slot conflict dev-libs/mpfr::0 when building 8.2.beta4

[strogdon]

I'm sure everyone will see this

!!! Multiple package instances within a single package slot have been pulled
!!! into the dependency graph, resulting in a slot conflict:

dev-libs/mpfr:0

  (dev-libs/mpfr-4.0.0-r1:0/6::gentoo, ebuild scheduled for merge) pulled in by
    >=dev-libs/mpfr-4.0.0 required by (sci-mathematics/sage-9999:0/0::sage-on-gentoo, ebuild scheduled for merge)
    ^^              ^^^^^                                                                                                                                               

  (dev-libs/mpfr-3.1.6:0/4::gentoo, installed) pulled in by
    dev-libs/mpfr:0/4= required by (sci-libs/linbox-1.5.2:0/0::sage-on-gentoo, installed)
                 ^^^^^

when building the subject beta4. But what to do, unmask dev-libs/mpfr-4.0.0-r1? If so won't this require rebuilding gcc? And can now gcc rebuild itself?

[kiwifb]

I am planning to do a post on gentoo-science at some point. Note that the fun has already started on sage-release and sage-devel because of mpfr-4.
So mpfr-4 is masked in package.mask

# Matthias Maier <tamiko@gentoo.org> (26 Dec 2017)
# gcc depends on mpfr and this version changes soname. Spare users with
# FEATURES=-preserve-libs from completely frying their system.
>=dev-libs/mpfr-4.0.0

So most users will be just fine. The mpfr upgrade will trigger multiple package recompilation but gcc still has to be done manually (probably listed under revdep-rebuild). The fun bit is the rebuild of packages will break at the next to last one: giac with an ICE. The last package to rebuild is sage. Rebuilding gcc gets rid of the ICE - the debug message associated with the ICE clearly point to mpfr-3 in gcc being involved. I think something in giac could be done to fix the ICE without recompiling gcc but it is hard to figure out.
Vanilla sage user using sage's gcc get hit by the ICE too since mpfr is upgraded before giac and gcc is not rebuilt by the upgrade of mpfr.

[strogdon]

So do you plan on sage-on-gentoo users doing their own unmask of mpfr or will you supply a sage-on-gentoo explicit unmask?

[kiwifb]

I don't know yet. We only have a unmask file for some funtoo users and it is probably obsolete. As far as I am concerned definite action will only be required when 8.2 is released - people on 9999 should know about unmasking things sometimes, it's fair game. There are two timelines I don't have any control on:

• release of sage-8.2
• unmasking of mpfr-4 in Gentoo

So it will really depend on what's happening when sage reach the "rc" stage.

[strogdon]

No ICE failures here in Prefix after unmasking mpfr-4.0.0-r1 when building giac in an attempt to build Sage. But giac cannot be rebuilt and neither can gcc. I feared this. Good thing it was Prefix. So beware!

[kiwifb]

Was your libmpfr.so.3 file preserved? Is gcc even working?

[strogdon]

Apparently not. The emerge @preserved-rebuild, which was requested, only rebuilt sci-libs/fplll-5.2.0. An emerge -1 giac fails as does emerge -1 gcc with

checking whether the C compiler works... no
configure: error: in `/storage/strogdon/gentoo-rap/var/tmp/portage/sci-mathematics/giac-1.4.9.45/work/giac-1.4.9':
configure: error: C compiler cannot create executables

[kiwifb]

OK, you are just in the situation that the mask was supposed to prevent. It looks like your prefix must have FEATURES=-preserve-libs. If it is the default, that's something we'll have to bring to gentoo-alt mailing list.
To recover you may be able to link the system libmpfr.so.3 inside the prefix until you fix the compiler.
Note that the affected executables are the real compilers: cc1, cc1plus, f951 and so on in usr/libexec/gcc/$host_triplet/$gcc_version/ not gcc, g++ and gfortran which are front end compiler drivers.

[strogdon]

FEATURES=-preserve-libs is not something I set and I don't recall any recent problems with preserving libs. The linking to system mpfr will probably not work. The host is debian.

[kiwifb]

OK, forensic:

• is there a libmpfr.so.3 inside the prefix?
• if there is, does it link to an existing libmpfr.so.3.xx?
• output of emerge --info gcc
• send me /storage/strogdon/gentoo-rap/var/tmp/portage/sci-mathematics/giac-1.4.9.45/work/giac-1.4.9/config.log privately for further diagnostics.

[strogdon]

OK linking to the debian mpfr seems to have done the trick. I now have a compiler and giac was successfully rebuild.

ls /storage/strogdon/gentoo-rap/usr/lib/libmpfr*
/storage/strogdon/gentoo-rap/usr/lib/libmpfr.so
/storage/strogdon/gentoo-rap/usr/lib/libmpfr.so.4
/storage/strogdon/gentoo-rap/usr/lib/libmpfr.so.4.1.6

[kiwifb]

I think you may want to do some kind of report to gentoo-alt, this is suspicious behavior in prefix.

[strogdon]

Bug https://bugs.gentoo.org/646090. I'm not exactly sure how to refer to 'old preserved libs`, by soname or by package version name? Feel free to comment to correct any inaccuracies.

[strogdon]

It's interesting that in Prefix I didn't get an ICE when building giac. But I do get that on Gentoo.

[kiwifb]

To be honest, it smells funny. That implies something is not linked to the right version in the right place (TM).

[kiwifb]

mpfr-4 is out of mask. Hopefully everything is right here.