Hi Dima and John, Yes, this seems to be one of the problems I am having. I did indeed migrate from another Mac, so it probably copied over the homebrew in /usr/local
MacBook-Pro-3:lib anne$ which brew /usr/local/bin/brew Now I need to figure out how to get rid of it. Best wishes, Anne On Thursday, September 26, 2024 at 1:11:03 PM UTC-7 John H Palmieri wrote: > If you migrated from an x86 Mac and as a result copied some of the old > homebrew files in /usr/local, then the files now in /usr/local on the new > Mac could be causing problems. As Dima noted, the homebrew installation on > an Apple Silicon machine should be in /opt/. I suggested trying to get rid > of whatever is in /usr/local. (Carefully, of course.) > > Regards, > John > > On Thursday, September 26, 2024 at 1:01:31 PM UTC-7 dim...@gmail.com > 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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