Created attachment 438684 [details, diff] ncbi-tools-2.2.26-r2.ebuild.patch On Gentoo:Prefix I get: make CFLAGS1="-DNDEBUG -O2 -pipe -O2 -pipe -march=native -c " LDFLAGS1="-O2 -pipe -O2 -pipe -march=native -Wl,-O1" OTHERLIBS="-lm" SHELL="/scratch/mmokrejs/gentoo/scratch/mmokrejs/gentoo/bin/sh" ... where you can see the '/scratch/mmokrejs/gentoo' is included twice. We can at least undo this in the ebuild.
Alternatively you can just drop the line: -e "/NCBI_MAKE_SHELL *=/s:=.*:= \"${EPREFIX}/bin/sh\":g" \ or if you really want a clean solution that figure out why the following sed \ -re "s:/usr(/bin/.*sh):\1:g" \ -e "s:(/bin/.*sh):${EPREFIX}\1:g" \ -i $(find "${S}" -type f) || die matched lines with '^NCBI_MAKE_SHELL =' which are then re-processed *again*.
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=59b2be273d92b67c4c7f581657151a5e7cbb63ae commit 59b2be273d92b67c4c7f581657151a5e7cbb63ae Author: Jakov Smolić <jsmolic@gentoo.org> AuthorDate: 2021-08-30 17:17:23 +0000 Commit: Jakov Smolić <jsmolic@gentoo.org> CommitDate: 2021-08-30 17:38:50 +0000 sci-biology/ncbi-tools: Remove last-rited package Closes: https://bugs.gentoo.org/649930 Closes: https://bugs.gentoo.org/782790 Closes: https://bugs.gentoo.org/741188 Closes: https://bugs.gentoo.org/715636 Closes: https://bugs.gentoo.org/710338 Closes: https://bugs.gentoo.org/701340 Closes: https://bugs.gentoo.org/586982 Closes: https://bugs.gentoo.org/295584 Signed-off-by: Jakov Smolić <jsmolic@gentoo.org> profiles/package.mask | 6 - sci-biology/ncbi-tools/Manifest | 1 - sci-biology/ncbi-tools/files/21ncbi-r1 | 6 - .../files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch | 81 ---------- .../files/ncbi-tools-2.2.26-bfr-overflow.patch | 103 ------------- .../files/ncbi-tools-2.2.26-format-security.patch | 124 --------------- .../ncbi-tools/files/ncbi-tools-extra_vib.patch | 37 ----- sci-biology/ncbi-tools/files/ncbi-tools-lop.patch | 15 -- sci-biology/ncbi-tools/files/ncbirc | 2 - sci-biology/ncbi-tools/metadata.xml | 8 - sci-biology/ncbi-tools/ncbi-tools-2.2.26-r3.ebuild | 169 --------------------- 11 files changed, 552 deletions(-)
It is still developed, see https://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2021/Aug_18_2021/README.html , albeit in c++. However, for those of use who have issues on some hosts to get that compiled, we were happy to use an older implementation in C. Why didn't you just just go the --without-x or --disable-x way? Why dropping the whole bundle? Please restore the package.
(In reply to Martin Mokrejš from comment #3) > It is still developed, see > https://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2021/Aug_18_2021/ > README.html , albeit in c++. However, for those of use who have issues on > some hosts to get that compiled, we were happy to use an older > implementation in C. > > Why didn't you just just go the --without-x or --disable-x way? Why dropping > the whole bundle? > > Please restore the package. Please see https://bugs.gentoo.org/701340#c13
