On Thu, Sep 26, 2024 at 10:30 PM Anne Schilling
<anne1.schill...@gmail.com> wrote:
>
> 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.

https://docs.brew.sh/FAQ#how-do-i-uninstall-homebrew

I presume if you run this while brew is /usr/local/bin/brew it will
uninstall everything related to it, and leave the Homebrew in /opt
untouched.


>
> 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
>>> >>>> >> >> >>
>>> >>>> >> >> >>
>>> >>>> >> >> >>
>>> >>>> >> >> >
>>> >>>> >> >> > --
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>>> >>>> >> >> > https://groups.google.com/d/msgid/sage-devel/51990537-59a2-4fce-9993-b322ada6c10fn%40googlegroups.com.
>>> >>>> >> >
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