Error when installing Sage from source

[Ishaan Jolly]

Hi,

I am very new to Sage, and software development in particular. I recently tried cloning the GitHub repo, and installing Sage from root. However, on running make, I failed. I was wondering if some assitance could be provided. Here is the error message:

[ppl-1.2.p1] Package 'ppl' is currently not installed
[ppl-1.2.p1] No legacy uninstaller found for 'ppl'; nothing to do
[ppl-1.2.p1] Configuring ppl-1.2.p1
[ppl-1.2.p1] configure: WARNING: unrecognized options: --disable-maintainer-mode
[ppl-1.2.p1] checking build system type... Invalid configuration `arm64-apple-darwin20.0.0': machine `arm64-apple' not recognized
[ppl-1.2.p1] configure: error: /bin/bash ./config.sub arm64-apple-darwin20.0.0 failed
[ppl-1.2.p1] checking build system type... Invalid configuration `arm64-apple-darwin20.0.0': machine `arm64-apple' not recognized
[ppl-1.2.p1] configure: error: /bin/bash ./config.sub arm64-apple-darwin20.0.0 failed
[ppl-1.2.p1] *************************************************************************************
[ppl-1.2.p1] Error configuring ppl-1.2.p1 See the file
[ppl-1.2.p1]     /Users/ishaanjolly/Programs/sage/local/var/tmp/sage/build/ppl-1.2.p1/src/config.log
[ppl-1.2.p1] for details.
[ppl-1.2.p1] *************************************************************************************
[ppl-1.2.p1] Error configuring PPL with both C and C++ interfaces, trying
[ppl-1.2.p1] again with only the C++ interface.
[ppl-1.2.p1] Configuring ppl-1.2.p1
[ppl-1.2.p1] configure: WARNING: unrecognized options: --disable-maintainer-mode
[ppl-1.2.p1] checking build system type... Invalid configuration `arm64-apple-darwin20.0.0': machine `arm64-apple' not recognized
[ppl-1.2.p1] configure: error: /bin/bash ./config.sub arm64-apple-darwin20.0.0 failed
[ppl-1.2.p1] checking build system type... Invalid configuration `arm64-apple-darwin20.0.0': machine `arm64-apple' not recognized
[ppl-1.2.p1] configure: error: /bin/bash ./config.sub arm64-apple-darwin20.0.0 failed
[ppl-1.2.p1] *************************************************************************************
[ppl-1.2.p1] Error configuring ppl-1.2.p1 See the file
[ppl-1.2.p1]     /Users/ishaanjolly/Programs/sage/local/var/tmp/sage/build/ppl-1.2.p1/src/config.log
[ppl-1.2.p1] for details.
[ppl-1.2.p1] *************************************************************************************
[ppl-1.2.p1]
[ppl-1.2.p1] real    0m1.080s
[ppl-1.2.p1] user    0m0.244s
[ppl-1.2.p1] sys    0m0.302s
[ppl-1.2.p1] ************************************************************************
[ppl-1.2.p1] Error installing package ppl-1.2.p1
[ppl-1.2.p1] ************************************************************************
[ppl-1.2.p1] Please email sage-devel (http://groups.google.com/group/sage-devel)
[ppl-1.2.p1] explaining the problem and including the log files
[ppl-1.2.p1]   /Users/ishaanjolly/Programs/sage/logs/pkgs/ppl-1.2.p1.log
[ppl-1.2.p1] and
[ppl-1.2.p1]   /Users/ishaanjolly/Programs/sage/config.log
[ppl-1.2.p1] Describe your computer, operating system, etc.
[ppl-1.2.p1] If you want to try to fix the problem yourself, *don't* just cd to
[ppl-1.2.p1] /Users/ishaanjolly/Programs/sage/local/var/tmp/sage/build/ppl-1.2.p1 and type 'make' or whatever is appropriate.
[ppl-1.2.p1] Instead, the following commands setup all environment variables
[ppl-1.2.p1] correctly and load a subshell for you to debug the error:
[ppl-1.2.p1]   (cd '/Users/ishaanjolly/Programs/sage/local/var/tmp/sage/build/ppl-1.2.p1' && '/Users/ishaanjolly/Programs/sage/sage' --buildsh)
[ppl-1.2.p1] When you are done debugging, you can type "exit" to leave the subshell.
[ppl-1.2.p1] ************************************************************************
make[4]: *** [ppl-SAGE_LOCAL-no-deps] Error 1
make[3]: *** [/Users/ishaanjolly/Programs/sage/local/var/lib/sage/installed/ppl-1.2.p1] Error 2
make[2]: *** [all-start] Error 2

real    3m17.156s
user    2m26.222s
sys    0m18.146s
***************************************************************
Error building Sage.

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

* package:         ppl-1.2.p1
  last build time: 14 May 20:50
  log file:        /Users/ishaanjolly/Programs/sage/logs/pkgs/ppl-1.2.p1.log
  build directory: /Users/ishaanjolly/Programs/sage/local/var/tmp/sage/build/ppl-1.2.p1

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.

make[1]: *** [all-start] Error 1
make: *** [all] Error 2

And here is the log file:

[Matthias Koeppe]

Please take a look at the notes for the Apple Silicon platform at https://trac.sagemath.org/wiki/ReleaseTours/sage-9.6#Sources

If the problem persists, please send the top-level config.log file

[Ishaan Jolly]

Unfortunately, this error continues to persist. My machine (M1 mac) is not able to find ppl and Sage is not able to build it from source.  The error log suggests to write here so just making an attempt. It would be lovely if some could please assist me with this.

```

[ppl-1.2.p1] C compiler: arm64-apple-darwin20.0.0-clang
[ppl-1.2.p1] C compiler version:
[ppl-1.2.p1] clang version 13.0.1
[ppl-1.2.p1] Target: arm64-apple-darwin20.0.0
[ppl-1.2.p1] Thread model: posix
[ppl-1.2.p1] InstalledDir: /Users/ishaanjolly/miniforge3/envs/ox/bin
[ppl-1.2.p1] ****************************************************

[ppl-1.2.p1] Package 'ppl' is currently not installed
[ppl-1.2.p1] No legacy uninstaller found for 'ppl'; nothing to do
[ppl-1.2.p1] Configuring ppl-1.2.p1
[ppl-1.2.p1] configure: WARNING: unrecognized options: --disable-maintainer-mode
[ppl-1.2.p1] checking build system type... Invalid configuration `arm64-apple-darwin20.0.0': machine `arm64-apple' not recognized

[ppl-1.2.p1] configure: error: /opt/homebrew/bin/bash ./config.sub arm64-apple-darwin20.0.0 failed

[ppl-1.2.p1] checking build system type... Invalid configuration `arm64-apple-darwin20.0.0': machine `arm64-apple' not recognized

[ppl-1.2.p1] configure: error: /opt/homebrew/bin/bash ./config.sub arm64-apple-darwin20.0.0 failed
[ppl-1.2.p1] ********************************************************************************

[ppl-1.2.p1] Error configuring ppl-1.2.p1 See the file

[ppl-1.2.p1]     /Users/ishaanjolly/sage/local/var/tmp/sage/build/ppl-1.2.p1/src/config.log
[ppl-1.2.p1] for details.
[ppl-1.2.p1] ********************************************************************************

[ppl-1.2.p1] Error configuring PPL with both C and C++ interfaces, trying
[ppl-1.2.p1] again with only the C++ interface.
[ppl-1.2.p1] Configuring ppl-1.2.p1
[ppl-1.2.p1] configure: WARNING: unrecognized options: --disable-maintainer-mode
[ppl-1.2.p1] checking build system type... Invalid configuration `arm64-apple-darwin20.0.0': machine `arm64-apple' not recognized

[ppl-1.2.p1] configure: error: /opt/homebrew/bin/bash ./config.sub arm64-apple-darwin20.0.0 failed

[ppl-1.2.p1] checking build system type... Invalid configuration `arm64-apple-darwin20.0.0': machine `arm64-apple' not recognized

[ppl-1.2.p1] configure: error: /opt/homebrew/bin/bash ./config.sub arm64-apple-darwin20.0.0 failed
[ppl-1.2.p1] ********************************************************************************

[ppl-1.2.p1] Error configuring ppl-1.2.p1 See the file

[ppl-1.2.p1]     /Users/ishaanjolly/sage/local/var/tmp/sage/build/ppl-1.2.p1/src/config.log
[ppl-1.2.p1] for details.
[ppl-1.2.p1] ********************************************************************************
[ppl-1.2.p1]
[ppl-1.2.p1] real    0m1.068s
[ppl-1.2.p1] user    0m0.254s
[ppl-1.2.p1] sys    0m0.322s

[ppl-1.2.p1] ************************************************************************
[ppl-1.2.p1] Error installing package ppl-1.2.p1
[ppl-1.2.p1] ************************************************************************
[ppl-1.2.p1] Please email sage-devel (http://groups.google.com/group/sage-devel)
[ppl-1.2.p1] explaining the problem and including the log files

[ppl-1.2.p1]   /Users/ishaanjolly/sage/logs/pkgs/ppl-1.2.p1.log
[ppl-1.2.p1] and
[ppl-1.2.p1]   /Users/ishaanjolly/sage/config.log

[ppl-1.2.p1] Describe your computer, operating system, etc.
[ppl-1.2.p1] If you want to try to fix the problem yourself, *don't* just cd to

[ppl-1.2.p1] /Users/ishaanjolly/sage/local/var/tmp/sage/build/ppl-1.2.p1 and type 'make' or whatever is appropriate.

[ppl-1.2.p1] Instead, the following commands setup all environment variables
[ppl-1.2.p1] correctly and load a subshell for you to debug the error:

[ppl-1.2.p1]   (cd '/Users/ishaanjolly/sage/local/var/tmp/sage/build/ppl-1.2.p1' && '/Users/ishaanjolly/sage/sage' --buildsh)

[ppl-1.2.p1] When you are done debugging, you can type "exit" to leave the subshell.
[ppl-1.2.p1] ************************************************************************
make[4]: *** [ppl-SAGE_LOCAL-no-deps] Error 1

make[3]: *** [/Users/ishaanjolly/sage/local/var/lib/sage/installed/ppl-1.2.p1] Error 2

make[2]: *** [all-start] Error 2

real    0m3.750s
user    0m2.353s
sys    0m0.732s

***************************************************************
Error building Sage.

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

* package:         ppl-1.2.p1

  last build time: 2 Jun 18:37
  log file:        /Users/ishaanjolly/sage/logs/pkgs/ppl-1.2.p1.log
  build directory: /Users/ishaanjolly/sage/local/var/tmp/sage/build/ppl-1.2.p1

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

```

Please see the attached ppl-1.2 p1.log file below.

Thank you for your time!

[Matthias Koeppe]

As I wrote before: "If the problem persists, please send the top-level config.log file"

[Ishaan Jolly]

Very sorry, it still doesn't work. Please find the config.log file along with this email. Would be very grateful if someone can please assist me. Thank you!

[Matthias Koeppe]

With the config.log posted, it looks like you are trying to use homebrew together with conda.

Either deactivate the conda environment and follow the instructions for homebrew,

or follow the instructions for conda in the Sage installation manual.

[Ishaan Jolly]

When running ./configure it says to conda activate ENVIRONMENT. I thought due to this that sage built is dependent on conda for this reason. Clearly, this doesn't seem to be the case, so how might I get pass this?

[Matthias Koeppe]

As I said: "Either deactivate the conda environment [...]

or follow the instructions for conda [...]."

Which of the two do you pick?

[Ishaan Jolly]

Hi Matthias,

Thanks, I chose conda deactivate. I had base conda working so that's what caused the issue. Thanks for pointing it out. Unfortunately, I have still not managed to install Sage.

It now says

```

* package:         openblas-0.3.20
  last build time: 5 Jun 20:02
  log file:        /Users/ishaanjolly/SageMath/sage/logs/pkgs/openblas-0.3.20.log
  build directory: /Users/ishaanjolly/SageMath/sage/local/var/tmp/sage/build/openblas-0.3.20

```

I already have openblas installed through brew. If you could please see the config.log file?

[Matthias Koeppe]

At the end of the configure run, the following message was printed:

    hint: installing the following system packages, if not already present, is recommended and may avoid having to build them (though some may have to be built anyway): 

 $ brew install arb boost ecl flint fplll glpk gmp gsl xz libmpc mpfi mpfr ntl openblas openssl pari pari-elldata pari-galdata pari-galpol pari-seadata ppl python3 qhull r readline singular suite-sparse zeromq

[Matthias Koeppe]

Another message:

    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/ishaanjolly/SageMath/sage/.homebrew-build-env

[Ishaan Jolly]

I already have the packages listed in brew. Here's the list of packages I have: 

```

aom            jpeg            node@16
arb            jpeg-turbo        nspr
arpack            jpeg-xl            nss
assimp            lame            ntl
autoconf        leptonica        open-mpi
automake        libarchive        openblas
bash            libass            opencore-amr
bdw-gc            libatomic_ops        openexr
berkeley-db        libavif            openjpeg
bison            libb2            openldap
boost            libbluray        openssl@1.1
brotli            libcbor            openssl@3
bzip2            libde265        opus
c-ares            libevent        osi
ca-certificates        libffi            p11-kit
cairo            libfido2        pandoc
cbc            libheif            pango
cgal            libiconv        pari
cgl            libidn            pari-elldata
cjson            libidn2            pari-galdata
clp            liblqr            pari-galpol
cmake            libmng            pari-seadata
cmocka            libmpc            pcre
coinutils        libnghttp2        pcre2
crystal            libogg            pdf2svg
curl            libomp            perl
dav1d            libpng            pixman
dbus            libpthread-stubs    pkg-config
docbook            libraw            polymake
docbook-xsl        librist            poppler
double-conversion    librsvg            ppl
ecl            libsamplerate        primesieve
eigen            libsndfile        protobuf
ffmpeg            libsodium        pyt...@3.10
flac            libsoxr            python@3.8
flint            libssh2            python@3.9
fontconfig        libtasn1        qhull
fplll            libtiff            qt
freetype        libtool            r
frei0r            libunistring        rav1e
fribidi            libuv            readline
gcc            libvidstab        rtmpdump
gd            libvmaf            rubberband
gdbm            libvorbis        sdl2
gdk-pixbuf        libvpx            shared-mime-info
gengetopt        libx11            singular
gettext            libxau            six
ghostscript        libxcb            snappy
giflib            libxdmcp        spatialindex
git-lfs            libxext            speex
glib            libxrender        sqlite
glpk            libyaml            srt
gmp            little-cms2        suite-sparse
gnu-getopt        llvm            swig
gnutls            lz4            tbb
go            lzo            tcl-tk
gobject-introspection    m4            tesseract
gpatch            macos-term-size        texinfo
graphite2        mbedtls            theora
graphviz        md4c            tox
gsl            metis            unbound
gts            mongodb-community    webp
guile            mongodb-database-tools    wget
harfbuzz        mongosh            x264
highs            mpdecimal        x265
hunspell        mpfi            xmlto
hwloc            mpfr            xorgproto
icu4c            mysql            xvid
igraph            nauty            xz
imagemagick        ncurses            zeromq
imath            netpbm            zimg
isl            nettle            zlib
jasper            ninja            zstd
jbig2dec        node@14

```

Sorry for the copy paste. I will try to direct to .homebrew-build-env although I did do this step.

[Ishaan Jolly]

Hi all,

I just wanted to close off this thread. I was able to successfully install Sage! I did make the build, though. It seems there were some issues with my brew installations.

Thanks a lot, Matthias, and hopefully, now I can get on to what I initially set out to contribute.

Ishaan

[Ishaan Jolly]

Just thought of asking when making a symbolic link and being able to do `sage` from the terminal. I think I am facing a small problem in the photo below:

I was wondering if someone could please assist me with this. Thanks.

--
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/7225be20-01c7-4493-b6a9-290d2a93282cn%40googlegroups.com.

[Niranjana K M]

Hi,

    It should be

     /usr/local/bin/sage 

while making the symbolic link.

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/CAMKq_Jb0%2BUoiByTDLNjeeLswOdajWeMN0AZPjHmFvZWg4wZ%2B4Q%40mail.gmail.com.

[Ishaan Jolly]

It says `(base) ishaanjolly@Ishaans-MacBook-Pro ~ % sudo ln -s $(./sage -sh -c 'ls $SAGEROOT/venv/bin/sage') /usr/local/bin/sage

zsh: no such file or directory: ./sage`

Did I do something wrong? I set SAGEROOT=/Users/ishaanjolly/SageMath/sage

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/CAMcUJ1u%3Du%3D5xHFCo%3DnoP-qPr1j70qjXC%3DpspW3PNMnxo8%3Dt%2BvQ%40mail.gmail.com.

[Matthias Koeppe]

It's SAGE_ROOT, not SAGEROOT

[Ishaan Jolly]

Um, yes, however it still does not work.

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/c8f131cf-9f3e-42b1-86de-f677b1b1a2c0n%40googlegroups.com.

[Matthias Koeppe]

You need to run this command from the source directory of Sage, not from your home directory.

[Ishaan Jolly]

Thanks Mattihas ! :) It works.

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/62229df7-95ac-4f79-aee0-319b561f48bcn%40googlegroups.com.

[Ishaan Jolly]

Oops, I meant Matthias - my apologies.