Not preserving old libs is relative to the above portage and installed dev-libs/mpfr-3.1.6 which installs libmpfr.so.4.1.6. Profile: Available profile symlink targets: [1] prefix/linux/amd64 [2] prefix/linux-standalone/amd64 [3] prefix/linux-standalone/amd64/legacy [4] default/linux/amd64/17.0/no-multilib/prefix/kernel-3.2+ * [5] default/linux/amd64/17.0/no-multilib/prefix/kernel-2.6.32+ [6] default/linux/amd64/17.0/no-multilib/prefix/kernel-2.6.16+ with gcc version 7.2.0 (Gentoo 7.2.0-r1 p1.1) A recent emerge of the latest sage-9999 from the sage-on-gentoo overlay requires emerge -1 sage Calculating dependencies... done! [ebuild U #] dev-libs/mpfr-4.0.0-r1 [3.1.6] [ebuild N #] sci-mathematics/sage-9999 USE="debug doc-html doc-pdf sagenb testsuite -X -bliss -latex -libbraiding -libhomfly -modular_decomposition" L10N="en -ca -de -es -fr -hu -it -ja -pt -ru -tr" PYTHON_TARGETS="python2_7 -python3_6" Presently, mpfr-4.0.0-r1 is package masked. --- # 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-r1 --- I do not have 'FEATURES=-preserve-libs' set in make.conf. After unmasking mpfr-4.0.0-r1 the emerge of sage gives emerge -1p sage These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild r U #] dev-libs/mpfr-4.0.0-r1 [3.1.6] [ebuild rR ] dev-libs/mpc-1.1.0-r1 [ebuild rR ] sci-libs/mpfi-1.5.2 [ebuild rR ] sci-mathematics/flint-2.5.2-r1 [ebuild rR ] sci-mathematics/arb-2.12.0 [ebuild rR ] sci-libs/linbox-1.5.2 [ebuild rR ] sci-mathematics/giac-1.4.9.45 [ebuild rR ] app-text/texlive-core-2017-r3 [ebuild N #] sci-mathematics/sage-9999 USE="debug doc-html doc-pdf sagenb testsuite -X -bliss -latex -libbraiding -libhomfly -modular_decomposition" L10N="en -ca -de -es -fr -hu -it -ja -pt -ru -tr" PYTHON_TARGETS="python2_7 -python3_6" After proceeding with the emerge @preserved-rebuild required one rebuild of sci-libs/fplll which oddly completed. sage-9999 was not actually installed due to a patching error. Everything else was rebuilt during the emerge step. eix -I fplll [I] sci-libs/fplll Available versions: 4.0.4 5.0.3(0/2.0)[1] 5.1.0-r1(0/3.0)[1] 5.2.0(0/4.0)[1] {static-libs} Installed versions: 5.2.0(0/4.0)[1](05:55:43 PM 01/28/2018)(-static-libs) Homepage: https://github.com/fplll/fplll Description: Different implementations of the floating-point LLL reduction algorithm [1] "sage-on-gentoo" /storage/strogdon/gentoo-rap/var/lib/layman/sage-on-gentoo Upon completing the @preserved-rebuild request I discovered that my gcc was broken. See https://github.com/cschwan/sage-on-gentoo/issues/497 for more elaborate documentation. To recover I linked to the host (debian) libmpfr (libmpfr.so.4.1.0) and rebuilt the Prefix libmpfr.so.4.1.6 using dev-libs/mpfr-3.1.6. So there was a required rebuild but the old mpfr libs were not preserved which broke gcc. I didn't check before the rebuild of fplll as to whether the old libs were present, but since the rebuild completed I suspect they were. Which may suggest that @preserved-rebuild removed them.
There are further issues with this particular upgrade but the main point is that gcc broke because libmpfr.so.3{,.xx} has been removed when it should have been preserved. My understanding is that by default libraries are preserved in FEATURES so this shouldn't have happened.
Possibly a fault of the mpfr-4.0.0-r1 ebuild rather than portage, see bug 642316.
Check if the ebuild that you used had this commit: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=02da1bfffe30537bf7fe7680fc628acc9d6ec289
(In reply to Zac Medico from comment #3) > Check if the ebuild that you used had this commit: > > https://gitweb.gentoo.org/repo/gentoo.git/commit/ > ?id=02da1bfffe30537bf7fe7680fc628acc9d6ec289 Yes, the ebuild I used had the commit.
(In reply to Zac Medico from comment #3) > Check if the ebuild that you used had this commit: > > https://gitweb.gentoo.org/repo/gentoo.git/commit/ > ?id=02da1bfffe30537bf7fe7680fc628acc9d6ec289 It should, he specified mpfr-4.0.0-r1. And that commit goes from 4.0.0 to 4.0.0-r1. My last comment on #642316 was for a different issue where some code will trigger ICE if you upgrade mpfr then mpc but not gcc immediately after that.
OK, 2nd attempt. I unmasked mpfr-4.0.0-r1 and installed it. Old mpfr libs are preserved 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 /storage/strogdon/gentoo-rap/usr/lib/libmpfr.so.6 /storage/strogdon/gentoo-rap/usr/lib/libmpfr.so.6.0.0 However, gcc is not in my list of rebuilds emerge -p @preserved-rebuild These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] sci-libs/fplll-5.2.0 I'm now sure if I simply run emerge @preserved-rebuild the old mpfr libs will be deleted and my gcc will be broken. Instead, at this point, I rebuilt gcc and then performed the @preserved-rebuild. This then required a manual emerge of dev-python/fpylll because of 'stale' links to the old mpfr libs. But my gcc seems fine.
Created attachment 586400 [details, diff] prefix-preserve-libs.patch Hi Zac, I have been bitten by the same bug, and finally found the root cause is that portage looked into ROOT for consumers of a shared library, which returns nothing on Prefix. Here is a patch that fixes this long standing bug. Benda
(In reply to Benda Xu from comment #7) > Created attachment 586400 [details, diff] [details, diff] > prefix-preserve-libs.patch Looks good, except it should use self._dbapi.settings['EROOT'], since portage.const.EPREFIX is not necessarily correct for a cross-prefix configuration which has two independent EPREFIX values.
(In reply to Zac Medico from comment #8) > (In reply to Benda Xu from comment #7) > > Created attachment 586400 [details, diff] [details, diff] [details, diff] > > prefix-preserve-libs.patch > > Looks good, except it should use self._dbapi.settings['EROOT'], since > portage.const.EPREFIX is not necessarily correct for a cross-prefix > configuration which has two independent EPREFIX values. Agreed. I have overlooked it, sorry. Benda
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/proj/portage.git/commit/?id=1120e6f62feb1aa0d3202beb00c01537d352f420 commit 1120e6f62feb1aa0d3202beb00c01537d352f420 Author: Benda Xu <heroxbd@gentoo.org> AuthorDate: 2019-08-10 02:26:12 +0000 Commit: Zac Medico <zmedico@gentoo.org> CommitDate: 2019-08-11 18:07:43 +0000 lib/p/util/_dyn_libs/LinkageMapELF.py: get dep graph from EROOT. On Prefix, the preserve-libs feature should search for shared libraries consumers from EROOT instead of ROOT. Bug: https://bugs.gentoo.org/646090 Signed-off-by: Zac Medico <zmedico@gentoo.org> lib/portage/util/_dyn_libs/LinkageMapELF.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-)
Thanks, Zac!
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=08557524dc6c8eec3a366e43ab2587d2cdd8f133 commit 08557524dc6c8eec3a366e43ab2587d2cdd8f133 Author: Zac Medico <zmedico@gentoo.org> AuthorDate: 2019-08-19 04:24:07 +0000 Commit: Zac Medico <zmedico@gentoo.org> CommitDate: 2019-08-19 05:06:15 +0000 sys-apps/portage: Bump to version 2.3.72 #463952 glsa-check: install in /usr/bin #646090 preserve-libs: get dep graph from EROOT #690484 detect internal collisions for /usr merge #690786 repoman: support metadata/layout.conf restrict-allowed #691776 unpack: Unconditionally die if an unpacker returns an error #691638 Show get/setfattr stderr #692024 econf: Unconditionally die on error in EAPIs 0 to 3 #692262 QA Notice: EXPORT_FUNCTIONS is called before inherit in kernel-2.eclass #692412 emerge IndexError for ambiguous package atom with pypy Bug: https://bugs.gentoo.org/691278 Bug: https://bugs.gentoo.org/463952 Bug: https://bugs.gentoo.org/646090 Bug: https://bugs.gentoo.org/690484 Bug: https://bugs.gentoo.org/690786 Bug: https://bugs.gentoo.org/691776 Bug: https://bugs.gentoo.org/691638 Bug: https://bugs.gentoo.org/692024 Bug: https://bugs.gentoo.org/692262 Bug: https://bugs.gentoo.org/692412 Package-Manager: Portage-2.3.71, Repoman-2.3.17 Signed-off-by: Zac Medico <zmedico@gentoo.org> sys-apps/portage/Manifest | 1 + sys-apps/portage/portage-2.3.72.ebuild | 264 +++++++++++++++++++++++++++++++++ 2 files changed, 265 insertions(+)
