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
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'
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'
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(+)