Before deleting anything, you could try expunging all mention of /usr/local from your PATH and other variables wherever they're set (.profile or .bashrc or .zshrc or whatever), and start a clean Terminal session with the new settings. At this point you may need to install homebrew (if it thinks it's only installed in /usr/local). Then source .homebrew-build-env, check PATH and other variables again, run ./configure and install whatever packages Sage recommends. If this all happens to work, then you can start going through /usr/local to see if there is anything there that didn't come from homebrew that you want to keep.
On Thursday, September 26, 2024 at 2:52:48 PM UTC-7 dim...@gmail.com wrote: > ---------- Forwarded message --------- > From: Dima Pasechnik <dim...@gmail.com> > Date: Thu, Sep 26, 2024 at 9:17 PM > Subject: Re: [sage-devel] trouble installing sage > To: <an...@math.ucdavis.edu> > > > Hi Anna, > > Oh no... > Well, try > > unset LDFLAGS > unset CPPFLAGS > unset PKG_CONFIG_PATH > brew uninstall openblas > brew install openblas > > but I really don't know what kind of collateral damage "brew reinstall > openblas --build-from-source" > has done. > > It might be that you'd have to purge Homebrew > (see https://github.com/homebrew/install#uninstall-homebrew) > and reinstall it from scratch. > > > It's still puzzling that it went into /usr/local, and not into /opt ? > Do you have 2 installations of Homebrew, one in /opt, and another in > /usr/local? > The 2nd one must go... > > > HTH > Dima > > > > > On Thu, Sep 26, 2024 at 8:44 PM Anne Schilling <an...@math.ucdavis.edu> > wrote: > > > No, this is still the same machine, but somehow last night I also > followed Kyukwan's suggestion and did > > > > > brew reinstall openblas --build-from-source > > > > And then following your advice of doing as Romans do in Rome was asked > to do > > > > export LDFLAGS="-L/usr/local/opt/openblas/lib" > > export CPPFLAGS="-I/usr/local/opt/openblas/include" > > export PKG_CONFIG_PATH="/usr/local/opt/openblas/lib/pkgconfig" > > > > How do I undo this? > > > > Best, > > > > Anne > > > > On 9/26/24 12:17 PM, Dima Pasechnik wrote: > > > Hi Anne, > > > > > > I am sorry, why all of a sudden you have Homebrew installed in > > > /usr/local, even though in the previous iteration it was in /opt ? > > > Do you have a wrong arch copy of Homebrew on your M1 machine? > > > (and if so, why?) > > > > > > Or is it a different, x86_64, machine? > > > > > > Assuming you're on an arm64, your brew should be in /opt/, not on > > > /usr/local, too. > > > Wrong order of things in PATH? > > > Please make sure that /opt things come before /usr/local things in > your path, > > > and re-run the whole things. > > > > > > Best > > > Dima > > > > > > > > > On Thu, Sep 26, 2024 at 7:58 PM Anne Schilling > > > <anne1.s...@gmail.com> wrote: > > >> Hi Dima, > > >> > > >> I appreciate all your help! > > >> > > >> In a new terminal, I did > > >> > > >> source .homebrew-build-env > > >> echo $PKG_CONFIG_PATH > > >> > /usr/local/opt/sqlite/lib/pkgconfig:/usr/local/opt/readline/lib/pkgconfig:/usr/local/opt/openssl/lib/pkgconfig:/usr/local/opt/openblas/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/local/opt/sqlite/lib/pkgconfig:/usr/local/opt/readline/lib/pkgconfig:/usr/local/opt/openssl/lib/pkgconfig:/usr/local/opt/openblas/lib/pkgconfig:/usr/local/lib/pkgconfig: > > >> > > >> ./configure > > >> make > > >> > > >> ... > > >> [openblas-0.3.26] /Users/anne/sage/sage/config.log > > >> [openblas-0.3.26] Describe your computer, operating system, etc. > > >> [openblas-0.3.26] If you want to try to fix the problem yourself, > *don't* just cd to > > >> [openblas-0.3.26] > /Users/anne/sage/sage/local/var/tmp/sage/build/openblas-0.3.26 and type > 'make' or whatever is appropriate. > > >> [openblas-0.3.26] Instead, the following commands setup all > environment variables > > >> [openblas-0.3.26] correctly and load a subshell for you to debug the > error: > > >> [openblas-0.3.26] (cd > '/Users/anne/sage/sage/local/var/tmp/sage/build/openblas-0.3.26' && > '/Users/anne/sage/sage/sage' --buildsh) > > >> [openblas-0.3.26] When you are done debugging, you can type "exit" to > leave the subshell. > > >> [openblas-0.3.26] > ************************************************************************ > > >> [openblas-0.3.26] real 4m38.340s user 3m6.887s sys 1m6.485s > > >> make[4]: *** [openblas-SAGE_LOCAL-no-deps] Error 1 > > >> make[3]: *** > [/Users/anne/sage/sage/local/var/lib/sage/installed/openblas-0.3.26] Error 2 > > >> make[2]: *** [all-start] Error 2 > > >> *************************************************************** > > >> Error building Sage. > > >> > > >> The following package(s) may have failed to build (not necessarily > > >> during this run of 'make all-start'): > > >> > > >> * package: m4ri-20200125 > > >> last build time: Sep 26 11:51 > > >> log file: /Users/anne/sage/sage/logs/pkgs/m4ri-20200125.log > > >> build directory: > /Users/anne/sage/sage/local/var/tmp/sage/build/m4ri-20200125 > > >> > > >> * package: openblas-0.3.26 > > >> last build time: Sep 26 11:55 > > >> log file: /Users/anne/sage/sage/logs/pkgs/openblas-0.3.26.log > > >> build directory: > /Users/anne/sage/sage/local/var/tmp/sage/build/openblas-0.3.26 > > >> > > >> It is safe to delete any log files and build directories, but they > > >> contain information that is helpful for debugging build problems. > > >> WARNING: If you now run 'make' again, the build directory of the > > >> same version of the package will, by default, be deleted. Set the > > >> environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this. > > >> > > >> real 8m1.762s user 12m32.628s sys 5m29.871s > > >> make[1]: *** [all-start] Error 1 > > >> make: *** [all] Error 2 > > >> > > >> Best wishes, > > >> > > >> Anne > > >> > > >> On Thursday, September 26, 2024 at 1:10:39 AM UTC-7 dim...@gmail.com > wrote: > > >>> Hi Anne, > > >>> sorry for this mess. > > >>> This config.log (which you sent only to me) looks fine, openblas is > detected. What's not fine is > > >>> PKG_CONFIG_PATH value, which is over 4K characters long. > > >>> That's insanely long, with lots and lots of repeated entries. > > >>> It's actually not the only environment variable which grows with > each sourcing. > > >>> There are also LIBRARY_PATH, CPATH, PATH, etc (you can read > > >>> .homebrew-build-environment for a complete list) > > >>> :-( > > >>> It could be that's they are so long that it breaks things. > > >>> > > >>> This came from repeated sourcing of .homebrew-build-env > > >>> Our instructions say that "source .homebrew-build-env" should only be > > >>> run once in given terminal session. > > >>> That's obviously not well-aligned with repeatedly installing more and > > >>> more homebrew packages, after which round > > >>> values of PKG_CONFIG_PATH might need to be updated, and needs another > > >>> round of "source .homebrew-build-env". > > >>> > > >>> Indeed, PKG_CONFIG_PATH grows after each sourcing, > > >>> as you can check by repeatedly running > > >>> > > >>> source .homebrew-build-env > > >>> echo $PKG_CONFIG_PATH > > >>> > > >>> I'll open a GitHub issue to deal with it. > > >>> As a workaround, could you please open a new ternimal, run there > > >>> "source .homebrew-build-env" followed by "./configure", and check > > >>> that PKG_CONFIG_PATH > > >>> is of reasonable length (by running "echo $PKG_CONFIG_PATH"), > > >>> something like I see on our M1 machine: > > >>> > PKG_CONFIG_PATH='/opt/homebrew/opt/sqlite/lib/pkgconfig:/opt/homebrew/opt/readline/lib/pkgconfig:/opt/homebrew/opt/openssl/lib/pkgconfig:/opt/homebrew/opt/openblas/lib/pkgconfig:/opt/homebrew/lib/pkgconfig:' > > >>> > > >>> Then run "make", if it's OK. > > >>> > > >>> HTH > > >>> Dima > > >>> > > >>> On Thursday, September 26, 2024 at 12:49:24 AM UTC+1 > anne1.s...@gmail.com wrote: > > >>>> Hi Dima, > > >>>> > > >>>> Yes, I have openblas installed via brew and just reinstalled it > again and get the same error message. > > >>>> > > >>>> Best wishes, > > >>>> > > >>>> Anne > > >>>> > > >>>> On Wednesday, September 25, 2024 at 1:41:01 PM UTC-7 > dim...@gmail.com wrote: > > >>>>> On Wed, Sep 25, 2024 at 8:18 PM Anne Schilling > > >>>>> <anne1.s...@gmail.com> wrote: > > >>>>>> Thanks! I followed the instructions, then ran ./configure and > make and got the following: > > >>>>> Do you have openblas installed via brew? > > >>>>> This would be probably the easiest - otherwise we might need an > > >>>>> upgrade of openblas > > >>>>> (ours it probably too old for macOS 15.0) > > >>>>> > > >>>>> > > >>>>> > > >>>>>> ... > > >>>>>> CNAME=\"\" -DNO_AFFINITY -I. -O2 -DMAX_STACK_ALLOC=2048 -Wall > -DF_INTERFACE_GFORT -fPIC -DSMP_SERVER -DNO_WARMUP -DMAX_CPU_NUMBER=10 > -DMAX_PARALLEL_NUMBER=1 -DUSE_TLS -DBUILD_SINGLE=1 -DBUILD_DOUBLE=1 > -DBUILD_COMPLEX=1 -DBUILD_COMPLEX16=1 -DVERSION=\"0.3.26\" -UASMNAME > -UASMFNAME -UNAME -UCNAME -UCHAR_NAME -UCHAR_CNAME -DASMNAME=_samax_k > -DASMFNAME=_samax_k_ -DNAME=samax_k_ -DCNAME=samax_k > -DCHAR_NAME=\"samax_k_\" -DCHAR_CNAME=\"samax_k\" -DNO_AFFINITY -I.. > -UDOUBLE -UCOMPLEX -UCOMPLEX -UDOUBLE -DUSE_ABS -UUSE_MIN > ../kernel/arm64/amax.S -o samax_k.o > > >>>>>> [openblas-0.3.26] [spkg-install] make[6]: *** No rule to make > target `../kernel/arm64/amin.S', needed by `samin_k.o'. Stop. > > >>>>>> [openblas-0.3.26] [spkg-install] make[5]: *** [libs] Error 1 > > >>>>>> [openblas-0.3.26] [spkg-install] > ******************************************************************************** > > >>>>>> [openblas-0.3.26] [spkg-install] Error building openblas-0.3.26 > > >>>>>> [openblas-0.3.26] [spkg-install] > ******************************************************************************** > > >>>>>> [openblas-0.3.26] > ************************************************************************ > > >>>>>> [openblas-0.3.26] Error installing package openblas-0.3.26 > > >>>>>> [openblas-0.3.26] > ************************************************************************ > > >>>>>> [openblas-0.3.26] Please email sage-devel ( > http://groups.google.com/group/sage-devel) > > >>>>>> [openblas-0.3.26] explaining the problem and including the log > files > > >>>>>> [openblas-0.3.26] > /Users/anne/sage/sage/logs/pkgs/openblas-0.3.26.log > > >>>>>> [openblas-0.3.26] and > > >>>>>> [openblas-0.3.26] /Users/anne/sage/sage/config.log > > >>>>>> [openblas-0.3.26] Describe your computer, operating system, etc. > > >>>>>> [openblas-0.3.26] If you want to try to fix the problem yourself, > *don't* just cd to > > >>>>>> [openblas-0.3.26] > /Users/anne/sage/sage/local/var/tmp/sage/build/openblas-0.3.26 and type > 'make' or whatever is appropriate. > > >>>>>> [openblas-0.3.26] Instead, the following commands setup all > environment variables > > >>>>>> [openblas-0.3.26] correctly and load a subshell for you to debug > the error: > > >>>>>> [openblas-0.3.26] (cd > '/Users/anne/sage/sage/local/var/tmp/sage/build/openblas-0.3.26' && > '/Users/anne/sage/sage/sage' --buildsh) > > >>>>>> [openblas-0.3.26] When you are done debugging, you can type > "exit" to leave the subshell. > > >>>>>> [openblas-0.3.26] > ************************************************************************ > > >>>>>> [openblas-0.3.26] real 4m31.252s user 3m3.040s sys 1m4.242s > > >>>>>> make[4]: *** [openblas-SAGE_LOCAL-no-deps] Error 1 > > >>>>>> make[3]: *** > [/Users/anne/sage/sage/local/var/lib/sage/installed/openblas-0.3.26] Error 2 > > >>>>>> make[2]: *** [all-start] Error 2 > > >>>>>> *************************************************************** > > >>>>>> Error building Sage. > > >>>>>> > > >>>>>> The following package(s) may have failed to build (not necessarily > > >>>>>> during this run of 'make all-start'): > > >>>>>> > > >>>>>> * package: m4ri-20200125 > > >>>>>> last build time: Sep 25 12:11 > > >>>>>> log file: /Users/anne/sage/sage/logs/pkgs/m4ri-20200125.log > > >>>>>> build directory: > /Users/anne/sage/sage/local/var/tmp/sage/build/m4ri-20200125 > > >>>>>> > > >>>>>> * package: openblas-0.3.26 > > >>>>>> last build time: Sep 25 12:15 > > >>>>>> log file: /Users/anne/sage/sage/logs/pkgs/openblas-0.3.26.log > > >>>>>> build directory: > /Users/anne/sage/sage/local/var/tmp/sage/build/openblas-0.3.26 > > >>>>>> > > >>>>>> It is safe to delete any log files and build directories, but they > > >>>>>> contain information that is helpful for debugging build problems. > > >>>>>> WARNING: If you now run 'make' again, the build directory of the > > >>>>>> same version of the package will, by default, be deleted. Set the > > >>>>>> environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this. > > >>>>>> > > >>>>>> real 4m31.928s user 9m1.974s sys 2m44.265s > > >>>>>> make[1]: *** [all-start] Error 1 > > >>>>>> make: *** [all] Error 2 > > >>>>>> > > >>>>>> Best wishes, > > >>>>>> > > >>>>>> Anne > > >>>>>> > > >>>>>> On Wednesday, September 25, 2024 at 9:33:00 AM UTC-7 > dim...@gmail.com wrote: > > >>>>>>> Well, while in Rome, do as Romans do? :-) > > >>>>>>> From your log: > > >>>>>>> > > >>>>>>> hint: On your system (homebrew), you can install the required > system > > >>>>>>> packages as follows: > > >>>>>>> > > >>>>>>> $ brew install autoconf automake libtool pkg-config > > >>>>>>> > > >>>>>>> On Wed, Sep 25, 2024 at 4:45 PM Anne Schilling > > >>>>>>> <anne1.s...@gmail.com> wrote: > > >>>>>>>> Hi Dima and Kwankyu, > > >>>>>>>> > > >>>>>>>> Thank you so much for your help! > > >>>>>>>> > > >>>>>>>> Dima, I have > > >>>>>>>> > > >>>>>>>> export PATH=$PATH:/Users/anne/Library/ > > >>>>>>>> > > >>>>>>>> in my .bashrc file. But when I take out this line the command > > >>>>>>>> > > >>>>>>>> ./bootstrap > > >>>>>>>> > > >>>>>>>> gives a failure > > >>>>>>>> > > >>>>>>>> ... > > >>>>>>>> /bootstrap:85: installing src/doc/en/reference/spkg/*.rst > > >>>>>>>> ./bootstrap: installing > /Users/anne/sage/sage/build/pkgs/sagemath_environment/src/pyproject.toml > > >>>>>>>> ./bootstrap: installing > /Users/anne/sage/sage/build/pkgs/sagemath_environment/src/requirements-editable.txt > > >>>>>>>> ./bootstrap: installing > /Users/anne/sage/sage/build/pkgs/sagemath_environment/src/requirements.txt > > >>>>>>>> ./bootstrap: installing > /Users/anne/sage/sage/build/pkgs/sagemath_mcqd/src/pyproject.toml > > >>>>>>>> ./bootstrap: installing > /Users/anne/sage/sage/build/pkgs/sagemath_mcqd/src/requirements.txt > > >>>>>>>> ./bootstrap: installing > /Users/anne/sage/sage/build/pkgs/sagemath_meataxe/src/pyproject.toml > > >>>>>>>> ./bootstrap: installing > /Users/anne/sage/sage/build/pkgs/sagemath_meataxe/src/requirements.txt > > >>>>>>>> ./bootstrap: installing > /Users/anne/sage/sage/build/pkgs/sagemath_objects/src/pyproject.toml > > >>>>>>>> ./bootstrap: installing > /Users/anne/sage/sage/build/pkgs/sagemath_objects/src/requirements-editable.txt > > >>>>>>>> ./bootstrap: installing > /Users/anne/sage/sage/build/pkgs/sagemath_objects/src/requirements.txt > > >>>>>>>> ./bootstrap: installing > /Users/anne/sage/sage/build/pkgs/sagemath_repl/src/pyproject.toml > > >>>>>>>> ./bootstrap: installing > /Users/anne/sage/sage/build/pkgs/sagemath_repl/src/requirements-editable.txt > > >>>>>>>> ./bootstrap: installing > /Users/anne/sage/sage/build/pkgs/sagemath_repl/src/requirements.txt > > >>>>>>>> ./bootstrap: installing > /Users/anne/sage/sage/build/pkgs/sagemath_sirocco/src/pyproject.toml > > >>>>>>>> ./bootstrap: installing > /Users/anne/sage/sage/build/pkgs/sagemath_sirocco/src/requirements.txt > > >>>>>>>> ./bootstrap: installing > /Users/anne/sage/sage/build/pkgs/sagemath_tdlib/src/pyproject.toml > > >>>>>>>> ./bootstrap: installing > /Users/anne/sage/sage/build/pkgs/sagemath_tdlib/src/requirements.txt > > >>>>>>>> ./bootstrap-conda:84: generate conda environment files > > >>>>>>>> ./bootstrap: line 143: aclocal: command not found > > >>>>>>>> Bootstrap failed. Either install autotools; or run bootstrap > with > > >>>>>>>> the -d option to download the auto-generated files instead. > > >>>>>>>> > > >>>>>>>> hint: On your system (homebrew), you can install the required > system packages as follows: > > >>>>>>>> $ brew install autoconf automake libtool pkg-config > > >>>>>>>> > > >>>>>>>> Homebrew can issue suggestions regarding keg-only packages. > > >>>>>>>> The following command is to automatically apply these > suggestions > > >>>>>>>> for packages relevant for Sage to make them available for the > build. > > >>>>>>>> Run it once to apply the suggestions for the current session. > > >>>>>>>> Add it to your shell profile to apply them for all future > sessions. > > >>>>>>>> > > >>>>>>>> $ source /Users/anne/sage/sage/.homebrew-build-env > > >>>>>>>> > > >>>>>>>> Best wishes, > > >>>>>>>> > > >>>>>>>> Anne > > >>>>>>>> > > >>>>>>>> On Wednesday, September 25, 2024 at 1:00:48 AM UTC-7 > dim...@gmail.com wrote: > > >>>>>>>>> these PATH entries look very suspect. > > >>>>>>>>> You don't want any of these Python things in your PATH. > > >>>>>>>>> > > >>>>>>>>> PATH: /Library/Frameworks/Python.framework/Versions/3.7/bin/ > > >>>>>>>>> PATH: /Library/Frameworks/Python.framework/Versions/2.7/bin/ > > >>>>>>>>> PATH: > /Library/Frameworks/Python.framework/Versions/Current/bin/ > > >>>>>>>>> > > >>>>>>>>> On Tue, Sep 24, 2024 at 11:32 PM Anne Schilling > > >>>>>>>>> <anne1.s...@gmail.com> wrote: > > >>>>>>>>>> Ok, sorry, here is the result after > > >>>>>>>>>> > > >>>>>>>>>> make distclean > > >>>>>>>>>> source .homebrew-build-env > > >>>>>>>>>> ./bootstrap > > >>>>>>>>>> ./configure --enable-system-site-packages > > >>>>>>>>>> > > >>>>>>>>>> Best wishes, > > >>>>>>>>>> > > >>>>>>>>>> Anne > > >>>>>>>>>> > > >>>>>>>>>> On Tuesday, September 24, 2024 at 3:22:06 PM UTC-7 John H > Palmieri wrote: > > >>>>>>>>>>> On Tuesday, September 24, 2024 at 3:19:07 PM UTC-7 > dim...@gmail.com wrote: > > >>>>>>>>>>> > > >>>>>>>>>>> From the log: > > >>>>>>>>>>> > > >>>>>>>>>>> ./configure --enable-system-site-packagesls (SIC!) > > >>>>>>>>>>> > > >>>>>>>>>>> > > >>>>>>>>>>> ## Checking whether SageMath should install SPKG scipy... ## > > >>>>>>>>>>> ## ------------------------------------------------------ ## > > >>>>>>>>>>> configure:90867: checking whether any of openblas is > installed as or > > >>>>>>>>>>> will be installed as SPKG > > >>>>>>>>>>> configure:90877: result: no > > >>>>>>>>>>> configure:90881: checking if --enable-system-site-packages > was used > > >>>>>>>>>>> configure:90939: result: no; skipping check > > >>>>>>>>>>> configure:90976: no suitable system package found for SPKG > scipy > > >>>>>>>>>>> > > >>>>>>>>>>> So please run > > >>>>>>>>>>> > > >>>>>>>>>>> ./configure --enable-system-site-packages > > >>>>>>>>>>> > > >>>>>>>>>>> without a typo. > > >>>>>>>>>>> > > >>>>>>>>>>> > > >>>>>>>>>>> And it might not hurt to first run "make distclean" before > doing everything else (in case you're not already doing this). > > >>>>>>>>>>> > > >>>>>>>>>>> -- > > >>>>>>>>>>> John > > >>>>>>>>>>> > > >>>>>>>>>>> > > >>>>>>>>>>> > > >>>>>>>>>> -- > > >>>>>>>>>> You received this message because you are subscribed to the > Google Groups "sage-devel" group. > > >>>>>>>>>> To unsubscribe from this group and stop receiving emails from > it, send an email to sage-devel+...@googlegroups.com. > > >>>>>>>>>> To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/51990537-59a2-4fce-9993-b322ada6c10fn%40googlegroups.com > . > > >>>>>>>> -- > > >>>>>>>> You received this message because you are subscribed to the > Google Groups "sage-devel" group. > > >>>>>>>> To unsubscribe from this group and stop receiving emails from > it, send an email to sage-devel+...@googlegroups.com. > > >>>>>>>> To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/da1e14fb-20a7-4e34-bc63-19016b03f588n%40googlegroups.com > . > > >>>>>> -- > > >>>>>> You received this message because you are subscribed to the > Google Groups "sage-devel" group. > > >>>>>> To unsubscribe from this group and stop receiving emails from it, > send an email to sage-devel+...@googlegroups.com. > > >>>>>> To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/fdbca53b-c231-496f-a2d5-36d5062a33ecn%40googlegroups.com > . > > >> -- > > >> You received this message because you are subscribed to the Google > Groups "sage-devel" group. > > >> To unsubscribe from this group and stop receiving emails from it, > send an email to sage-devel+...@googlegroups.com. > > >> To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/5668cf7f-387f-40e1-a87d-93ba0a910a7dn%40googlegroups.com > . > > > -- You received this message because you are subscribed to the Google Groups "sage-devel" group. 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