Bug 642944 – sci-libs/ssm-1.4 : /.../ld: /.../libmmdb2.a(mmdb_mattype.o): relocation R_X86_64_PC32 against symbol _ZN4mmdb15GetMatrixMemoryERPPdjjjj can not be used when making a shared object; recompile with -fPIC

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Toralf Förster 2018-01-01 10:55:25 UTC]

/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmmdb2.a(mmdb_cryst.o): warning: relocation against `_ZN4mmdb15StreamInitCrystERPNS_2io6StreamE' in readonly section `.text'
/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmmdb2.a(mmdb_mattype.o): relocation R_X86_64_PC32 against symbol `_ZN4mmdb15GetMatrixMemoryERPPdjjjj' can not be used when making a shared object; recompile with -fPIC
/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: final link failed: Bad value
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:513: libssm.la] Error 1

  -------------------------------------------------------------------

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.0-no-multilib-hardened_20171229-184738

  -------------------------------------------------------------------

gcc-config -l:
 [1] x86_64-pc-linux-gnu-7.2.0 *

Available Python interpreters, in order of preference:
  [1]   python3.5
  [2]   python2.7 (fallback)
Available Ruby profiles:
  [1]   ruby22 (with Rubygems) *
java-config:
The following VMs are available for generation-2:
*)	IcedTea JDK 3.6.0 [icedtea-bin-8]
Available Java Virtual Machines:
  [1]   icedtea-bin-8  system-vm

emerge -qpv sci-libs/ssm
[ebuild  N    ] sci-libs/ssm-1.4  USE="ccp4 -static-libs"

[Comment 1 Toralf Förster 2018-01-01 10:55:28 UTC]

Created attachment 512456 [details]
emerge-info.txt

[Comment 2 Toralf Förster 2018-01-01 10:55:31 UTC]

Created attachment 512458 [details]
emerge-history.txt

[Comment 3 Toralf Förster 2018-01-01 10:55:34 UTC]

Created attachment 512460 [details]
environment

[Comment 4 Toralf Förster 2018-01-01 10:55:37 UTC]

Created attachment 512462 [details]
etc.portage.tbz2

[Comment 5 Toralf Förster 2018-01-01 10:55:40 UTC]

Created attachment 512464 [details]
logs.tbz2

[Comment 6 Toralf Förster 2018-01-01 10:55:43 UTC]

Created attachment 512466 [details]
sci-libs:ssm-1.4:20180101-063224.log

[Comment 7 Toralf Förster 2018-01-01 10:55:46 UTC]

Created attachment 512468 [details]
temp.tbz2

[Comment 8 François Bissey 2018-01-02 05:17:53 UTC]

It looks like the problem is with `sci-libs/mmdb` it only installed a static library - not built with any PIC flags - when ssm is built to use a shared library (or at least a static one compiled with PIC). 

I wasn't particularly impressed with those two packages and ccp4 when I had to deal with them on the HPC cluster I used to take care of.

[Comment 9 Larry the Git Cow 2018-01-06 13:35:41 UTC]

The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=87ac2c93178e64c1e36a9cd01c0cd346cea6ce7d

commit 87ac2c93178e64c1e36a9cd01c0cd346cea6ce7d
Author:     Justin Lecher <[e-mail]>
AuthorDate: 2018-01-06 12:53:57 +0000
Commit:     Justin Lecher <[e-mail]>
CommitDate: 2018-01-06 13:35:36 +0000

    sci-libs/mmdb: Build shared libs
    
    Closes: https://bugs.gentoo.org/641534
    Closes: https://bugs.gentoo.org/642944
    Signed-off-by: Justin Lecher <[e-mail]>
    Package-Manager: Portage-2.3.19, Repoman-2.3.6

 sci-libs/mmdb/{mmdb-2.0.5.ebuild => mmdb-2.0.5-r1.ebuild} | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)