Error when makeing Sage

[Éricles Lima]

I get an error when running the `make` step of the Sage building as described in the readme.

More specifically, I get:

"

Error building Sage.

The following package(s) may have failed to build (not necessarily
during this run of 'make all-start'):

* package:         python3-3.12.5
  last build time: Jan 2 22:25

"

I'm running on a Lenovo LOQ, with Ubuntu 24.04.1.

The error message indicates to get in touch with the two log files that I send in attachment.

I'm afraid this might have something to do with my miniconda install, but I'm not sure what. Searched for similar problems, but didn't find much.

Any help is appreciated!

Also, happy new year :)

[Eric Gourgoulhon]

If you are on Ubuntu 24.04, I would advise to install SageMath along these lines:

https://sagemanifolds.obspm.fr/install_ubuntu.html

Best wishes,

Eric.

[Henri Girard]

It's easier to make it with eric suggestion I don't want to use conda in ubuntu because debs python are natives

I even compile with 25.04 ubuntu dev version

best

HG

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[Éricles Lima]

But that's basically what I did before - the steps on that sagemanifolds website are basically the same listed on the github: clone -> make configure -> ./configure -> make

And the error it gets me is the same (failure to build python3-3.12.5).

I tried deactivating conda to see whether I'd get a different behavior, but it only added one item to the error log (now it fails to build linbox-1.7.0+sage-2024-05-18 as well).

Does someone have an idea what's going on? :/

[Dima Pasechnik]

Your error indicates that your system Python3 was rejected for some reason.
Please post the top-level config.log - it contains the needed details.

> To view this discussion visit https://groups.google.com/d/msgid/sage-support/994b0c78-9667-4347-91c4-067b00b750b6n%40googlegroups.com.

[Éricles Lima]

Is there more than one config.log?

I considering copying the one I found below, but the formatting became too awful, so I add it again as an attachment here (it's also attached to my first message in this discussion)

Thanks beforehand! Also, let me know if there's any more information you need

[Dima Pasechnik]

On Fri, Jan 3, 2025 at 12:15 PM Éricles Lima
<ericlesaq...@gmail.com> wrote:
>
> Is there more than one config.log?
>
> I considering copying the one I found below, but the formatting became too awful, so I add it again as an attachment here (it's also attached to my first message in this discussion)
>
> Thanks beforehand! Also, let me know if there's any more information you need
>
>
>
> Em sexta-feira, 3 de janeiro de 2025 às 13:26:16 UTC-3, dim...@gmail.com escreveu:
>>
>> Your error indicates that your system Python3 was rejected for some reason.
>> Please post the top-level config.log - it contains the needed details.
>>

there is a line

configure:155509: result: python3: using system
package; SPKG will not be installed

which means that

>> Error building Sage.
>>
>> The following package(s) may have failed to build (not necessarily
>> during this run of 'make all-start'):
>>
>> * package: python3-3.12.5
>> last build time: Jan 2 22:25

actually does not refer to the current error.
(or something is off)

Can you remove logs/install.log and logs/pkgs/*

and run

make

again?
If it fails, send logs/install.log

> To view this discussion visit https://groups.google.com/d/msgid/sage-support/f2fbdb17-2797-4e20-b9ee-f8f452f8dda0n%40googlegroups.com.

[Éricles Lima]

It's funny... why should removing log files change the error obtained?

Anyway, it did. Now it fails when building gmpy:

Error building Sage.

The following package(s) may have failed to build (not necessarily
during this run of 'make all-start'):

* package:         gmpy2-2.2.0a1
  last build time: Jan 5 15:54

  log file:        /home/ericles/Documents/Aprendizado/Unicamp/Mestrado/Lattices/sage/sage/logs/pkgs/gmpy2-2.2.0a1.log

Then, as I look in the log file (that I attach here), it there's a 404 Not Found complaint:

Attempting to download package gmpy2-2.2.0a1.tar.gz from mirrors
https://github.com/sagemath/sage/releases/download/10.6/gmpy2-2.2.0a1.tar.gz
[xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx]
ERROR [transfer|run:135]: [Errno socket error] [Errno 404] Not Found: '//github.com/sagemath/sage/releases/download/10.6/gmpy2-2.2.0a1.tar.gz'
https://github.com/sagemath/sage/releases/download/10.5/gmpy2-2.2.0a1.tar.gz

And, indeed, the link github.com/sagemath/sage/releases/download/10.6/gmpy2-2.2.0a1.tar.gz is invalid.

I searched and it seems people had compatibility problems of python with gmpy before, so I downgraded my python to v=3.10. It didn't work though.

Any ideas?

[Dima Pasechnik]

On 5 January 2025 14:04:20 GMT-06:00, "Éricles Lima"

<ericlesaq...@gmail.com> wrote:
>It's funny... why should removing log files change the error obtained?

less scrolling to look for the real error.

>
>Anyway, it did. Now it fails when building gmpy:
>
>
>
>
>
>
>

>*Error building Sage.The following package(s) may have failed to build (not
>necessarilyduring this run of 'make all-start'):* package:
>gmpy2-2.2.0a1 last build time: Jan 5 15:54*
>* log file:
> /home/ericles/Documents/Aprendizado/Unicamp/Mestrado/Lattices/sage/sage/logs/pkgs/gmpy2-2.2.0a1.log*
>
>Then, as I look in the log file (that I attach here), it there's a *404 Not
>Found *complaint:
>
>
>
>
>
>
>*Attempting to download package gmpy2-2.2.0a1.tar.gz from
>mirrorshttps://github.com/sagemath/sage/releases/download/10.6/[xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx]ERROR

>[transfer|run:135]: [Errno socket error] [Errno 404] Not Found:

>'//github.com/sagemath/sage/releases/download/10.6/gmpy2-2.2.0a1.tar.gz'https://github.com/sagemath/sage/releases/download/10.5/gmpy2-2.2.0a1.tar.gz*
>
>And, indeed, the link *github.com/sagemath/sage/releases/download/10.6/gmpy2-2.2.0a1.tar.gz
>*is invalid.

Did you scroll to the end of this log file? By right, gmpy2 can be found in
https://files.pythonhosted.org/packages/source/g/gmpy2/gmpy2-VERSION.tar.gz
where VERSION is in
build/pkgs/gmpy2/package-version.txt
(which is 2.2.0a1)

So you either had a catastrophic internet connectivity disruption, or
the error is different, not related
to downloading.

>
>I searched and it seems people had compatibility problems of python with
>gmpy before, so I downgraded my python to v=3.10. It didn't work though.
>Any ideas?

Please dig up the real error.
gmpy2 - this version - does work with Python 3.12/11/10...

>> https://groups.google.com/d/msgid/sage-support/994b0c78-9667-4347-91c4-067b00b750b6n%40googlegroups.com
>> .

>> >
>> > --
>> > You received this message because you are subscribed to the Google
>> Groups "sage-support" group.
>> > To unsubscribe from this group and stop receiving emails from it, send
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>> > To view this discussion visit

>> https://groups.google.com/d/msgid/sage-support/f2fbdb17-2797-4e20-b9ee-f8f452f8dda0n%40googlegroups.com
>> .
>>
>

[Jan Groenewald]

Hi

On Mon, 6 Jan 2025 at 02:03, Dima Pasechnik <dim...@gmail.com> wrote:

On 5 January 2025 14:04:20 GMT-06:00, "Éricles Lima"
<ericlesaq...@gmail.com> wrote:
>*Attempting to download package gmpy2-2.2.0a1.tar.gz from
>mirrorshttps://github.com/sagemath/sage/releases/download/10.6/[xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx]ERROR
>[transfer|run:135]: [Errno socket error] [Errno 404] Not Found:
>'//github.com/sagemath/sage/releases/download/10.6/gmpy2-2.2.0a1.tar.gz'https://github.com/sagemath/sage/releases/download/10.5/gmpy2-2.2.0a1.tar.gz*
>
>And, indeed, the link *github.com/sagemath/sage/releases/download/10.6/gmpy2-2.2.0a1.tar.gz
>*is invalid.

 Note 10.5 vs 10.6 in the link.

10.5 is working.

Regards,

Jan

 

 

[Éricles Lima]

Now I downgraded to python 10.5, and it stopped yielding that error (also, there's evidence gmpy2 had issues with newer python version , but I'm not entirely sure that is related).

However, it's now failing on building scipy :/

There's a similar error in this thread of this group, but it seems to fail at a different step, so I'm not sure it's related.

A relevant part of the log file is as follows

[spkg-install] [343/1610] Linking target scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so
[spkg-install] FAILED: scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so
[spkg-install] /home/ericles/miniconda3/bin/x86_64-conda-linux-gnu-gfortran  -o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/meson-g
enerated_..__interpolativemodule.c.o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_dfft.f.o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_id_rand
.f.o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_id_rtrans.f.o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_idd_frm.f.o scipy/linalg/_interpol
ative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_idd_house.f.o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_idd_id.f.o scipy/linalg/_interpolative.cpython-312-x86_64-lin
ux-gnu.so.p/src_id_dist_src_idd_id2svd.f.o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_idd_qrpiv.f.o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_
src_idd_sfft.f.o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_idd_snorm.f.o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_idd_svd.f.o scipy/lina
lg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_iddp_aid.f.o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_iddp_asvd.f.o scipy/linalg/_interpolative.cpython-
312-x86_64-linux-gnu.so.p/src_id_dist_src_iddp_rid.f.o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_iddp_rsvd.f.o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/
src_id_dist_src_iddr_aid.f.o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_iddr_asvd.f.o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_iddr_rid.f
.o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_iddr_rsvd.f.o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_idz_frm.f.o scipy/linalg/_interpolat
ive.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_idz_house.f.o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_idz_id.f.o scipy/linalg/_interpolative.cpython-312-x86_64-linux
-gnu.so.p/src_id_dist_src_idz_id2svd.f.o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_idz_qrpiv.f.o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_sr
c_idz_sfft.f.o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_idz_snorm.f.o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_idz_svd.f.o scipy/linalg
/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_idzp_aid.f.o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_idzp_asvd.f.o scipy/linalg/_interpolative.cpython-31
2-x86_64-linux-gnu.so.p/src_id_dist_src_idzp_rid.f.o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_idzp_rsvd.f.o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/sr
c_id_dist_src_idzr_aid.f.o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_idzr_asvd.f.o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_idzr_rid.f.o
 scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_idzr_rsvd.f.o scipy/linalg/_interpolative.cpython-312-x86_64-linux-gnu.so.p/src_id_dist_src_prini.f.o -L/home/ericles/miniconda3/b
in/../lib/gcc/x86_64-conda-linux-gnu/13.3.0 -L/home/ericles/miniconda3/lib/gcc/x86_64-conda-linux-gnu/13.3.0 -L/home/ericles/miniconda3/bin/../lib/gcc -L/home/ericles/miniconda3/lib/gcc -L/home/ericles/Documen
ts/Aprendizado/Unicamp/Mestrado/Lattices/sage/sage/local/lib/../lib -L/home/ericles/Documents/Aprendizado/Unicamp/Mestrado/Lattices/sage/sage/local/lib -L/home/ericles/miniconda3/bin/../lib/gcc/x86_64-conda-li
nux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/lib/../lib -L/home/ericles/miniconda3/x86_64-conda-linux-gnu/lib -L/home/ericles/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../lib -L/hom
e/ericles/miniconda3/lib -L/home/ericles/miniconda3/bin/../x86_64-conda-linux-gnu/sysroot/lib/../lib -L/home/ericles/miniconda3/x86_64-conda-linux-gnu/sysroot/lib64 -L/home/ericles/miniconda3/bin/../x86_64-con
da-linux-gnu/sysroot/usr/lib/../lib -L/home/ericles/miniconda3/x86_64-conda-linux-gnu/sysroot/usr/lib64 -L/home/ericles/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gn
u/lib -L/home/ericles/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../.. -L/home/ericles/miniconda3/bin/../x86_64-conda-linux-gnu/sysroot/lib -L/home/ericles/miniconda3/bin/../x86_64-conda-linux-
gnu/sysroot/usr/lib -I/home/ericles/miniconda3/include -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-rpath-link,/home/ericles/Documents/Aprendizado/Unicamp/Mestrado/Lattices/sage/sage/
local/lib -Wl,-rpath,/home/ericles/Documents/Aprendizado/Unicamp/Mestrado/Lattices/sage/sage/local/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/ericles/miniconda3/lib -Wl,-rpath-link,/home/ericles/miniconda3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/ericles/miniconda3/include -Wl,--start-group scipy/lib_fortranobject.a -Wl,--version-script=/home/ericles/Documents/Aprendizado/Unicamp/Mestrado/Lattices/sage/sage/local/var/lib/sage/venv-python3.12.5/var/tmp/sage/build/scipy-1.12.0/src/scipy/_build_utils/link-version-pyinit.map /home/ericles/miniconda3/lib/libopenblas.so -lgfortran -lm -Wl,--end-group
[spkg-install] /home/ericles/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/ericles/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/lib/../lib/libgfortran.a(async.o): relocation R_X86_64_TPOFF32 against symbol `thread_unit' can not be used when making a shared object; recompile with -fPIC
[spkg-install] /home/ericles/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: failed to set dynamic section sizes: bad value
[spkg-install] collect2: error: ld returned 1 exit status

[spkg-install] [344/1610] Compiling C object scipy/special/_test_internal.cpython-312-x86_64-linux-gnu.so.p/meson-generated__test_internal.c.o
[spkg-install] [345/1610] Compiling Fortran object scipy/special/libspecfun.a.p/specfun_specfun.f.o
[spkg-install] [346/1610] Generating 'scipy/special/cython_special.cpython-312-x86_64-linux-gnu.so.p/cython_special.c'
[spkg-install] [347/1610] Compiling C object scipy/linalg/_matfuncs_sqrtm_triu.cpython-312-x86_64-linux-gnu.so.p/meson-generated__matfuncs_sqrtm_triu.c.o
[spkg-install] [348/1610] Compiling C object scipy/linalg/_solve_toeplitz.cpython-312-x86_64-linux-gnu.so.p/meson-generated__solve_toeplitz.c.o
[spkg-install] [349/1610] Compiling C++ object scipy/special/_ufuncs_cxx.cpython-312-x86_64-linux-gnu.so.p/meson-generated__ufuncs_cxx.cpp.o
[spkg-install] [350/1610] Compiling C object scipy/linalg/_fblas.cpython-312-x86_64-linux-gnu.so.p/meson-generated_..__fblasmodule.c.o
[spkg-install] [351/1610] Generating 'scipy/linalg/cython_lapack.cpython-312-x86_64-linux-gnu.so.p/cython_lapack.c'
[spkg-install] [352/1610] Generating 'scipy/linalg/_decomp_update.cpython-312-x86_64-linux-gnu.so.p/_decomp_update.c'
[spkg-install] warning: scipy/linalg/_decomp_update.pyx:1227:13: noexcept clause is ignored for function returning Python object
[spkg-install] warning: scipy/linalg/_decomp_update.pyx:1359:19: noexcept clause is ignored for function returning Python object
[spkg-install] warning: scipy/linalg/_decomp_update.pyx:1381:22: noexcept clause is ignored for function returning Python object
[spkg-install] warning: scipy/linalg/_decomp_update.pyx:1832:18: noexcept clause is ignored for function returning Python object
[spkg-install] warning: scipy/linalg/_decomp_update.pyx:1980:18: noexcept clause is ignored for function returning Python object
[spkg-install] [353/1610] Compiling C object scipy/linalg/cython_blas.cpython-312-x86_64-linux-gnu.so.p/meson-generated_cython_blas.c.o
[spkg-install] [354/1610] Compiling C object scipy/linalg/_decomp_lu_cython.cpython-312-x86_64-linux-gnu.so.p/meson-generated__decomp_lu_cython.c.o
[spkg-install] [355/1610] Compiling C object scipy/special/_ufuncs.cpython-312-x86_64-linux-gnu.so.p/meson-generated__ufuncs.c.o
[spkg-install] [356/1610] Generating scipy/linalg/flapack_module with a custom command
[spkg-install] ninja: build stopped: subcommand failed.
[spkg-install]
[spkg-install] ERROR Backend subprocess exited when trying to invoke build_wheel
[spkg-install] ********************************************************************************
[spkg-install] Error building a wheel for scipy-1.12.0
[spkg-install] ********************************************************************************
************************************************************************
Error installing package scipy-1.12.0
************************************************************************

I'm puzzled as to what is generating this.

But I'm just posting this just for record though, as what I did then is I got an older notebook, 

with older versions of everything, and then I managed to install sage with no problems, and I'll use that for now.

Thanks for your kind attention.

If I make some advance in this error at a later time, I'll post here later.

Also, if someone experiences a similar error and if I may be of help, feel free to get in touch.