Upgrade arb and fix FLINT includes

[jdemeyer]

Upstream: ​http://sage.ugent.be/www/jdemeyer/sage/arb-2.7.0.tar.bz2 (packaged from git repo since upstream doesn't seem to provide tarballs)

Pull request: ​https://github.com/fredrik-johansson/arb/pull/55

[fbissey]

One doctest failure after straight upgrading arb (linux 64bit).

sage -t --long usr/lib/python2.7/site-packages/sage/rings/real_arb.pyx
**********************************************************************
File "usr/lib/python2.7/site-packages/sage/rings/real_arb.pyx", line 2620, in sage.rings.real_arb.RealBall.log_gamma
Failed example:
    RBF(1/2).log_gamma()
Expected:
    [0.572364942924700 +/- 4.87e-16]
Got:
    [0.572364942924700 +/- 2.67e-16]
**********************************************************************
1 item had failures:
   1 of   3 in sage.rings.real_arb.RealBall.log_gamma
    [494 tests, 1 failure, 0.30 s]
----------------------------------------------------------------------
sage -t --long usr/lib/python2.7/site-packages/sage/rings/real_arb.pyx  # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 0.5 seconds
    cpu time: 0.3 seconds
    cumulative wall time: 0.3 seconds

[fbissey]

Oh there is a tarball at https://github.com/fredrik-johansson/arb/archive/2.7.0.tar.gz but of course as a lot of those coming from github it has to be renamed.

[jdemeyer]

Replying to fbissey:

Oh there is a tarball at https://github.com/fredrik-johansson/arb/archive/2.7.0.tar.gz

Right, this is what I meant with "packaged from git repo".

[jdemeyer]

Last 10 new commits:

​ab117da	complex_ball: abort() --> sig_error()
​1ee8c16	ref manual: rm reference to arb being optional
​865e6d5	{real,complex}_arb: more doc on precision issues
​d289538	{real,complex}_arb: move SEEALSO blocks after EXAMPLES
​fe1b071	RealBall: clarify doc of upper(), lower(), endpoints()
​a38574a	complex_arb is no longer experimental
​d5af324	{real,complex}_arb: minor doc fixes
​f43e94a	RealBall: minor change to __hash__
​7e6b5d0	real_arb: minor doc fix
​c4fe46c	Upgrade to arb 2.7.0 and fix flint includes

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​ac6e2c3

Fix arb doctest failure in log_gamma()

[fbissey]

I am surprised making arb a standard package didn't cause any issue on OS X 10.11. The library lack an install_name which has been the sources of trouble just building there. A small fix just like in cliquer's spkg-install would do the trick

if [ "$UNAME" = "Darwin" ]; then
    install_name_tool -id "${SAGE_LOCAL}"/lib/libarb.dylib "${SAGE_LOCAL}"/lib/libarb.dylib
fi

[jdemeyer]

Replying to fbissey:

I am surprised making arb a standard package didn't cause any issue on OS X 10.11. The library lack an install_name which has been the sources of trouble just building there.

Is this problem related to the upgrade of arb?

[fbissey]

Replying to jdemeyer:

Replying to fbissey:

I am surprised making arb a standard package didn't cause any issue on OS X 10.11. The library lack an install_name which has been the sources of trouble just building there.

Is this problem related to the upgrade of arb?

Arguably it should have been dealt with in #18546 or earlier.

[jdemeyer]

Replying to fbissey:

I am surprised making arb a standard package didn't cause any issue on OS X 10.11. The library lack an install_name which has been the sources of trouble just building there. A small fix just like in cliquer's spkg-install would do the trick

if [ "$UNAME" = "Darwin" ]; then
    install_name_tool -id "${SAGE_LOCAL}"/lib/libarb.dylib "${SAGE_LOCAL}"/lib/libarb.dylib
fi

This is now #19627.

[vbraun]

The arb testsuite dies with

$ SAGE_CHECK=yes ./sage -p arb
...
Successfully installed arb-2.7.0.p0
Running the test suite for arb-2.7.0.p0...
make[1]: warning: -jN forced in submake: disabling jobserver mode.
make[1]: Entering directory '/mnt/disk/home/release/Sage/local/var/tmp/sage/build/arb-2.7.0.p0/src'
make[1]: Nothing to be done for 'shared'.
make[1]: Leaving directory '/mnt/disk/home/release/Sage/local/var/tmp/sage/build/arb-2.7.0.p0/src'
make[1]: warning: -jN forced in submake: disabling jobserver mode.
make[1]: Entering directory '/mnt/disk/home/release/Sage/local/var/tmp/sage/build/arb-2.7.0.p0/src'
make[1]: Nothing to be done for 'static'.
make[1]: Leaving directory '/mnt/disk/home/release/Sage/local/var/tmp/sage/build/arb-2.7.0.p0/src'
make[1]: warning: -jN forced in submake: disabling jobserver mode.
make[1]: Entering directory '/mnt/disk/home/release/Sage/local/var/tmp/sage/build/arb-2.7.0.p0/src'
make[2]: Entering directory '/mnt/disk/home/release/Sage/local/var/tmp/sage/build/arb-2.7.0.p0/src'
make[2]: warning: -jN forced in submake: disabling jobserver mode.
make[2]: Nothing to be done for 'shared'.
make[2]: Leaving directory '/mnt/disk/home/release/Sage/local/var/tmp/sage/build/arb-2.7.0.p0/src'
make[2]: Entering directory '/mnt/disk/home/release/Sage/local/var/tmp/sage/build/arb-2.7.0.p0/src'
make[2]: warning: -jN forced in submake: disabling jobserver mode.
make[2]: Nothing to be done for 'static'.
make[2]: Leaving directory '/mnt/disk/home/release/Sage/local/var/tmp/sage/build/arb-2.7.0.p0/src'
make[1]: Leaving directory '/mnt/disk/home/release/Sage/local/var/tmp/sage/build/arb-2.7.0.p0/src'
make[1]: warning: -jN forced in submake: disabling jobserver mode.
make[1]: Entering directory '/mnt/disk/home/release/Sage/local/var/tmp/sage/build/arb-2.7.0.p0/src/fmpr'
    CC   ../build/fmpr/test/t-add
    CC   ../build/fmpr/test/t-set_fmpq
    CC   ../build/fmpr/test/t-root
    CC   ../build/fmpr/test/t-mul
    CC   ../build/fmpr/test/t-sub
    CC   ../build/fmpr/test/t-exp
    CC   ../build/fmpr/test/t-abs_bound_lt_2exp_si
    CC   ../build/fmpr/test/t-mul_si
    CC   ../build/fmpr/test/t-set_round_ui_2exp_fmpz
    CC   ../build/fmpr/test/t-get_d
test/t-mul_si.c:27:25: fatal error: long_extras.h: No such file or directory
compilation terminated.
../Makefile.subdirs:78: recipe for target '../build/fmpr/test/t-mul_si' failed
make[1]: *** [../build/fmpr/test/t-mul_si] Error 1
make[1]: *** Waiting for unfinished jobs....
make[1]: Leaving directory '/mnt/disk/home/release/Sage/local/var/tmp/sage/build/arb-2.7.0.p0/src/fmpr'
Makefile:169: recipe for target 'check' failed
make: *** [check] Error 2

Thoughts?

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​d6c3c85

Fix more includes

[jdemeyer]

I forgot to change some includes. With this patch, the testsuite passes. Since I'm just adding a few changes in the spirit of the old branch, I assume the positive review still stands.