| Summary: | sci-biology/qrna-2.0.3c-r3 - EvolScoreWithRNA; ISO C99 and later do not support implicit function | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Toralf Förster <toralf> |
| Component: | Current packages | Assignee: | Gentoo Science Biology related packages <sci-biology> |
| Status: | RESOLVED FIXED | ||
| Severity: | normal | ||
| Priority: | Normal | ||
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Bug Depends on: | |||
| Bug Blocks: | 870412 | ||
| Attachments: |
emerge-info.txt
emerge-history.txt environment etc.clang.tar.bz2 etc.portage.tar.bz2 logs.tar.bz2 sci-biology:qrna-2.0.3c-r3:20221204-082951.log temp.tar.bz2 |
||
Created attachment 839721 [details]
emerge-info.txt
Created attachment 839723 [details]
emerge-history.txt
Created attachment 839725 [details]
environment
Created attachment 839727 [details]
etc.clang.tar.bz2
Created attachment 839729 [details]
etc.portage.tar.bz2
Created attachment 839731 [details]
logs.tar.bz2
Created attachment 839733 [details]
sci-biology:qrna-2.0.3c-r3:20221204-082951.log
Created attachment 839735 [details]
temp.tar.bz2
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c19c464def01a163fc04351c151a98d4048095e3 commit c19c464def01a163fc04351c151a98d4048095e3 Author: Eli Schwartz <eschwartz93@gmail.com> AuthorDate: 2024-03-21 00:25:02 +0000 Commit: Sam James <sam@gentoo.org> CommitDate: 2024-03-21 05:57:37 +0000 sci-biology/qrna: add 2.0.4 This is the 2006 edition of the software. It has a bunch of useful fixes: - it fixes Modern C porting issues - it fixes LTO errors - it incorporates the glibc-2.10 patch just by upgrading! It's about time we upgrade, since it is 18 years later. Along the way we fix up the ebuild a bit: - bump to EAPI 8 - acquire an actual SRC_URI, not just the gentoo mirror - update the homepage along with the SRC_URI. The original homepage is dead, and the domain redirects to a new domain (whence comes the new distfile). It has some shortcomings too: - the distfile comes with free .svn directories, which have to be pruned. - the distfile comes without the 80mb demos To solve this, we use the old distfile (which I think only exists on Gentoo's mirror network) and gate it behind a USE=examples flag, in case anyone needs them. Closes: https://bugs.gentoo.org/862285 Closes: https://bugs.gentoo.org/884283 Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org> sci-biology/qrna/Manifest | 1 + sci-biology/qrna/files/qrna-2.0.4-ldflags.patch | 381 ++++++++++++++++++++++++ sci-biology/qrna/qrna-2.0.4.ebuild | 61 ++++ 3 files changed, 443 insertions(+) |
clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DASSERT -I../squid -c ../src/qrnaversion.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DASSERT -I../squid -c ../src/evolemissions.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DASSERT -I../squid -c ../src/evolscorewithmodels.c ../src/evolscorewithmodels.c:422:3: error: call to undeclared function 'EvolScoreWithRNA'; ISO C99 and later do not support implicit function declarations [-Werror,-Wimplicit-function-declaration] EvolScoreWithRNA(ofp, sqinfoX, isegX, sqinfoY, isegY, gss, 0, win, emo... ------------------------------------------------------------------- This is an unstable amd64 chroot image at a tinderbox (==build bot) name: 17.1-j4-20221203-182649 ------------------------------------------------------------------- GNUMAKEFLAGS="$GNUMAKEFLAGS --jobserver-style=pipe" GNUMAKEFLAGS="$GNUMAKEFLAGS --shuffle" CC=clang CXX=clang++ gcc-config -l: [1] x86_64-pc-linux-gnu-12 * clang/llvm (if any): clang version 15.0.6 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/lib/llvm/15/bin Configuration file: /etc/clang/clang.cfg /usr/lib/llvm/15 15.0.6 Python 3.10.8 Available Rust versions: [1] rust-bin-1.65.0 * The following VMs are available for generation-2: *) Eclipse Temurin JDK 17.0.5_p8 [openjdk-bin-17] 2) Eclipse Temurin JDK 8.352_p08 [openjdk-bin-8] Available Java Virtual Machines: [1] openjdk-bin-8 [2] openjdk-bin-17 system-vm php cli (if any): HEAD of ::gentoo commit 86202b966705bfd2e3bb5ed53bb44f24f93c31c5 Author: Repository mirror & CI <repomirrorci@gentoo.org> Date: Sun Dec 4 07:31:49 2022 +0000 2022-12-04 07:31:48 UTC emerge -qpvO sci-biology/qrna [ebuild N ] sci-biology/qrna-2.0.3c-r3