Macaulay2 / homebrew-tap

The Macaulay2 tap for Homebrew
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Error with 'cannot find -lbacktrace' #176

Closed Siwon-S-Kim closed 1 year ago

Siwon-S-Kim commented 1 year ago

Hello

Kernel: Linux 5.4.0-42-generic x86_64 GNU/Linux OS: Ubuntu 20.04.1 LTS (focal)

I was trying to install M2 without sudo command, with homebrew, and faced this problem. I am installing M2 to my account in server with ssh, so I hope this might not be problem with root access. I installed homebrew without root access on folder 'myid42/M' inside my user folder 'myid42', following "Alternative installs". (I don't remember exactly why but I think error I got from standard method suggested me to do so) And I must say that I am not familiar with Ubuntu nor Linux but trying my best without properly studying the basics. So let me know if I am missing any information.

(on ~/M/)

mkdir homebrew && curl -L https://github.com/Homebrew/brew/tarball/master | tar xz --strip 1 -C homebrew
eval "$(homebrew/bin/brew shellenv)"
brew update --force --quiet
chmod -R go-w "$(brew --prefix)/share/zsh"

Then I got this problem with latest message "cannot find -lbacktrace"

(base) myid42@lk4:~/M$ brew install M2
==> Fetching dependencies for macaulay2/tap/macaulay2: automake, libtool, and topcom
==> Fetching automake
==> Downloading https://ghcr.io/v2/homebrew/core/automake/manifests/1.16.5
Already downloaded: /home/myid42/.cache/Homebrew/downloads/6863d3ffa73c5a5cbf1f1ea9e47b60784d09b232ac9e56149c1b931d9ec44d8b--automake-1.16.5.bottle_manifest.json
==> Downloading https://ghcr.io/v2/homebrew/core/automake/blobs/sha256:59808c20f7dc565f106b432941b43c52f3d7f46a8d562ab27a4aabd424783158
Already downloaded: /home/myid42/.cache/Homebrew/downloads/0636fd23d95938f0a6e5eb2b50a90af1d0dd25f60cd244d5fec8311308396045--automake--1.16.5.x86_64_linux.bottle.tar.gz
==> Fetching libtool
==> Downloading https://ghcr.io/v2/homebrew/core/libtool/manifests/2.4.7
Already downloaded: /home/myid42/.cache/Homebrew/downloads/583066a50f4afbd11e5d6bd1d66fe9c16c2770a6d8a9f1b1dc5be930fa7194c5--libtool-2.4.7.bottle_manifest.json
==> Downloading https://ghcr.io/v2/homebrew/core/libtool/blobs/sha256:1cde2899a36adf5b04d25a9b8b4d6bec8a3099bc59ae68c63e479a4da8ca70b3
Already downloaded: /home/myid42/.cache/Homebrew/downloads/d3dad839b407eb637916b2f26564dd9981bd4b486203d16402e30735923916ce--libtool--2.4.7.x86_64_linux.bottle.tar.gz
==> Fetching macaulay2/tap/topcom
Warning: Building macaulay2/tap/topcom from source as the bottle needs:
- HOMEBREW_CELLAR: /home/linuxbrew/.linuxbrew/Cellar (yours is /home/myid42/M/homebrew/Cellar)
- HOMEBREW_PREFIX: /home/linuxbrew/.linuxbrew (yours is /home/myid42/M/homebrew)
==> Downloading https://www.wm.uni-bayreuth.de/de/team/rambau_joerg/TOPCOM-Downloads/TOPCOM-1_1_2.tgz
Already downloaded: /home/myid42/.cache/Homebrew/downloads/5431f89f15b97e2080075b0954b9e95c12a8bcce2721d0823a5f8f68c2da3cdc--TOPCOM-1_1_2.tgz
==> Fetching macaulay2/tap/macaulay2
Warning: Building macaulay2/tap/macaulay2 from source as the bottle needs:
- HOMEBREW_CELLAR: /home/linuxbrew/.linuxbrew/Cellar (yours is /home/myid42/M/homebrew/Cellar)
- HOMEBREW_PREFIX: /home/linuxbrew/.linuxbrew (yours is /home/myid42/M/homebrew)
==> Downloading https://github.com/Macaulay2/M2/commit/c4bf16f3278118ff1b6fdf20d4ad68441f4b26c5.patch?full_index=1
Already downloaded: /home/myid42/.cache/Homebrew/downloads/ac963ad48c0661b05ac4a1f73dd8e6849b57769bffc050d958df262ef5ff1ed2--c4bf16f3278118ff1b6fdf20d4ad68441f4b26c5.patch
==> Downloading https://github.com/Macaulay2/M2/archive/refs/tags/release-1.21.tar.gz
Already downloaded: /home/myid42/.cache/Homebrew/downloads/b03ad43a23f645eabed8b116df2ac468d83d4aaa15520e71a73159c95c0c5156--M2-release-1.21.tar.gz
==> Installing macaulay2 from macaulay2/tap
==> Installing dependencies for macaulay2/tap/macaulay2: automake, libtool, and topcom
==> Installing macaulay2/tap/macaulay2 dependency: automake
==> Pouring automake--1.16.5.x86_64_linux.bottle.tar.gz
??  /home/myid42/M/homebrew/Cellar/automake/1.16.5: 131 files, 3.5MB
==> Installing macaulay2/tap/macaulay2 dependency: libtool
==> Pouring libtool--2.4.7.x86_64_linux.bottle.tar.gz
??  /home/myid42/M/homebrew/Cellar/libtool/2.4.7: 74 files, 3.8MB
==> Installing macaulay2/tap/macaulay2 dependency: topcom
==> autoreconf -vif
==> ./configure --prefix=/home/myid42/M/homebrew/Cellar/topcom/1.1.2_5 CPPFLAGS=-I/home/myid42/M/homebrew/opt/gmp/include -I/home/myid42/M/homebrew/opt/cddlib/include/cddlib
==> make install
??  /home/myid42/M/homebrew/Cellar/topcom/1.1.2_5: 151 files, 62.8MB, built in 1 minute 31 seconds
==> Installing macaulay2/tap/macaulay2
==> Patching
==> Applying c4bf16f3278118ff1b6fdf20d4ad68441f4b26c5.patch
patching file M2/Macaulay2/packages/Normaliz.m2
==> git clone https://github.com/Macaulay2/M2-emacs.git M2/Macaulay2/editors/emacs --branch main
==> git clone https://github.com/Macaulay2/memtailor.git M2/submodules/memtailor
==> git clone https://github.com/Macaulay2/mathic.git M2/submodules/mathic
==> git clone https://github.com/Macaulay2/mathicgb.git M2/submodules/mathicgb
==> cmake -GNinja -SM2 -BM2/BUILD/build-brew -DBUILD_NATIVE=OFF -DCMAKE_PREFIX_PATH=/home/myid42/M/homebrew/opt/bison;/home/myid42/M/homebrew/opt/cmake;/home/myid42/M/homebre
==> cmake --build M2/BUILD/build-brew --target M2-core M2-emacs M2-highlightjs
Last 15 lines from /home/myid42/.cache/Homebrew/Logs/macaulay2/06.cmake:
/tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/Macaulay2/e/SLP-defs.hpp:183:7: warning:   'int SLEvaluatorConcrete<M2::ARingQQGMP>::nInputs' [-Wreorder]
  183 |   int nInputs, nOutputs;
      |       ^~~~~~~
/tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/Macaulay2/e/SLP-imp.hpp:64:1: warning:   when initialized here [-Wreorder]
   64 | SLEvaluatorConcrete<RT>::SLEvaluatorConcrete(const SLEvaluatorConcrete<RT>& a)
      | ^~~~~~~~~~~~~~~~~~~~~~~
[401/408] /home/myid42/M/homebrew/Library/Homebrew/shims/linux/super/g++-12 -DBOOST_REGEX_NO_LIB -DNDEBUG -DOM_NDEBUG -DSING_NDEBUG -I/tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/Macaulay2/d -I/tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/Macaulay2/e -I/tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/Macaulay2/c -I/tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/BUILD/build-brew/Macaulay2/d -I/tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/Macaulay2/e/mathic -I/tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/Macaulay2/e/memtailor -I/tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/Macaulay2/e/mathicgb -I/home/myid42/M/homebrew/opt/readline/include -I/home/myid42/M/homebrew/opt/libxml2/include/libxml2 -I/home/myid42/M/homebrew/opt/eigen/include/eigen3 -I/home/myid42/M/homebrew/opt/mpsolve/include -I/home/myid42/M/homebrew/opt/frobby/include -I/home/myid42/M/homebrew/opt/factory/include -I/home/myid42/M/homebrew/opt/flint/include -I/home/myid42/M/homebrew/opt/ntl/include -I/home/myid42/M/homebrew/opt/mpfi/include -I/home/myid42/M/homebrew/opt/mpfr/include -I/home/myid42/M/homebrew/opt/bdw-gc/include -I/home/myid42/M/homebrew/opt/gdbm/include -I/home/myid42/M/homebrew/opt/libatomic_ops/include -I/tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/Macaulay2/system -isystem /home/myid42/M/homebrew/opt/gmp/include -isystem /home/myid42/M/homebrew/Cellar/boost/1.81.0_1/include -isystem /home/myid42/M/homebrew/opt/tbb/include -isystem /home/myid42/M/homebrew/opt/libffi/include -isystem /home/myid42/M/homebrew/Cellar/givaro/4.2.0/include -isystem /home/myid42/M/homebrew/Cellar/fflas-ffpack/2.5.0/include -O3 -DNDEBUG -Wuninitialized -g3 -I/tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/BUILD/build-brew/usr-host/include -I/tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/include -I/tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/BUILD/build-brew/include -Wall -Wextra -Wfatal-errors -Wcast-qual -Wno-unused-parameter -Wno-attributes -Wno-cast-qual -Wno-sign-compare -Wno-uninitialized -Wno-unused -Wno-array-bounds -Wno-deprecated-copy -Wno-unknown-pragmas -fopenmp -std=gnu++17 -MD -MT Macaulay2/d/CMakeFiles/M2-interpreter.dir/boostmath-tmp.cc.o -MF Macaulay2/d/CMakeFiles/M2-interpreter.dir/boostmath-tmp.cc.o.d -o Macaulay2/d/CMakeFiles/M2-interpreter.dir/boostmath-tmp.cc.o -c /tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/BUILD/build-brew/Macaulay2/d/boostmath-tmp.cc
[402/408] /home/myid42/M/homebrew/Library/Homebrew/shims/linux/super/g++-12 -DNDEBUG -DOM_NDEBUG -DSING_NDEBUG -I/tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/Macaulay2/e -I/tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/Macaulay2/d -I/tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/Macaulay2/c -I/tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/BUILD/build-brew/Macaulay2/d -I/tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/Macaulay2/e/mathic -I/tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/Macaulay2/e/memtailor -I/tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/Macaulay2/e/mathicgb -I/home/myid42/M/homebrew/opt/readline/include -I/home/myid42/M/homebrew/opt/libxml2/include/libxml2 -I/home/myid42/M/homebrew/opt/mpsolve/include -I/home/myid42/M/homebrew/opt/frobby/include -I/home/myid42/M/homebrew/opt/factory/include -I/home/myid42/M/homebrew/opt/flint/include -I/home/myid42/M/homebrew/opt/ntl/include -I/home/myid42/M/homebrew/opt/mpfi/include -I/home/myid42/M/homebrew/opt/mpfr/include -I/home/myid42/M/homebrew/opt/bdw-gc/include -I/home/myid42/M/homebrew/opt/gdbm/include -I/home/myid42/M/homebrew/opt/libatomic_ops/include -isystem /home/myid42/M/homebrew/opt/eigen/include/eigen3 -isystem /home/myid42/M/homebrew/opt/gmp/include -isystem /home/myid42/M/homebrew/Cellar/givaro/4.2.0/include -isystem /home/myid42/M/homebrew/Cellar/fflas-ffpack/2.5.0/include -isystem /home/myid42/M/homebrew/opt/tbb/include -O3 -DNDEBUG -Wuninitialized -g3 -I/tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/BUILD/build-brew/usr-host/include -I/tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/include -I/tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/BUILD/build-brew/include -Wall -Wextra -Wfatal-errors -Wcast-qual -Wno-unused-parameter -Wno-attributes -Wno-cast-qual -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated-copy -Wno-unknown-pragmas -Wno-ignored-qualifiers -Wno-implicit-fallthrough -fopenmp -std=gnu++17 -MD -MT Macaulay2/e/CMakeFiles/M2-engine.dir/eigen.cpp.o -MF Macaulay2/e/CMakeFiles/M2-engine.dir/eigen.cpp.o.d -o Macaulay2/e/CMakeFiles/M2-engine.dir/eigen.cpp.o -c /tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/Macaulay2/e/eigen.cpp
[403/408] : && /home/myid42/M/homebrew/Cellar/cmake/3.25.3/bin/cmake -E rm -f Macaulay2/e/libM2-engine.a && /home/myid42/M/homebrew/opt/binutils/bin/ar qc Macaulay2/e/libM2-engine.a  Macaulay2/d/CMakeFiles/M2-interpreter.dir/M2types.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/M2lib.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/M2mem.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/scclib.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/memdebug.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/debug.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/gmp_aux.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/gdbm_interface.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/arithmetic-tmp.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/atomic-tmp.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/M2-tmp.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/system-tmp.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/strings-tmp.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/varstrin-tmp.c.o 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Macaulay2/d/CMakeFiles/M2-interpreter.dir/evaluate-tmp.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/sets-tmp.cc.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/mysqldummy-tmp.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/pthread-tmp.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/actors-tmp.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/actors2-tmp.cc.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/actors3-tmp.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/actors4-tmp.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/xmlactors-tmp.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/actors5-tmp.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/actors6-tmp.cc.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/threads-tmp.cc.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/interface-tmp.cc.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/interface2-tmp.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/texmacs-tmp.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/boostmath-tmp.cc.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/ffi-tmp.c.o 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Macaulay2/e/memtailor/libmemtailor.a  /home/myid42/M/homebrew/opt/tbb/lib/libtbb.so.12.8  /home/myid42/M/homebrew/opt/gcc/lib/gcc/12/libgomp.so  /home/myid42/M/homebrew/opt/glibc/lib/libpthread.a && cd /tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/BUILD/build-brew/Macaulay2/bin && /home/myid42/M/homebrew/Cellar/cmake/3.25.3/bin/cmake -E echo --\ Linked\ libraries: && LD_LIBRARY_PATH=/tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/BUILD/build-brew/usr-host/lib: /home/myid42/M/homebrew/opt/glibc/bin/ldd /tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/BUILD/build-brew/usr-dist/x86_64-Linux-Ubuntu-20.04/bin/M2-binary && /home/myid42/M/homebrew/Cellar/cmake/3.25.3/bin/cmake -E echo --\ INSTALL_RPATH:\ /home/myid42/M/homebrew/Cellar/macaulay2/1.21_2/lib/Macaulay2/lib
FAILED: usr-dist/x86_64-Linux-Ubuntu-20.04/bin/M2-binary
: && /home/myid42/M/homebrew/Library/Homebrew/shims/linux/super/g++-12 -O3 -DNDEBUG -g3 -L/tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/BUILD/build-brew/usr-host/lib -fopenmp Macaulay2/system/CMakeFiles/M2-supervisor.dir/supervisor.cpp.o Macaulay2/system/CMakeFiles/M2-supervisor.dir/m2file.cpp.o Macaulay2/system/CMakeFiles/M2-supervisor.dir/tests.cpp.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/M2types.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/M2lib.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/M2mem.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/scclib.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/memdebug.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/debug.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/gmp_aux.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/gdbm_interface.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/arithmetic-tmp.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/atomic-tmp.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/M2-tmp.c.o 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Macaulay2/d/CMakeFiles/M2-interpreter.dir/interface2-tmp.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/texmacs-tmp.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/boostmath-tmp.cc.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/ffi-tmp.c.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/interp-tmp.cc.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/version-tmp.cc.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/boost-regex.cpp.o Macaulay2/d/CMakeFiles/M2-interpreter.dir/xml-c.c.o Macaulay2/bin/CMakeFiles/M2-binary.dir/timestamp.cpp.o Macaulay2/bin/CMakeFiles/M2-binary.dir/main.cpp.o Macaulay2/bin/CMakeFiles/M2-binary.dir/startup.c.o -o usr-dist/x86_64-Linux-Ubuntu-20.04/bin/M2-binary  -Wl,-rpath,/home/myid42/M/homebrew/opt/libffi/lib:/home/myid42/M/homebrew/Cellar/givaro/4.2.0/lib:/home/myid42/M/homebrew/opt/mpsolve/lib:/home/myid42/M/homebrew/opt/factory/lib:/home/myid42/M/homebrew/opt/flint/lib:/home/myid42/M/homebrew/opt/ntl/lib:/home/myid42/M/homebrew/opt/mpfi/lib:/home/myid42/M/homebrew/opt/mpfr/lib:/home/myid42/M/homebrew/opt/bdw-gc/lib:/home/myid42/M/homebrew/opt/gmp/lib:/home/myid42/M/homebrew/opt/openblas/lib:/home/myid42/M/homebrew/opt/libxml2/lib:/home/myid42/M/homebrew/opt/readline/lib:/home/myid42/M/homebrew/opt/gdbm/lib:/home/myid42/M/homebrew/opt/tbb/lib:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::  /home/myid42/M/homebrew/Cellar/boost/1.81.0_1/lib/libboost_stacktrace_backtrace-mt.a  Macaulay2/e/libM2-engine.a  -ldl  -lbacktrace  -ldl  -lquadmath  /home/myid42/M/homebrew/Cellar/boost/1.81.0_1/lib/libboost_regex-mt.a  -licudata  -licui18n  -licuuc  /home/myid42/M/homebrew/opt/libffi/lib/libffi.so  /home/myid42/M/homebrew/Cellar/givaro/4.2.0/lib/libgivaro.so  /home/myid42/M/homebrew/opt/mpsolve/lib/libmps.so  /home/myid42/M/homebrew/opt/frobby/lib/libfrobby.a  /home/myid42/M/homebrew/opt/factory/lib/libfactory.so  /home/myid42/M/homebrew/opt/flint/lib/libflint.so  /home/myid42/M/homebrew/opt/ntl/lib/libntl.so  /home/myid42/M/homebrew/opt/mpfi/lib/libmpfi.so  /home/myid42/M/homebrew/opt/mpfr/lib/libmpfr.so  /home/myid42/M/homebrew/opt/bdw-gc/lib/libgc.so  /home/myid42/M/homebrew/opt/gmp/lib/libgmpxx.so  /home/myid42/M/homebrew/opt/gmp/lib/libgmp.so  /home/myid42/M/homebrew/opt/openblas/lib/libopenblas.so  -lm  -ldl  /home/myid42/M/homebrew/opt/libxml2/lib/libxml2.so  /home/myid42/M/homebrew/opt/readline/lib/libreadline.so  /home/myid42/M/homebrew/opt/readline/lib/libhistory.so  /home/myid42/M/homebrew/opt/gdbm/lib/libgdbm.so  /home/myid42/M/homebrew/opt/libatomic_ops/lib/libatomic_ops.a  Macaulay2/e/mathicgb/libmathicgb.a  Macaulay2/e/mathic/libmathic.a  Macaulay2/e/memtailor/libmemtailor.a  /home/myid42/M/homebrew/opt/tbb/lib/libtbb.so.12.8  /home/myid42/M/homebrew/opt/gcc/lib/gcc/12/libgomp.so  /home/myid42/M/homebrew/opt/glibc/lib/libpthread.a && cd /tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/BUILD/build-brew/Macaulay2/bin && /home/myid42/M/homebrew/Cellar/cmake/3.25.3/bin/cmake -E echo --\ Linked\ libraries: && LD_LIBRARY_PATH=/tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/BUILD/build-brew/usr-host/lib: /home/myid42/M/homebrew/opt/glibc/bin/ldd /tmp/macaulay2-20230314-1391459-11640x/M2-release-1.21/M2/BUILD/build-brew/usr-dist/x86_64-Linux-Ubuntu-20.04/bin/M2-binary && /home/myid42/M/homebrew/Cellar/cmake/3.25.3/bin/cmake -E echo --\ INSTALL_RPATH:\ /home/myid42/M/homebrew/Cellar/macaulay2/1.21_2/lib/Macaulay2/lib
/home/myid42/M/homebrew/opt/binutils/bin/ld: cannot find -lbacktrace: No such file or directory
collect2: error: ld returned 1 exit status
ninja: build stopped: subcommand failed.

If reporting this issue please do so at (not Homebrew/brew or Homebrew/homebrew-core):
  https://github.com/macaulay2/homebrew-tap/issues

These open issues may also help:
The Homebrew tap Macaulay2/tap/fflas-ffpack prevents Sage from building https://github.com/Macaulay2/homebrew-tap/issues/68

I don't know if it would help but before having this error there was another error while installing dependency:

==> Installing macaulay2/tap/macaulay2 dependency: autoconf
==> Pouring autoconf--2.71.x86_64_linux.bottle.tar.gz
Error: Failure while executing; `/usr/bin/env tar --extract --no-same-owner --file /home/myid42/.cache/Homebrew/downloads/3f68a25ba78c87e7d08c6b529f89c0d5e80144bf3b5f8242e7d70bb64d597e6b--autoconf--2.71.x86_64_linux.bottle.tar.gz --directory /tmp/d20230314-993703-ie7dvh` exited with 1. Here's the output:
Too many open files
(base) myid42@lk4:~/M$ brew install autoconf

So I installed and reinstalled autoconf manually, and continued with command brew install M2 that's when I started to get same error message on missing file or directory whenever I try to reinstall or install.

I hope everything is clear as error report and does not violate community guidelines.

brew config:

HOMEBREW_VERSION: 4.0.6-65-g8a5e169
ORIGIN: https://github.com/Homebrew/brew
HEAD: 8a5e1697a64ab8b694fc1d4fd6c8e948fe6950be
Last commit: 4 hours ago
Core tap origin: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 203158f5c16f9ed61b2ae5531b410d48d2973d16
Core tap last commit: 42 minutes ago
Core tap branch: master
HOMEBREW_PREFIX: /home/myid42/M/homebrew
HOMEBREW_REPOSITORY: /home/myid42/M/homebrew
HOMEBREW_CELLAR: /home/myid42/M/homebrew/Cellar
HOMEBREW_CASK_OPTS: []
HOMEBREW_MAKE_JOBS: 32
HOMEBREW_NO_INSTALL_FROM_API: set
Homebrew Ruby: 2.6.8 => /home/myid42/M/homebrew/Library/Homebrew/vendor/portable-ruby/2.6.8_1/bin/ruby
CPU: 32-core 64-bit broadwell
Clang: N/A
Git: 2.25.1 => /bin/git
Curl: 7.68.0 => /bin/curl
Kernel: Linux 5.4.0-42-generic x86_64 GNU/Linux
OS: Ubuntu 20.04.1 LTS (focal)
Host glibc: 2.31
/usr/bin/gcc: 9.3.0
/usr/bin/ruby: N/A
glibc: 2.35_1
gcc@11: N/A
gcc: 12.2.0
xorg: N/A
mahrud commented 1 year ago

I hope everything is clear as error report and does not violate community guidelines.

The report is very clear and detailed, thank you!

I don't know what's going on with autoconf, but the issue with backtrace seems to be cause by cmake pointing to libboost_stacktrace_backtrace-mt.a instead of libboost_stacktrace_backtrace.a. I can look into it, but it might be a while ...

However, the only reason brew wants to rebuild from source is this warning:

Warning: Building macaulay2/tap/macaulay2 from source as the bottle needs:
- HOMEBREW_CELLAR: /home/linuxbrew/.linuxbrew/Cellar (yours is /home/myid42/M/homebrew/Cellar)
- HOMEBREW_PREFIX: /home/linuxbrew/.linuxbrew (yours is /home/myid42/M/homebrew)

Could you try seeing if applying this patch to $(brew --repo macaulay2/tap)/Formula/macaulay2.rb and rerunning brew install M2 forces brew to use the bottle instead?

diff --git a/Formula/macaulay2.rb b/Formula/macaulay2.rb
index 3fa06c0..4bed4c9 100644
--- a/Formula/macaulay2.rb
+++ b/Formula/macaulay2.rb
@@ -20,7 +20,7 @@ class Macaulay2 < Formula
     sha256 cellar: :any, arm64_ventura: "eb5ac622fbcc2a13895470b018557e53ad6c9c6d6e8150a47c358abeaab2edd5"
     sha256 cellar: :any, monterey:      "abc1029ff3ac237fa184978dc74fb4392eaaa03d12ea88670a31f58dd5136a76"
     sha256 cellar: :any, big_sur:       "bacd18b9869adc8e22246acf793d51fee83c2a49d3983ead69772e2566c6f165"
-    sha256               x86_64_linux:  "850f0c224d6e1fdee5f09efe75f5d261d3b6505b203281bc9dab203e61601887"
+    sha256 cellar: :any_skip_relocation, x86_64_linux: "850f0c224d6e1fdee5f09efe75f5d261d3b6505b203281bc9dab203e61601887"
   end

   head do

This may cause other issues, but you might get lucky.

I also made a new issue for making the M2 bottle truly relocatable.

Siwon-S-Kim commented 1 year ago

It worked! Thank you very much.

I used command brew --repo macaulay2/tap then edited file in a 'tap' ; homebrew/Library/Taps/macaulay2/homebrew-tap/Formula/macaulay2.rb .

Changed

-    sha256               x86_64_linux:  "850f0c224d6e1fdee5f09efe75f5d261d3b6505b203281bc9dab203e61601887"
+    sha256 cellar: :any_skip_relocation, x86_64_linux: "850f0c224d6e1fdee5f09efe75f5d261d3b6505b203281bc9dab203e61601887"

After that brew install M2 did show change. It tried to download some things and when I checked my computer later it was installed.

Again thank you very much.