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Bug 671130

Summary: sci-mathematics/Macaulay2-1.8.2.1-r1 fails to build at "make -C flint fetch"
Product: Gentoo Linux Reporter: Cyp <cyp561>
Component: Current packagesAssignee: Gentoo Science Mathematics related packages <sci-mathematics>
Status: RESOLVED WONTFIX    
Severity: normal CC: treecleaner
Priority: Normal Keywords: PMASKED
Version: unspecified   
Hardware: All   
OS: Linux   
Whiteboard:
Package list:
Runtime testing required: ---

Description Cyp 2018-11-14 11:55:08 UTC
I have sci-mathematics/flint-2.4.4-r1 installed.

Trying to emerge sci-mathematics/Macaulay2-1.8.2.1-r1, it seems to want to download it instead of using the installed one, and the emerge fails.

From emerging sci-mathematics/Macaulay2-1.8.2.1-r1:
> >>> Source configured.
> >>> Compiling source in /var/tmp/portage/sci-mathematics/Macaulay2-1.8.2.1-r1/work/M2/M2 ...
> make -j8 IgnoreExampleErrors=true -j1 
> make: Entering directory '/var/tmp/portage/sci-mathematics/Macaulay2-1.8.2.1-r1/work/M2/M2'
> : "checking for strings that look like undefined configure variables in all *.in files..."
> : creating or removing symbolic link to common staging area, if necessary,
> : based on comparision of these directories:
> :                      pre_prefix : /var/tmp/portage/sci-mathematics/Macaulay2-1.8.2.1-r1/work/M2/M2/usr-dist/common
> : abs_builddir/usr-dist/common : /var/tmp/portage/sci-mathematics/Macaulay2-1.8.2.1-r1/work/M2/M2/usr-dist/common
> rm -f srcdir .link-test
> echo "./" >srcdir
> rm -f M2
> echo 'exec /var/tmp/portage/sci-mathematics/Macaulay2-1.8.2.1-r1/work/M2/M2/usr-dist/x86_64-Linux-Gentoo/bin/M2 "$@"' >M2
> chmod a+x M2
> make -C libraries all
> make[1]: Entering directory '/var/tmp/portage/sci-mathematics/Macaulay2-1.8.2.1-r1/work/M2/M2/libraries'
> make -C mpir fetch
> make[2]: Entering directory '/var/tmp/portage/sci-mathematics/Macaulay2-1.8.2.1-r1/work/M2/M2/libraries/mpir'
> make[2]: Nothing to be done for 'fetch'.
> make[2]: Leaving directory '/var/tmp/portage/sci-mathematics/Macaulay2-1.8.2.1-r1/work/M2/M2/libraries/mpir'
> make -C mpfr fetch
> make[2]: Entering directory '/var/tmp/portage/sci-mathematics/Macaulay2-1.8.2.1-r1/work/M2/M2/libraries/mpfr'
> make[2]: Nothing to be done for 'fetch'.
> make[2]: Leaving directory '/var/tmp/portage/sci-mathematics/Macaulay2-1.8.2.1-r1/work/M2/M2/libraries/mpfr'
> make -C ntl fetch
> make[2]: Entering directory '/var/tmp/portage/sci-mathematics/Macaulay2-1.8.2.1-r1/work/M2/M2/libraries/ntl'
> make[2]: Nothing to be done for 'fetch'.
> make[2]: Leaving directory '/var/tmp/portage/sci-mathematics/Macaulay2-1.8.2.1-r1/work/M2/M2/libraries/ntl'
> make -C flint fetch
> make[2]: Entering directory '/var/tmp/portage/sci-mathematics/Macaulay2-1.8.2.1-r1/work/M2/M2/libraries/flint'
> error: for the third-party library or program source "flint"
>        the source code is not present in the file "/var/tmp/portage/sci-mathematics/Macaulay2-1.8.2.1-r1/work/M2/M2/BUILD/tarfiles/flint-2.4.5.tar.gz"
>        so either download a "fat" tar file of the Macaulay2 source code
>        or rerun the Macaulay2 "configure" command with the added option "--enable-download"
>        to enable automatic downloading of the source code over the internet
> make[2]: *** [../Makefile.library:212: /var/tmp/portage/sci-mathematics/Macaulay2-1.8.2.1-r1/work/M2/M2/BUILD/tarfiles/flint-2.4.5.tar.gz] Error 1
> make[2]: Leaving directory '/var/tmp/portage/sci-mathematics/Macaulay2-1.8.2.1-r1/work/M2/M2/libraries/flint'
> make[1]: *** [Makefile:7: fetch-in-flint] Error 2
> make[1]: Leaving directory '/var/tmp/portage/sci-mathematics/Macaulay2-1.8.2.1-r1/work/M2/M2/libraries'
> make: *** [GNUmakefile:144: all-in-libraries] Error 2
> make: Leaving directory '/var/tmp/portage/sci-mathematics/Macaulay2-1.8.2.1-r1/work/M2/M2'
>  * ERROR: sci-mathematics/Macaulay2-1.8.2.1-r1::gentoo failed (compile phase):
>  *   emake failed
Comment 1 Cyp 2018-11-14 15:44:17 UTC
Tried reemerging sci-mathematics/flint2.4.4-r1, and now it gets further, but fails here:
> mpn/.libs/preinv_divrem_1.o: In function `__gmpn_preinv_divrem_1':
> /var/tmp/portage/sci-mathematics/Macaulay2-1.8.2.1-r1/work/M2/M2/libraries/mpir/build/mpir-2.6.0/mpn/preinv_divrem_1.c:56: multiple definition of `__gmpn_preinv_divrem_1'
> mpn/.libs/divrem_euclidean_qr_1.o:divrem_euclidean_qr_1.as:(.text+0x0): first defined here
> mpn/.libs/addmul_2.o: In function `__gmpn_addmul_2':
> addmul_2.as:(.text+0x0): multiple definition of `__gmpn_addmul_2'
> mpn/.libs/redc_2.o:/var/tmp/portage/sci-mathematics/Macaulay2-1.8.2.1-r1/work/M2/M2/libraries/mpir/build/mpir-2.6.0/mpn/redc_2.c:38: first defined here
> collect2: error: ld returned 1 exit status
> make[5]: *** [Makefile:714: libmpir.la] Error 1
> make[5]: Leaving directory '/var/tmp/portage/sci-mathematics/Macaulay2-1.8.2.1-r1/work/M2/M2/libraries/mpir/build/mpir-2.6.0'
Comment 2 Cyp 2018-11-14 16:03:11 UTC
Seems sci-libs/mpir-2.6.0-r2 isn't installed, although it has previously been installed.

@preserved-rebuild:
> >>> package: sci-libs/mpir-2.6.0-r2
>  *  - /usr/lib64/libmpir.so.11
>  *  - /usr/lib64/libmpir.so.11.0.0
>  *      used by /usr/lib64/Macaulay2/x86_64-Linux-Gentoo/lib/libmpirxx.so.4.0.21 (sci-mathematics/Macaulay2-1.8.2.1-r1)

If trying to emerge mpir, I get the same error as when trying to emerge Macaulay2:
> mpn/.libs/preinv_divrem_1.o: In function `__gmpn_preinv_divrem_1':
> /var/tmp/portage/sci-libs/mpir-2.6.0-r2/work/mpir-2.6.0_build/mpn/preinv_divrem_1.c:56: multiple definition of `__gmpn_preinv_divrem_1'
> mpn/.libs/divrem_euclidean_qr_1.o:divrem_euclidean_qr_1.as:(.text+0x0): first defined here
> collect2: error: ld returned 1 exit status
> make[2]: *** [Makefile:845: libmpir.la] Error 1
> make[2]: Leaving directory '/var/tmp/portage/sci-libs/mpir-2.6.0-r2/work/mpir-2.6.0_build'
Comment 3 Larry the Git Cow gentoo-dev 2019-12-07 23:50:22 UTC
The bug has been referenced in the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e38c4220a19d1fb89f091f49c10fd0b0402773e2

commit e38c4220a19d1fb89f091f49c10fd0b0402773e2
Author:     David Seifert <soap@gentoo.org>
AuthorDate: 2019-12-07 23:49:08 +0000
Commit:     David Seifert <soap@gentoo.org>
CommitDate: 2019-12-07 23:49:08 +0000

    profiles: Mask sci-mathematics/Macaulay2 for removal
    
    Bug: https://bugs.gentoo.org/345233
    Bug: https://bugs.gentoo.org/459640
    Bug: https://bugs.gentoo.org/474782
    Bug: https://bugs.gentoo.org/474784
    Bug: https://bugs.gentoo.org/474788
    Bug: https://bugs.gentoo.org/474790
    Bug: https://bugs.gentoo.org/474792
    Bug: https://bugs.gentoo.org/620942
    Bug: https://bugs.gentoo.org/631876
    Bug: https://bugs.gentoo.org/671130
    Signed-off-by: David Seifert <soap@gentoo.org>

 profiles/package.mask | 7 +++++++
 1 file changed, 7 insertions(+)