Sage 8.3 build from source on Debian 7 fails

[wout.d...@gmail.com]

This is what I try to do:

  wget ftp://ftp.fu-berlin.de/unix/misc/sage/src/sage-8.3.tar.gz

  tar -xzf sage-8.3.tar.gz

  cd sage-8.3

  ./bootstrap

  ./configure --prefix=./local/sage

  make

I get the following errors when it is installing the Sage packages:

.../sage/var/tmp/sage/build/mpfr-4.0.1/src/missing: line 81: automake-1.15: command not found

WARNING: 'automake-1.15' is missing on your system.

         You should only need it if you modified 'Makefile.am' or

         'configure.ac' or m4 files included by 'configure.ac'.

         The 'automake' program is part of the GNU Automake package:

         <http://www.gnu.org/software/automake>

         It also requires GNU Autoconf, GNU m4 and Perl in order to run:

         <http://www.gnu.org/software/autoconf>

         <http://www.gnu.org/software/m4/>

         <http://www.perl.org/>

make[5]: *** [Makefile.in] Error 127

...

.../sage/var/tmp/sage/build/patch-2.7.5/src/build-aux/missing: line 81: automake-1.14: command not found

WARNING: 'automake-1.14' is missing on your system.

         You should only need it if you modified 'Makefile.am' or

         'configure.ac' or m4 files included by 'configure.ac'.

         The 'automake' program is part of the GNU Automake package:

         <http://www.gnu.org/software/automake>

         It also requires GNU Autoconf, GNU m4 and Perl in order to run:

         <http://www.gnu.org/software/autoconf>

         <http://www.gnu.org/software/m4/>

         <http://www.perl.org/>

make[4]: *** [Makefile.in] Error 127

...

.../sage/var/tmp/sage/build/patch-2.7.5/src/build-aux/missing: line 81: aclocal-1.14: command not found

WARNING: 'aclocal-1.14' is missing on your system.

         You should only need it if you modified 'acinclude.m4' or

         'configure.ac' or m4 files included by 'configure.ac'.

         The 'aclocal' program is part of the GNU Automake package:

         <http://www.gnu.org/software/automake>

         It also requires GNU Autoconf, GNU m4 and Perl in order to run:

         <http://www.gnu.org/software/autoconf>

         <http://www.gnu.org/software/m4/>

         <http://www.perl.org/>

make[2]: *** [aclocal.m4] Error 127

The system's automake version is 1.11.

I tried "autoreconf -ivf" instead of bootstrap but this doesn't change anything (basically the same thing).

I also tried installing automake 1.14 and 1.15 which results in similar messages by other packages related to a missing automake or aclocal version.

Any ideas?

[John H Palmieri]

You shouldn't have to do './bootstrap'. Try again from the beginning but leave that part off. (This may involve deleting the existing sage-8.3 directory and unpacking the tarball again.) Does that help?

[Dima Pasechnik]

indeed, bootstrap is only needed if you install from "bare" source rather than from a ready to install tarball. There you'd only need ./configure (in case you need some non-default settings) and make, or just make if defaults are OK.

[wout.d...@gmail.com]

At first I did use ./configure followed by make but I had the same issue. I thought maybe "./bootstrap" or "autoreconf -fi" would have solved the problem, but unfortunately no.

[Stephen Weston]

I have the same kind of problem on a RHEL 7.4 system. After investigating the issue, it appears that some Makefiles are trying to rebuild files (such as Makefile.in) because they are out-of-date with respect to their dependencies (such as Makefile.am) because, although they exist, their timestamp makes it appear that it needs to be rebuilt. It looks like in the process of untarring the upstream tarballs the timestamps aren't preserved, so they may be rebuilt erroneously.

It's odd that I hit different errors on a different runs, but patch-2.7.5 often fails with:

[patch-2.7.5] Building patch-2.7.5

[patch-2.7.5] make[2]: Entering directory `/gpfs/loomis/home.grace/fas/hpcprog/sw464/sage-8.3/local/var/tmp/sage/build/patch-2.7.5/src'

[patch-2.7.5] CDPATH="${ZSH_VERSION+.}:" && cd . && /usr/bin/bash /gpfs/loomis/home.grace/fas/hpcprog/sw464/sage-8.3/local/var/tmp/sage/build/patch-2.7.5/src/build-aux/missing aclocal-1.14 -I m4

[patch-2.7.5] /gpfs/loomis/home.grace/fas/hpcprog/sw464/sage-8.3/local/var/tmp/sage/build/patch-2.7.5/src/build-aux/missing: line 81: aclocal-1.14: command not found

[patch-2.7.5] WARNING: 'aclocal-1.14' is missing on your system.

[patch-2.7.5]          You should only need it if you modified 'acinclude.m4' or

[patch-2.7.5]          'configure.ac' or m4 files included by 'configure.ac'.

[patch-2.7.5]          The 'aclocal' program is part of the GNU Automake package:

[patch-2.7.5]          <http://www.gnu.org/software/automake>

[patch-2.7.5]          It also requires GNU Autoconf, GNU m4 and Perl in order to run:

[patch-2.7.5]          <http://www.gnu.org/software/autoconf>

[patch-2.7.5]          <http://www.gnu.org/software/m4/>

[patch-2.7.5]          <http://www.perl.org/>

[patch-2.7.5] make[2]: *** [aclocal.m4] Error 127

[patch-2.7.5] make[2]: Leaving directory `/gpfs/loomis/home.grace/fas/hpcprog/sw464/sage-8.3/local/var/tmp/sage/build/patch-2.7.5/src'

[patch-2.7.5] ********************************************************************************

[patch-2.7.5] Error building patch-2.7.5

Here's a listing of the timestamps where the make failure occurred:

$ ls -l

total 3520

-rw-r--r-- 1 sw464 hpcprog  67297 Sep  7 18:37 aclocal.m4

-rw-r--r-- 1 sw464 hpcprog    335 Sep  7 18:37 AUTHORS

-rwxr-xr-x 1 sw464 hpcprog  29454 Sep  7 18:37 bootstrap

drwxr-xr-x 3 sw464 hpcprog   4096 Sep  7 18:37 build-aux

-rw-r--r-- 1 sw464 hpcprog   1320 Sep  7 18:37 cfg.mk

-rw-r--r-- 1 sw464 hpcprog  47117 Sep  7 18:37 ChangeLog

-rw-r--r-- 1 sw464 hpcprog 142258 Sep  7 18:37 ChangeLog-2011

-rw-rw-r-- 1 sw464 hpcprog  63448 Sep  7 18:37 config.h

-rw-r--r-- 1 sw464 hpcprog  61280 Sep  7 18:37 config.hin

-rw-rw-r-- 1 sw464 hpcprog 417883 Sep  7 18:37 config.log

-rwxrwxr-x 1 sw464 hpcprog  68741 Sep  7 18:37 config.status

-rwxr-xr-x 1 sw464 hpcprog 657356 Sep  7 18:37 configure

-rw-r--r-- 1 sw464 hpcprog   5731 Sep  7 18:37 configure.ac

[snip]

The timestamps of the files in the upstream tarball are quite different, and don't cause "make" to trigger any rebuilds that require automake.

So what's going on during the installation process that causes this problem on RHEL 7.4, and possibly Debian 7 as well? I'm using a GPFS file system. Could that cause this problem?

[Dima Pasechnik]

This looks like a typical situation with old autotools. One is
seriously out of luck there.
Depending upon what you mean by "building from source" (it should
also be possible to build
from a distribution tarball...)
Would be be possible to install more up to date autotools?

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[Stephen Weston]

Are you building from a local filesystem or a distributed filesystem? It seems to build successfully for me when using a local hard drive, but fails when using a GPFS filesystem.

On Friday, August 10, 2018 at 2:18:55 PM UTC-4, wout.d...@gmail.com wrote:

[Stephen Weston]

I've been using autoconf 2.69 which appears to be the current version. I've tried automake 1.13, 1.14, 1.14.1, 1.15, 1.15.1, and combinations of those. Nothing worked while performing the build on GPFS. And note that I had no trouble when building Sage 6.9 in the past.

But the Sage documentation for building from source seems to say that autotools isn't a prerequisite for a source install unless you're modifying things like Malefile.am:

WARNING: 'automake-1.15' is missing on your system.

         You should only need it if you modified 'Makefile.am' or

         'configure.ac' or m4 files included by 'configure.ac'.

Since I'm not modifying anything, it seems like something stranger is going on.

Note that I've downloaded the sage-8.3.tar.gz tarball (containing the upstream tarballs) from the Sage mirrors, as well as from github. Both failed in the same way.