commit: 15a450fc0413b28c5a1f35b66177045544284fd9 Author: Michał Górny <mgorny <AT> gentoo <DOT> org> AuthorDate: Sun Feb 8 19:16:58 2026 +0000 Commit: Michał Górny <mgorny <AT> gentoo <DOT> org> CommitDate: Sun Feb 8 19:16:58 2026 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=15a450fc
sci-biology/rnaview: Remove last-rited pkg Bug: https://bugs.gentoo.org/944877 Signed-off-by: Michał Górny <mgorny <AT> gentoo.org> profiles/package.mask | 5 -- sci-biology/rnaview/Manifest | 1 - .../rnaview/files/rnaview-20040713-implicit.patch | 13 ---- .../rnaview/files/rnaview-20040713-makefile.patch | 87 ---------------------- sci-biology/rnaview/metadata.xml | 16 ---- sci-biology/rnaview/rnaview-20040713-r5.ebuild | 31 -------- 6 files changed, 153 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 41c7392a7eba..bbb1c854b220 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -203,11 +203,6 @@ app-emacs/docker-tramp >=dev-python/autobahn-25.10 >=dev-python/txaio-25.10 -# David Seifert <[email protected]> (2025-12-01) -# Last release over 20 years ago, ancient codebase, lots of QA warnings, no -# other distro packages this anymore. Removal on 2025-12-31. Bug #944877. -sci-biology/rnaview - # David Seifert <[email protected]> (2025-11-30) # Last release over 15 years ago, GTK+2, EAPI 7, broken C constructs, removed # by other distros already. Removal on 2025-12-30. Bug #944347. diff --git a/sci-biology/rnaview/Manifest b/sci-biology/rnaview/Manifest deleted file mode 100644 index 784acf0a7aa7..000000000000 --- a/sci-biology/rnaview/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST rnaview-20040713.tar.bz2 433916 BLAKE2B e6f52fbb90a11290728c0a67b8ccde42c1c20967c8b9810c0c1103a300d1cf1a4ee1c9e501c203ae3f3dfda29fb5851603f095931c3efedd86143793115e633b SHA512 c63bb728bad0f358ab36f4ca18f4f9ef046811f21d3b8f3c6fdd3e6e6fcb367a9a52710476c5daea001f8f3262f72b64f0c0546f0c1423f463f2e0d288809e8e diff --git a/sci-biology/rnaview/files/rnaview-20040713-implicit.patch b/sci-biology/rnaview/files/rnaview-20040713-implicit.patch deleted file mode 100644 index 90ea72ab6f8c..000000000000 --- a/sci-biology/rnaview/files/rnaview-20040713-implicit.patch +++ /dev/null @@ -1,13 +0,0 @@ -Fix implicit function declaration - ---- a/src/xml2ps.c -+++ b/src/xml2ps.c -@@ -36,7 +36,7 @@ - void read_sugar_syn(char *inpfile, long **sugar_syn); - void get_sugar_syn(FILE *inp, char *value_ch); - void get_chain_broken(long nres, double **a, double **b, long *chain_broken); -- -+extern void get_BDIR(char *BDIR, char *filename); - - - FILE *psfile; diff --git a/sci-biology/rnaview/files/rnaview-20040713-makefile.patch b/sci-biology/rnaview/files/rnaview-20040713-makefile.patch deleted file mode 100644 index 1af72f581fbf..000000000000 --- a/sci-biology/rnaview/files/rnaview-20040713-makefile.patch +++ /dev/null @@ -1,87 +0,0 @@ - Makefile | 20 +++++++++++++++++--- - rnaml2ps/Makefile | 19 ++++++++++++------- - 2 files changed, 29 insertions(+), 10 deletions(-) - -diff --git a/Makefile b/Makefile -index 452e6c4..00d35f0 100644 ---- a/Makefile -+++ b/Makefile -@@ -1,4 +1,4 @@ --CC = cc -+CC ?= cc - - - -@@ -56,12 +56,17 @@ OBJ_FILE = $(OBJ)/rnaview.o \ - $(OBJ)/multiple.o \ - $(OBJ)/statistics.o - -+.PHONY: clean all install -+ -+SUBDIRS = rnaml2ps -+ - all: $(RNAVIEW) -+ for dir in ${SUBDIRS} ; do ( cd $$dir ; ${MAKE} all ) ; done - --CFLAGS = $(LINCLUDES) -+CFLAGS += $(LINCLUDES) - - $(RNAVIEW) : $(HFILES) $(OBJ_FILE) -- $(CC) $(CFLAGS) -o $@ $(OBJ_FILE) $(LDFLAGS) -lm $(MALLOCLIB) -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(OBJ_FILE) -lm $(MALLOCLIB) - - - -@@ -111,6 +116,15 @@ $(OBJ)/statistics.o : $(SRC)/statistics.c - clean: - @rm -f $(OBJ)/*.o - @rm -f $(ALLTARGETS) -+ for dir in ${SUBDIRS} ; do ( cd $$dir ; ${MAKE} clean ) ; done -+ -+install: -+ install -D -m 0755 bin/rnaview $(DESTDIR)/usr/bin/rnaview -+ mkdir -p $(DESTDIR)/usr/share/rnaview/BASEPARS -+ install -m 0644 BASEPARS/* $(DESTDIR)/usr/share/rnaview/BASEPARS -+ mkdir -p $(DESTDIR)/usr/share/rnaview/test -+ install -m 0644 test/* $(DESTDIR)/usr/share/rnaview/test -+ for dir in ${SUBDIRS} ; do ( cd $$dir ; ${MAKE} install ) ; done - - export: - mkdir -p $(EXPORT_DIR) -diff --git a/rnaml2ps/Makefile b/rnaml2ps/Makefile -index d207655..2278ccc 100644 ---- a/rnaml2ps/Makefile -+++ b/rnaml2ps/Makefile -@@ -1,20 +1,25 @@ --CFLAGS = -O --CC = cc -+CFLAGS ?= -O -+CC ?= cc - - # ++++++++++++++++++++++++++++ Program RNADRAW - RNADRAW = rnaml2ps - OBJS_RNADRAW = rnaml2ps.o nrutil.o - -+all: $(RNADRAW) -+ - $(RNADRAW): $(OBJS_RNADRAW) -- $(CC) -o $(RNADRAW) $(OBJS_RNADRAW) -lm -+ $(CC) $(LDFLAGS) -o $(RNADRAW) $(OBJS_RNADRAW) -lm - - nrutil.o : nrutil.c -- cc -c nrutil.c -+ $(CC) $(CFLAGS) -c nrutil.c - - rnaml2ps.o : rnaml2ps.c -- cc -c rnaml2ps.c -+ $(CC) $(CFLAGS) -c rnaml2ps.c - - --.PHONY : clean -+.PHONY : clean all install - clean: -- rm *.o -+ rm -f *.o -+ -+install: -+ install -D -m 0755 $(RNADRAW) $(DESTDIR)/usr/bin/$(RNADRAW) diff --git a/sci-biology/rnaview/metadata.xml b/sci-biology/rnaview/metadata.xml deleted file mode 100644 index 396eccdc212f..000000000000 --- a/sci-biology/rnaview/metadata.xml +++ /dev/null @@ -1,16 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> - The RNAView program generates 2-dimensional displays of RNA/DNA - secondary structures with tertiary interactions. RNAView - automatically identifies and classifies the types of base pairs that - are formed in nucleic acid structures, fully implementing Leontis and - Westhof's (RNA (2001) 7, 499-512), convention for edge-to-edge - hydrogen bonding interactions. - </longdescription> -</pkgmetadata> diff --git a/sci-biology/rnaview/rnaview-20040713-r5.ebuild b/sci-biology/rnaview/rnaview-20040713-r5.ebuild deleted file mode 100644 index c0c4289ba24b..000000000000 --- a/sci-biology/rnaview/rnaview-20040713-r5.ebuild +++ /dev/null @@ -1,31 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit toolchain-funcs - -DESCRIPTION="Generates 2D displays of RNA/DNA secondary structures with tertiary interactions" -HOMEPAGE="http://ndbserver.rutgers.edu/services/download/index.html"; -SRC_URI="mirror://gentoo/${P}.tar.bz2" - -LICENSE="public-domain" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -PATCHES=( - "${FILESDIR}"/${P}-makefile.patch - "${FILESDIR}"/${P}-implicit.patch -) - -src_configure() { - tc-export CC -} - -src_install() { - default - - newenvd - 22rnaview <<- EOF - RNAVIEW="${EPREFIX}/usr/share/rnaview" - EOF -}
