You also were saying that you have MAXIMA set to an installation of Maxima.
Note that Sage won't be able to use it. Sage uses Maxima in two ways: as a Python module embedding ECL (with Maxima installed there) and (something we work on to get rid of) interacting with Maxima built with ECL with pexpect (Unix pipes, more or less). While the latter may in principle use different Maxima installation, this is not implemented. On Sun, Feb 5, 2023 at 12:56 PM Dima Pasechnik <[email protected]> wrote: > > On Sun, Feb 5, 2023 at 12:44 PM 'Nasser M. Abbasi' via sage-release > <[email protected]> wrote: > > > > > > I agree with you. I think the best thing for me, is just to make a brand > > new Virtual box, and install a new Linux and start everything from clean > > system. It will take me 2-3 days as I have to install few things I need, > > Then will try installing sagemath again after that. > > you can try to temporarily move /usr/local somewhere, and see if it > helps; no need to rebuild the whole Sage then, just rebuild > scipy: > > make scipy-clean scipy-uninstall > make scipy > > Then start sage > > ./sage > > and run > > sage: import scipy > > there. If this works, run > > make > > to see if it finishes fine. > > > > > Thanks for the help. > > --Nasser > > > > On Sunday, February 5, 2023 at 5:58:14 AM UTC-6 Dima Pasechnik wrote: > >> > >> I suspect you have an installation of openblas, or/and some other > >> blas/lapack, in /usr/local - and this results in scipy being unable > >> to link it correctly. > >> > >> > >> (or perhaps it's not /usr/local, but some other location known to > >> pkg-config) > >> > >> numpy and scipy accumulated ~20 years of layer upon layer of old > >> outdated code for recognising BLAS/LAPACK libraries, it's such a > >> nightmare to debug. > >> > >> > >> > >> On Sun, Feb 5, 2023 at 10:36 AM 'Nasser M. Abbasi' via sage-release > >> <[email protected]> wrote: > >> > > >> > Here is the output for the new command you posted > >> > > >> > >ldd > >> > >local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/numpy/core/_multiarray_umath.cpython-310-x86_64-linux-gnu.so > >> > linux-vdso.so.1 (0x00007ffd883d4000) > >> > libcblas.so.3 => /usr/lib/libcblas.so.3 (0x00007f25a6532000) > >> > libopenblas.so.3 => /usr/lib/libopenblas.so.3 (0x00007f25a5260000) > >> > libm.so.6 => /usr/lib/libm.so.6 (0x00007f25a5178000) > >> > libc.so.6 => /usr/lib/libc.so.6 (0x00007f25a4f91000) > >> > /usr/lib64/ld-linux-x86-64.so.2 (0x00007f25a6a5b000) > >> > libgomp.so.1 => /usr/lib/libgomp.so.1 (0x00007f25a4f48000) > >> > libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x00007f25a4f28000) > >> > > > >> > > >> > I've also put in same folder here a file called log_folders.tar.gz which > >> > is backup of the logs/ folder in my build tree of 9.8 rc0 so it will > >> > have the logs you asked for. > >> > > >> > any other information needed please let me know. > >> > --Nasser > >> > > >> > > >> > On Sunday, February 5, 2023 at 4:17:44 AM UTC-6 Dima Pasechnik wrote: > >> >> > >> >> On Sun, Feb 5, 2023 at 9:58 AM Dima Pasechnik <[email protected]> wrote: > >> >> > > >> >> > 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* > >> >> > >> >> please also check that > >> >> > >> >> ldd > >> >> local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/numpy/core/_multiarray_umath.cpython-310-x86_64-linux-gnu.so > >> >> > >> >> has openblas in its output. > >> >> > >> >> > > >> >> > > >> >> > > > > >> >> > > > >> >> > > "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 :-)) > >> >> > >> >>>> > >> >> > >> >>>> > >> >> > >> >>>> > >> >> > >> >>>> > > >> >> > >> >>>> > > >> >> > >> >>>> > > >> >> > >> >>>> > -- > >> >> > >> >>>> > You received this message because you are subscribed to the > >> >> > >> >>>> > Google Groups "sage-release" group. > >> >> > >> >>>> > To unsubscribe from this group and stop receiving emails > >> >> > >> >>>> > from it, send an email to [email protected]. > >> >> > >> >>>> > To view this discussion on the web visit > >> >> > >> >>>> > https://groups.google.com/d/msgid/sage-release/d6aecaee-279a-45f8-a645-36483d72a382n%40googlegroups.com. > >> >> > >> >>> > >> >> > >> >>> -- > >> >> > >> >>> You received this message because you are subscribed to the > >> >> > >> >>> Google Groups "sage-release" group. > >> >> > >> >>> To unsubscribe from this group and stop receiving emails from > >> >> > >> >>> it, send an email to [email protected]. > >> >> > >> >>> > >> >> > >> >>> To view this discussion on the web visit > >> >> > >> >>> https://groups.google.com/d/msgid/sage-release/4a516a44-b761-4f02-ac10-e121cadc54d3n%40googlegroups.com. > >> >> > >> > > >> >> > >> > -- > >> >> > >> > You received this message because you are subscribed to the > >> >> > >> > Google Groups "sage-release" group. > >> >> > >> > To unsubscribe from this group and stop receiving emails from > >> >> > >> > it, send an email to [email protected]. > >> >> > >> > To view this discussion on the web visit > >> >> > >> > https://groups.google.com/d/msgid/sage-release/4d86cb2d-8c03-4101-904e-21a1a1ce8b93n%40googlegroups.com. > >> >> > > > >> >> > > -- > >> >> > > You received this message because you are subscribed to the Google > >> >> > > Groups "sage-release" group. > >> >> > > To unsubscribe from this group and stop receiving emails from it, > >> >> > > send an email to [email protected]. > >> >> > > To view this discussion on the web visit > >> >> > > https://groups.google.com/d/msgid/sage-release/2660c6b9-57cd-4d75-b0f8-97636bbfaf71n%40googlegroups.com. > >> > > >> > -- > >> > You received this message because you are subscribed to the Google > >> > Groups "sage-release" group. > >> > To unsubscribe from this group and stop receiving emails from it, send > >> > an email to [email protected]. > >> > To view this discussion on the web visit > >> > https://groups.google.com/d/msgid/sage-release/f362b0db-0f36-4c03-9949-473954352652n%40googlegroups.com. > > > > -- > > You received this message because you are subscribed to the Google Groups > > "sage-release" group. > > To unsubscribe from this group and stop receiving emails from it, send an > > email to [email protected]. > > To view this discussion on the web visit > > https://groups.google.com/d/msgid/sage-release/dcab8085-34af-40db-aaf7-e26db1c4dae6n%40googlegroups.com. -- You received this message because you are subscribed to the Google Groups "sage-release" group. 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