On Sun, Feb 5, 2023 at 9:04 AM 'Nasser M. Abbasi' via sage-release
<[email protected]> wrote:
>
>
> Here is the output
>
> >ldd
> >/home/me/TMP/sage-9.8.rc0/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/scipy/special/_ufuncs.cpython-310-x86_64-linux-gnu.so
> linux-vdso.so.1 (0x00007ffc53be9000)
> libgfortran.so.5 => /usr/lib/libgfortran.so.5 (0x00007fc232878000)
> libm.so.6 => /usr/lib/libm.so.6 (0x00007fc232790000)
> libmvec.so.1 => /usr/lib/libmvec.so.1 (0x00007fc232696000)
> libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x00007fc232676000)
> libc.so.6 => /usr/lib/libc.so.6 (0x00007fc23248f000)
> libquadmath.so.0 => /usr/lib/../lib/libquadmath.so.0 (0x00007fc232444000)
> /usr/lib64/ld-linux-x86-64.so.2 (0x00007fc232ce1000)
here is how it looks on a non-broken installation.
$ ldd
local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/scipy/special/_ufuncs.cpython-310-x86_64-linux-gnu.so
linux-vdso.so.1 (0x00007ffe6b935000)
libopenblas.so.0 => /lib64/libopenblas.so.0 (0x00007fe561400000)
libgfortran.so.5 => /lib64/libgfortran.so.5 (0x00007fe561000000)
libm.so.6 => /lib64/libm.so.6 (0x00007fe563865000)
libmvec.so.1 => /lib64/libmvec.so.1 (0x00007fe561303000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fe563845000)
libc.so.6 => /lib64/libc.so.6 (0x00007fe560c00000)
libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007fe560fb8000)
/lib64/ld-linux-x86-64.so.2 (0x00007fe563ad3000)
As you see, in your case libopenblas.so is not there, and you have an
error due to this.
Why scipy builds such a broken module, I don't know. I'd say it's a scipy bug.
Please post logs/pkgs/numpy* and logs/pkgs/scipy*
> >
>
> "You should add fpylll at the end of the line in
>
> build/pkgs/sagemath_doc_html/dependencies
>
> and run ./configure and make again"
>
> Ok thanks. Will give this a try.
>
> "sage in a different directory which is in your PATH typically breaks things"
>
> but it is NOT in the path. This is the reason I do
>
> unset SAGE_ROOT
> unset SAGE_LOCAL
>
> before building any new release. I make sure current installed sagemath (in
> different folder) is not visible.
>
> --Nasser
>
> On Saturday, February 4, 2023 at 9:15:14 AM UTC-6 Dima Pasechnik wrote:
>>
>> On Sat, Feb 4, 2023 at 1:51 PM 'Nasser M. Abbasi' via sage-release
>> <[email protected]> wrote:
>> >
>> > "Was it an incremental build. If so,
>> > make distclean
>> > and
>> > build again from scratch."
>> >
>> > It was not an incremental build. I extracted the gzip file and did the
>> > steps I showed. So I do not need to do "make distclean" since everything
>> > is new.
>> >
>> > But I repeated now everything again using "make distclean" and got same
>> > error.
>> >
>> > "Probably the problem is linking with openblas. Do you have a number of
>> > openblas versions accessible to the linker?"
>> >
>> > I have no idea. What command should I use to check?
>>
>> run
>>
>> ldd
>> /home/me/TMP/sage-9.8.rc0/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/scipy/special/_ufuncs.cpython-310-x86_64-linux-gnu.so
>>
>> Post its output
>> - there should be an openblas mentioned, the question is which one.
>>
>> As far as fpylll is concerned, you've hit the bug fixed in not yet merged
>> https://trac.sagemath.org/ticket/34940
>>
>> You should add fpylll at the end of the line in
>>
>> build/pkgs/sagemath_doc_html/dependencies
>>
>> and run ./configure and make again
>>
>>
>>
>>
>> >
>> > I am just following the instruction to download and install sagemath.
>> >
>> > I have giac and maxima and fricas and texlive already installed on this
>> > virtual box already. I also have sagemath 9.7 installed in different
>> > folder.
>> >
>> > --Nasser
>> >
>> >
>> > On Saturday, February 4, 2023 at 5:27:59 AM UTC-6 Dima Pasechnik wrote:
>> >>
>> >> Hello,
>> >> Was it an incremental build. If so,
>> >> make distclean
>> >> and
>> >> build again from scratch.
>> >>
>> >> Anyhow, if you look in your istall.log you'll see problems with a number
>> >> of packages, e.g. fpylll, scipy.
>> >>
>> >> [sagemath_doc_html-none] [manifolds] ImportError:
>> >> /home/me/TMP/sage-9.8.rc0/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/scipy/special/_ufuncs.cpython-310-x86_64-linux-gnu.so:
>> >> undefined symbol: dstevr_
>> >>
>> >> Probably the problem is linking with openblas. Do you have a number of
>> >> openblas versions accessible to the linker?
>> >>
>> >>
>> >>
>> >> By the way,
>> >> what are you trying to achieve with exporting
>> >> MAXIMA ?
>> >> Sage does not support using external Maxima at the moment,
>> >>
>> >>
>> >>
>> >>
>> >> On Sat, 4 Feb 2023, 08:12 'Nasser M. Abbasi' via sage-release,
>> >> <[email protected]> wrote:
>> >>>
>> >>> I get this error on Linux virtual box running
>> >>>
>> >>> lsb_release -a
>> >>> LSB Version: n/a
>> >>> Distributor ID: ManjaroLinux
>> >>> Description: Manjaro Linux
>> >>> Release: 22.0.0
>> >>> Codename: Sikaris
>> >>>
>> >>> After extracting the gzip file, these are the commands I did
>> >>>
>> >>> unset SAGE_ROOT
>> >>> unset SAGE_LOCAL
>> >>> export GIAC=/usr/local/bin/giac
>> >>> export MAXIMA=/usr/local/bin/maxima
>> >>> ./configure --with-system-python=no
>> >>> make
>> >>>
>> >>> At the end I see
>> >>>
>> >>> -------------
>> >>> sagemath_doc_html-none] File
>> >>> "/home/me/TMP/sage-9.8.rc0/src/sage_docbuild/sphinxbuild.py", line 263,
>> >>> in raise_errors
>> >>> [sagemath_doc_html-none] raise OSError(self._error)
>> >>> [sagemath_doc_html-none] OSError:
>> >>> /home/me/TMP/sage-9.8.rc0/src/sage/manifolds/chart.py:docstring of
>> >>> sage.manifolds.chart.RealChart.plot:104: WARNING: Exception occurred in
>> >>> plotting chart-1
>> >>> [sagemath_doc_html-none]
>> >>> [sagemath_doc_html-none] Note: incremental documentation builds
>> >>> sometimes cause spurious
>> >>> [sagemath_doc_html-none] error messages. To be certain that these are
>> >>> real errors, run
>> >>> [sagemath_doc_html-none] "make doc-clean doc-uninstall" first and try
>> >>> again.
>> >>> [sagemath_doc_html-none] make[6]: *** [Makefile:28:
>> >>> doc-inventory--reference-manifolds] Error 1
>> >>> [sagemath_doc_html-none] make[5]: *** [Makefile:45:
>> >>> doc-inventory-reference] Error 2
>> >>> make[4]: *** [Makefile:3262: sagemath_doc_html-SAGE_DOCS-no-deps] Error 2
>> >>> make[3]: *** [Makefile:3262:
>> >>> /home/me/TMP/sage-9.8.rc0/local/var/lib/sage/installed/sagemath_doc_html-none]
>> >>> Error 2
>> >>> make[2]: *** [Makefile:2766: all-start] Error 2
>> >>> make[2]: Leaving directory '/home/me/TMP/sage-9.8.rc0/build/make'
>> >>>
>> >>> real 71m30.833s
>> >>> user 103m7.355s
>> >>> sys 5m48.306s
>> >>> ***************************************************************
>> >>> Error building Sage.
>> >>>
>> >>> The following package(s) may have failed to build (not necessarily
>> >>> during this run of 'make all-start'):
>> >>>
>> >>> 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.
>> >>> ----------------------------
>> >>>
>> >>> The following folder contains config.log and install.log files
>> >>>
>> >>> Thank you
>> >>> --Nasser
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> On Friday, February 3, 2023 at 3:40:20 AM UTC-6 Dima Pasechnik wrote:
>> >>>>
>> >>>> On Fri, Feb 3, 2023 at 7:33 AM Sébastien Labbé <[email protected]> wrote:
>> >>>> >
>> >>>> >
>> >>>> >
>> >>>> > On Thursday, February 2, 2023 at 7:37:27 PM UTC+1
>> >>>> > [email protected] wrote:
>> >>>> > On Thursday, February 2, 2023 at 9:30:30 AM UTC-8 Sébastien Labbé
>> >>>> > wrote:
>> >>>> > ./bootstrap: 9: m4: Permission denied
>> >>>> > make: *** [Makefile:365 : configure] Erreur 1
>> >>>> >
>> >>>> > Do you have "." in PATH?
>> >>>> >
>> >>>> >
>> >>>> > No
>> >>>> >
>> >>>> > What does "which m4" say?
>> >>>> >
>> >>>> >
>> >>>> > It returns nothing! Thanks for the hint. I found the problem: when
>> >>>> > reading the sage README to install sage from scratch on this new
>> >>>> > machine, I installed the basic stuff as follows:
>> >>>> >
>> >>>> > $ sudo apt install gcc gfortran g++ make m4 perl ranlib tar bc
>> >>>> > [...]
>> >>>> > E: Impossible de trouver le paquet ranlib
>> >>>> >
>> >>>> > But this returned an error on ranlib and I assumed it had installed
>> >>>> > the other packages in the list but no, it did not (gcc, gfortran,
>> >>>> > etc. were not installed as well).
>> >>>> >
>> >>>> > Is ranlib really needed for sage? Can we remove it from the README?
>> >>>>
>> >>>> ranlib is a standard tool, and is used by various build systems. On
>> >>>> Debian it's a part of binutils package.
>> >>>>
>> >>>> README is not platform-specific, and it does not tell you to install
>> >>>> *package* called ranlib.
>> >>>> However, we should add there an advice to look for what packages to
>> >>>> install in
>> >>>> build/pkgs/_prereq/distros/
>> >>>> (e.g. for Debian it's in build/pkgs/_prereq/distros/debian.txt)
>> >>>>
>> >>>> (Once our GitHub is live in few days, it's a very quick PR to do :-))
>> >>>>
>> >>>>
>> >>>>
>> >>>> >
>> >>>> >
>> >>>> >
>> >>>> > --
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>> >>>
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