-self -Wstrict-aliasing -Wextra -Weffc++ -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int -Wno-gnu-static-float-init -c -o ED4_visualizeSAI.o ED4_visualizeSAI.cxx -I. -I/private/tmp/arbA7-20241022-54506-yh9dov/arbsrc_18910/INCLUDE -I/include -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/usr/local/Cellar/pcre2/10.44/include -I/usr/local/Cellar/glib/2.82.2/include/glib-2.0 -I/usr/local/Cellar/glib/2.82.2/lib/glib-2.0/include -I/usr/local/opt/gettext/include 2>&1 | /private/tmp/arbA7-20241022-54506-yh9dov/arbsrc_18910/SOURCE_TOOLS/postcompile.pl --compiler=16.0.0 ED4_visualizeSAI.cxx clang++ -O3 -arch x86_64 -Wno-error=implicit-function-declaration -pipe -fmessage-length=0 -fshow-column -funit-at-a-time -fPIC -fno-common -fstrict-aliasing -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DDARWIN -Wwrite-strings -Wunused -Wno-aggregate-return -DIN_ARB_EDIT4 -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute -Wctor-dtor-privacy -Wmissing-noreturn -Winit-self -Wstrict-aliasing -Wextra -Weffc++ -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int -Wno-gnu-static-float-init -c -o ED4_window.o ED4_window.cxx -I. -I/private/tmp/arbA7-20241022-54506-yh9dov/arbsrc_18910/INCLUDE -I/include -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/usr/local/Cellar/pcre2/10.44/include -I/usr/local/Cellar/glib/2.82.2/include/glib-2.0 -I/usr/local/Cellar/glib/2.82.2/lib/glib-2.0/include -I/usr/local/opt/gettext/include 2>&1 | /private/tmp/arbA7-20241022-54506-yh9dov/arbsrc_18910/SOURCE_TOOLS/postcompile.pl --compiler=16.0.0 ED4_window.cxx clang++ -O3 -arch x86_64 -Wno-error=implicit-function-declaration -pipe -fmessage-length=0 -fshow-column -funit-at-a-time -fPIC -fno-common -fstrict-aliasing -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DDARWIN -Wwrite-strings -Wunused -Wno-aggregate-return -DIN_ARB_EDIT4 -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute -Wctor-dtor-privacy -Wmissing-noreturn -Winit-self -Wstrict-aliasing -Wextra -Weffc++ -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int -Wno-gnu-static-float-init -c -o EDB_root_bact.o EDB_root_bact.cxx -I. -I/private/tmp/arbA7-20241022-54506-yh9dov/arbsrc_18910/INCLUDE -I/include -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/usr/local/Cellar/pcre2/10.44/include -I/usr/local/Cellar/glib/2.82.2/include/glib-2.0 -I/usr/local/Cellar/glib/2.82.2/lib/glib-2.0/include -I/usr/local/opt/gettext/include 2>&1 | /private/tmp/arbA7-20241022-54506-yh9dov/arbsrc_18910/SOURCE_TOOLS/postcompile.pl --compiler=16.0.0 EDB_root_bact.cxx clang++ -O3 -arch x86_64 -Wno-error=implicit-function-declaration -pipe -fmessage-length=0 -fshow-column -funit-at-a-time -fPIC -fno-common -fstrict-aliasing -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DDARWIN -Wwrite-strings -Wunused -Wno-aggregate-return -DIN_ARB_EDIT4 -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute -Wctor-dtor-privacy -Wmissing-noreturn -Winit-self -Wstrict-aliasing -Wextra -Weffc++ -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int -Wno-gnu-static-float-init -c -o graph_aligner_gui.o graph_aligner_gui.cxx -I. -I/private/tmp/arbA7-20241022-54506-yh9dov/arbsrc_18910/INCLUDE -I/include -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/OpenGL.framework/Headers -I/usr/include/krb5 -I/usr/local/Cellar/pcre2/10.44/include -I/usr/local/Cellar/glib/2.82.2/include/glib-2.0 -I/usr/local/Cellar/glib/2.82.2/lib/glib-2.0/include -I/usr/local/opt/gettext/include 2>&1 | /private/tmp/arbA7-20241022-54506-yh9dov/arbsrc_18910/SOURCE_TOOLS/postcompile.pl --compiler=16.0.0 graph_aligner_gui.cxx ar -csq EDIT4.a ED4_ProteinViewer.o ED4_base.o ED4_block.o ED4_colStat.o ED4_consensus.o ED4_container.o ED4_cursor.o ED4_dots.o ED4_dump.o ED4_edit_string.o ED4_flags.o ED4_main.o ED4_manager.o ED4_naligner.o ED4_nds.o ED4_no_class.o ED4_objspec.o ED4_plugins.o ED4_protein_2nd_structure.o ED4_root.o ED4_search.o ED4_seq_colors.o ED4_terminal.o ED4_text_terminals.o ED4_tools.o ED4_visualizeSAI.o ED4_window.o EDB_root_bact.o graph_aligner_gui.o /Library/Developer/CommandLineTools/usr/bin/ranlib: file: EDIT4.a(ED4_dump.o) has no symbols [35:24.N] ------------------------------------------------ Make EDIT4 [done] make[1]: [arb] Error 2 make: [all] Error 2

Could you please help me solving it ?

Thanks in advance :)

jgerken commented 1 day ago

Did you try to install the HEAD version of ARB?

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

There is an issue with the latest release that it can't be build with Homebrew which is fixed in the latest development version of ARB. Can you give it try, please?

CyrielleDeb commented 1 day ago

Hello ! I will give it a try today and come back to you as soon as it's done :)

CyrielleDeb commented 1 day ago

Hi !

This warning popped up when I tried "brew install --HEAD arb-project/arb/arb" , during the Patching process :

Warning: Calling gsub!(before, after, false) is deprecated! Use gsub!(before, after, audit_result: false) instead. Please report this issue to the arb-project/homebrew-arb tap (not Homebrew/brew or Homebrew/homebrew-core), or even better, submit a PR to fix it: /usr/local/Homebrew/Library/Taps/arb-project/homebrew-arb/Formula/arb.rb:110

Followed by this :

==> make ALL ARB_64=1 OPENGL=1 MACH=DARWIN DARWIN=1 LINUX=0 DEBIAN=0 REDHAT=0 DEBUG=0 TRACESYM=1

It doesn't seem to be compiling ever since.

jgerken commented 1 day ago

The warning you can ignore. At the moment it still works. The make call afterwards is normal. That's actually building ARB.

CyrielleDeb commented 1 day ago

It seemed to have successfully installed ARB, but when I tried to launch it this happened :

clairedastorg@MacBookAir ~ % arb Using ARBHOME='/usr/local/Cellar/arb/HEAD-19499/ArbHome' Using properties from /Users/clairedastorg/.arb_prop Directory /Users/clairedastorg/.arb_prop not found - creating ... Directory /Users/clairedastorg/.arb_pts not found - creating ... Directory /Users/clairedastorg/.arb_prop/macros not found - creating ... Please wait while the program ARB is starting ..... Waiting for '/Users/clairedastorg/.arb_tmp/sockets/arb_launcher.82549'.. Mer 23 oct 2024 14:04:45 CEST arb server.log created by arb_launcher [arb_launcher[0]: log for ARB_PID='82549'] [arb_launcher[0]: Starting 'arb_ntree'..] Using properties from '/usr/local/Cellar/arb/HEAD-19499/ArbHome/lib/arb_default/ntree.arb' Using properties from '/usr/local/Cellar/arb/HEAD-19499/ArbHome/lib/arb_default/status.arb' Error: Can't open display: :0 Error: Can't open display: :0 ARB: Loading 'ntree.arb' ARB: Loading '/usr/local/Cellar/arb/HEAD-19499/ArbHome/lib/arb_default/ntree.arb' done

[arb_launcher[0]: 'arb_ntree' has terminated with error 1] [arb_launcher[0]: All launched processes terminated] [arb_launcher[0]: cleaning up arb session] PID TTY TIME CMD rmdir: /Users/clairedastorg/.arb_prop/logs/20241023_140445.82574: Directory not empty

Session log has been stored in /Users/clairedastorg/.arb_prop/logs/session.20241023_140445.82574.tgz and is also accessible via /Users/clairedastorg/ARB_last_session.tgz

ARB terminated abnormally [Mer 23 oct 2024 14:04:52 CEST] [press ENTER or wait 3 days]

jgerken commented 1 day ago

Did you also install Xquartz?

brew install --cask xquartz

The error message is related to connection issue to the X server which is provided by XQuartz under macOS. If it is already installed, you can try the following: