Issue build sagemath 7.2 from source.

[Pietro Liguori]

Hi all,

I try to build sagemath 7.2 from source. My computer is Red Hat Enterprise Linux Server release 5.11 (Tikanga) x86_64.

after make command i have:

Error building Sage.

The following package(s) may have failed to build (not necessarily

during this run of 'make all'):

* package: automake-1.15

  log file: /home/pietrol/Sage/sage-7.2/logs/pkgs/automake-1.15.log

  build directory: /home/pietrol/Sage/sage-7.2/local/var/tmp/sage/build/automake-1.15

* package: brial-0.8.4.3

  log file: /home/pietrol/Sage/sage-7.2/logs/pkgs/brial-0.8.4.3.log

  build directory: /home/pietrol/Sage/sage-7.2/local/var/tmp/sage/build/brial-0.8.4.3

* package: brial

  log file: /home/pietrol/Sage/sage-7.2/logs/pkgs/brial.log

  build directory: /home/pietrol/Sage/sage-7.2/local/var/tmp/sage/build/brial

The build directory may contain configuration files and other potentially

helpful information. WARNING: if you now run 'make' again, the build

directory will, by default, be deleted. Set the environment variable

SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this.

make: *** [all] Error 1

Please some one help me! 

[Dima Pasechnik]

please post some log files you got, e.g. /home/pietrol/Sage/sage-7.2/logs/pkgs/automake-1.15.log

I suspect that RedHat 5 is a system we do not test on, as it's pretty rare, and it's supposed to be updated

in 2014... Any chance you can upgrade?

[Pietro Liguori]

Here automake-1.15.log

Attempting to download package automake-1.15

Downloading the Sage mirror list

CRITICAL [mirror_list|_refresh:164]: Downloading the mirror list failed

************************************************************************

Traceback (most recent call last):

  File "/home/pietrol/Sage/sage-7.2/build/bin/../sage_bootstrap/cmdline.py", line 224, in run

    print(MirrorList().fastest)

  File "/home/pietrol/Sage/sage-7.2/build/bin/../sage_bootstrap/mirror_list.py", line 63, in __init__

    self.mirrors = self._load()

  File "/home/pietrol/Sage/sage-7.2/build/bin/../sage_bootstrap/mirror_list.py", line 78, in _load

    return ast.literal_eval(mirror_list)

  File "/home/pietrol/Sage/sage-7.2/local/lib/python/ast.py", line 49, in literal_eval

    node_or_string = parse(node_or_string, mode='eval')

  File "/home/pietrol/Sage/sage-7.2/local/lib/python/ast.py", line 37, in parse

    return compile(source, filename, mode, PyCF_ONLY_AST)

  File "<unknown>", line 0

    

    ^

SyntaxError: unexpected EOF while parsing

************************************************************************

Error downloading fastest mirror

************************************************************************

Attempting to download package automake-1.15

Downloading the Sage mirror list

CRITICAL [mirror_list|_refresh:164]: Downloading the mirror list failed

************************************************************************

Traceback (most recent call last):

  File "/home/pietrol/Sage/sage-7.2/build/bin/../sage_bootstrap/cmdline.py", line 224, in run

    print(MirrorList().fastest)

  File "/home/pietrol/Sage/sage-7.2/build/bin/../sage_bootstrap/mirror_list.py", line 63, in __init__

    self.mirrors = self._load()

  File "/home/pietrol/Sage/sage-7.2/build/bin/../sage_bootstrap/mirror_list.py", line 78, in _load

    return ast.literal_eval(mirror_list)

  File "/home/pietrol/Sage/sage-7.2/local/lib/python/ast.py", line 49, in literal_eval

    node_or_string = parse(node_or_string, mode='eval')

  File "/home/pietrol/Sage/sage-7.2/local/lib/python/ast.py", line 37, in parse

    return compile(source, filename, mode, PyCF_ONLY_AST)

  File "<unknown>", line 0

    

    ^

SyntaxError: unexpected EOF while parsing

************************************************************************

Error downloading fastest mirror

************************************************************************

[Pietro Liguori]

I'm can't upgrade this a company machine .

[Jeroen Demeyer]

On 2016-05-17 13:33, Pietro Liguori wrote:
> Hi all,
> I try to build sagemath 7.2 from source. My computer is Red Hat
> Enterprise Linux Server release 5.11 (Tikanga) x86_64.

I suggest you run "make distclean" and "make" again. If that also fails,
send the logfile of the package which failed.

[Pietro Liguori]

after make distclean and make the issue is related to gcc.

the last portion of log

See `config.log' for more details.

make[5]: *** [configure-stage1-target-libgcc] Error 1

make[5]: Leaving directory `/home/pietrol/Sage/sage-7.2/local/var/tmp/sage/build/gcc-4.9.3.p1/gcc-build'

make[4]: *** [stage1-bubble] Error 2

make[4]: Leaving directory `/home/pietrol/Sage/sage-7.2/local/var/tmp/sage/build/gcc-4.9.3.p1/gcc-build'

make[3]: *** [all] Error 2

make[3]: Leaving directory `/home/pietrol/Sage/sage-7.2/local/var/tmp/sage/build/gcc-4.9.3.p1/gcc-build'

real 12m43.553s

user 7m5.534s

sys 1m20.565s

************************************************************************

Error installing package gcc-4.9.3.p1

************************************************************************

Please email sage-devel (http://groups.google.com/group/sage-devel)

explaining the problem and including the relevant part of the log file

  /home/pietrol/Sage/sage-7.2/logs/pkgs/gcc-4.9.3.p1.log

Describe your computer, operating system, etc.

If you want to try to fix the problem yourself, *don't* just cd to

/home/pietrol/Sage/sage-7.2/local/var/tmp/sage/build/gcc-4.9.3.p1 and type 'make' or whatever is appropriate.

Instead, the following commands setup all environment variables

correctly and load a subshell for you to debug the error:

  (cd '/home/pietrol/Sage/sage-7.2/local/var/tmp/sage/build/gcc-4.9.3.p1' && '/home/pietrol/Sage/sage-7.2/sage' --sh)

When you are done debugging, you can type "exit" to leave the subshell.

************************************************************************

Il giorno martedì 17 maggio 2016 13:43:43 UTC+2, Pietro Liguori ha scritto:

[Dima Pasechnik]

This looks like a firewall issue. We did see this few times. You probably also see a lot of these

"Downloading the mirror list failed" on the main log, (in logs/install.log)

I suppose your IT needs to whitelist something for you...

[Jeroen Demeyer]

Please send the complete log

/home/pietrol/Sage/sage-7.2/logs/pkgs/gcc-4.9.3.p1.log

together with

/home/pietrol/Sage/sage-7.2/local/var/tmp/sage/build/gcc-4.9.3.p1/build/config.log

or any other config.log located inside
/home/pietrol/Sage/sage-7.2/local/var/tmp/sage/build/gcc-4.9.3.p1

[Dima Pasechnik]

I have an account on an HPC RedHat system, where I cannot build Sage, as gcc is too old to build the gcc Sage needs...

[Pietro Liguori]

inside /home/pietrol/Sage/sage-7.2/local/var/tmp/sage/build/gcc-4.9.3.p1 there isn't log file

[Pietro Liguori]

Sorry in \Sage\sage-7.2\local\var\tmp\sage\build\gcc-4.9.3.p1\gcc-build there is config.log

[Dima Pasechnik]

gcc version 3.4.3

is a non-starter.

You need at least gcc 4.something

[Dima Pasechnik]

https://access.redhat.com/solutions/19458

says that RHEL 5 should have gcc 4.1.x by default, and gcc 4.4 for "forward compatibility testing".

So that's now for your IT to provide you a gcc newer than gcc 3.4...

[Pietro Liguori]

gcc version is 4.9.3 !

[John H Palmieri]

On Tuesday, May 17, 2016 at 9:25:23 AM UTC-7, Pietro Liguori wrote:

gcc version is 4.9.3 !

That is the version Sage is trying to build, but it needs some version to get started. Early in the log file, it says

"gcc version 3.4.3"

This is the version installed on your machine, and it is too old to build gcc 4.9.3.

[Pietro Liguori]

ok, now i have gcc 4.9.3 and a the end of make there is issue related to brial package. 

attached log file.

[Dima Pasechnik]

oops, a dependence on automake (from http://trac.sagemath.org/ticket/20381, I think), should not have happened!

Either wait for this to be fixed, or install automake 1.15 or newer...

[Pietro Liguori]

Please tell me how to install manually automake. Please consider that i'm on machine without admin right.

Il giorno martedì 17 maggio 2016 13:43:43 UTC+2, Pietro Liguori ha scritto:

[Dima Pasechnik]

On Wednesday, May 18, 2016 at 1:46:11 PM UTC+1, Pietro Liguori wrote:

Please tell me how to install manually automake. Please consider that i'm on machine without admin right.

try

 

    ./sage -i autotools

(not sure if your ./sage is already is the state to do this, but it's worth a try)

Otherwise, (assuming './sage -sh' works)

fire up the Sage shell (i.e. ./sage -sh)

and there do the usual ./configure && make business 

(see https://www.lrde.epita.fr/~adl/autotools.html)

Finally, you can install things in your home directory...

In fact, IT support should install autotools for you, it's a downright standard piece of software on Linux,

comes in packages (RPMs)...

HTH,

Dima

[Pietro Liguori]

there is a way to install package from local hard disk.

[Dima Pasechnik]

on the other hand this looks really strange. Is this error reproducible?

(just run make again and see if it stops at the same place)

Is your home directory on a NFS? This might trigger weird building problems, IIRC.

[Pietro Liguori]

Yes nfs. The error still there if I redo make

[sgouezel]

Could you check if Trac #20634 solves your problem? If you are not familiar with git, the simplest way here is simply to add the line

touch aclocal.m4 configure Makefile.in

in the file build/pkgs/brial/spkg-install, just before the line

./configure \

[Pietro Liguori]

Ok another step done. Now the issue is related to numpy.

[Dima Pasechnik]

if you look at the log you will see it's actually not about numpy, but about its dependence, Atlas.

Have you got Atlas package successfully installed?

Please post logs/pkgs/atlas-3.10.2.p2.log

An alternative would be to use the system supplied ones, see

http://doc.sagemath.org/html/en/installation/source.html#environment-variables

(search for SAGE_ATLAS_LIB)

[Pietro Liguori]

Too long file

[Dima Pasechnik]

hmm, so it looks OK. 

Can you try make again (perhaps there was a parallel build problem, and atlas was not ready for numpy...)

On Friday, May 20, 2016 at 2:25:59 PM UTC+1, Pietro Liguori wrote:

Too long file