gentoo resync : 09.07.2022

6 files changed, 218 insertions, 82 deletions

diff --git a/sci-biology/trnascan-se/Manifest b/sci-biology/trnascan-se/Manifest
index 5f9151c72b1e..3fb1acc44f13 100644
--- a/sci-biology/trnascan-se/Manifest
+++ b/sci-biology/trnascan-se/Manifest
@@ -1,4 +1,5 @@
-AUX trnascan-se-1.31-ldflags.patch 973 BLAKE2B 1aeae4e2e5a513caea6eced215e891a42e3ed650d02cf68f3874e20bc5b6b833cb4041ee3cc8fb4fba774143e247908e68f53d4a2b65bd77c32f857366be9621 SHA512 ff677ce9ac3ed9299f6a3bf977642e2a6c300a1b801436bb5d3787968cfe28357a0ec23d0438f0b15c06324cd7e1bbbda590c8fb5574577a3f653779316931df
+AUX trnascan-se-1.31-makefile.patch 5126 BLAKE2B 792cbd1226966c9f518672a730e8476f65cb0b4056b52e5416d43a6a1b5264666ae22fce88e4d7bfcf48d537ac4ec4d26ba8e737e60d31fbbc867de98d4315f2 SHA512 543ea32ed47279f5930485f5406d3b2912cba1df99681b2eb7e5d6df28579f48a07c9aba9ffe46819990543f5dbe69de6b086b8f86ed67de76e174dcc80563c4
+AUX trnascan-se-1.31-portable-perl-shebangs.patch 634 BLAKE2B 8089d6320bce63e560791c62a9baecea1dd1f8e54c618360072463507c73087a6412742669624db0539ec4b1cf2a4db0b6edb9b064eaf67e8ad1c3b77643004e SHA512 a910b02e35cb9dcc94f6f9ec3c44936e0f7faa1ec81d9bf6f397cb516b3bd20ba7cd8e334e452e94302b4254876187c36ec8f94ebb2bd8039c8fc3e1a2b5720f
 DIST trnascan-se-1.31.tar.gz 740960 BLAKE2B 995bfb7ad9f9d46543f15a36134aaec6c27921144c8900a323dbd6152f25e1faa587b5c817dcb8cb838dc1fde8ec7537e5fd6ca8930a4dd1aaadce41c575d651 SHA512 ba55bc8dfa7e5aee9c9a86c135a55b767cda083b74668bd9af4aaaeb693f9c3a17dc8bade5793de12b775564f09fbb861b0ab4f25bf83ccb0954fecd01bb328d
-EBUILD trnascan-se-1.31.ebuild 1191 BLAKE2B 8d492f11917a53e478d1f146bd55ee57b2c1ede4b1206fc419f86fd9acc1f73c30459b159836f8b0c946161cee16ba0cf0131d2635ce67708bd70c56c682f194 SHA512 d79fa9d244d4f3ab98fff94aca074bd23cc953c0b812a270daca2e80c440fcdcfd38e92cba2eea6ccd2ad9873c8fb898f46b9f4356c638d01fa0f2b21e23c55b
+EBUILD trnascan-se-1.31-r2.ebuild 925 BLAKE2B c3903dc93120d03a61d02efaae2ba9fff10cc0e804ea70f03b9ac86b9935b58721a319c0e51a452190444b91942192415d8c2406883aaca6fa07881d628b1f55 SHA512 fe165c6732fe579e739fdff25738ea8996974ef41cf927452aa51a91cfba1dc7485b6172adc81bb583fef442d44f5414c4ac2608b214dfc1c315c97799eb140f
 MISC metadata.xml 602 BLAKE2B 8f0a2a924d5e25b00f3850b903de327eff6811931047cd282386837db9d7905fa0a384b36821aea7c869d5da38969a6efbb43c3f1fd1d82dba50919bdda64172 SHA512 ace918d99f937c74013b854b34eaaeb0404dab2e5e9c21bcf876b471a617db7008cd1a7062a83dd00ba3e69027391a0b81915be8560a10d3ff9062c21862c0c2
diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch b/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch
deleted file mode 100644
index f28b1e8f6bb0..000000000000
--- a/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-diff --git a/Makefile b/Makefile
-index 53e5c5b..a2d3feb 100644
---- a/Makefile
-+++ b/Makefile
-@@ -109,17 +109,17 @@ MPOBJ = mpviterbi.o mp-dbviterbi.o
- all: 	$(PROGS) tRNAscan-SE setpaths
- 
- covels-SE:  $(OBJ) scan_main.o
--	$(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
-+	$(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
- 
- coves-SE: $(OBJ) score_main.o
--	$(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS)
-+	$(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS)
- 
- eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o
--	$(CC) $(CFLAGS)  -o eufindtRNA eufind_main.o \
-+	$(CC) $(CFLAGS)  $(LDFLAGS) -o eufindtRNA eufind_main.o \
- 	pavesi.o $(SQUIDOBJ) $(LIBS)
- 
- trnascan-1.4: trnascan.o
--	$(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c
-+	$(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" $(LDFLAGS) -o trnascan-1.4 trnascan.c
- 
- tRNAscan-SE:
- 	$(PERLDIR)/$(PERLBIN) checkversion.pl
diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-makefile.patch b/sci-biology/trnascan-se/files/trnascan-se-1.31-makefile.patch
new file mode 100644
index 000000000000..acf3c2a6d862
--- /dev/null
+++ b/sci-biology/trnascan-se/files/trnascan-se-1.31-makefile.patch
@@ -0,0 +1,140 @@
+--- a/Makefile
++++ b/Makefile
+@@ -20,9 +20,9 @@
+ PERLBIN = perl
+ 
+ ## where you want things installed
+-BINDIR  = $(HOME)/bin
+-LIBDIR  = $(HOME)/lib/tRNAscan-SE
+-MANDIR  = $(HOME)/man
++BINDIR = $(EPREFIX)/usr/bin
++LIBDIR = $(EPREFIX)/usr/share/trnascan-se
++MANDIR = $(EPREFIX)/usr/share/man
+ 
+ ## NOTE !!  If you later manually move the location of 
+ ## binaries or data files in the BINDIR or LIBDIR directories,
+@@ -33,10 +33,8 @@
+ TEMPDIR = /tmp
+ 
+ ## your compiler
+-CC = gcc	  # GNU cc (if available) otherwise use vendor's cc
+ 
+ ## any special compiler flags you want
+-CFLAGS = -O    # ok for most machines (remove -O for DEC OSF/1 cc compiler)
+ 
+ ## machine specific definitions
+ #  You shouldn't need any. The specific #define's in squid are historical.
+@@ -58,7 +56,7 @@
+ #######
+ 
+ SHELL  = /bin/sh
+-LIBS   = -lm
++LIBS   += -lm
+ .SUFFIXES : .c .o
+ 
+ DOCS = README MANUAL INSTALL COPYING GNULICENSE FILES Release.history
+@@ -109,20 +107,20 @@
+ all: 	$(PROGS) tRNAscan-SE setpaths
+ 
+ covels-SE:  $(OBJ) scan_main.o
+-	$(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
++	$(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
+ 
+ coves-SE: $(OBJ) score_main.o
+-	$(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS)
++	$(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS)
+ 
+ eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o
+-	$(CC) $(CFLAGS)  -o eufindtRNA eufind_main.o \
++	$(CC) $(LDFLAGS) $(CFLAGS) -o eufindtRNA eufind_main.o \
+ 	pavesi.o $(SQUIDOBJ) $(LIBS)
+ 
+-trnascan-1.4: trnascan.o
+-	$(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c
++trnascan-1.4: trnascan.c
++	$(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c
+ 
+ tRNAscan-SE:
+-	$(PERLDIR)/$(PERLBIN) checkversion.pl
++	$(PERLBIN) checkversion.pl
+ 	sed 's#/tmp#$(TEMPDIR)#g' tRNAscan-SE.src | \
+ 	sed 's#bindir = ""#bindir =\"$(BINDIR)/"#g' | \
+ 	sed 's#/usr/local/lib/tRNAscanSE#$(LIBDIR)#g' | \
+@@ -200,11 +198,11 @@
+ noambig: trnascan-1.4-NA eufindtRNA-NA
+ 
+ trnascan-1.4-NA:  trnascan.o
+-	$(CC) $(CFLAGS) -DNO_AMBIG -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4-NA trnascan.c
++	$(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -DNO_AMBIG -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4-NA trnascan.c
+ 
+ eufindtRNA-NA: $(SQUIDOBJ) eufind_main.o
+-	$(CC) $(CFLAGS) -DNO_AMBIG -c -o pavesi-NA.o pavesi.c 
+-	$(CC) $(CFLAGS) -o eufindtRNA-NA eufind_main.o \
++	$(CC) $(CFLAGS) $(CPPFLAGS) -DNO_AMBIG -c -o pavesi-NA.o pavesi.c 
++	$(CC) $(LDFLAGS) $(CFLAGS) -o eufindtRNA-NA eufind_main.o \
+ 	pavesi-NA.o $(SQUIDOBJ) $(LIBS)	
+ 
+ 
+@@ -220,7 +218,7 @@
+ 	rmdir -ps $(MANDIR)
+ 
+ .c.o:
+-	$(CC) $(CFLAGS) $(MDEFS) -c $<		
++	$(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -c $<		
+ 
+ ## programs from Sean Eddy's sequence i/o function library not
+ ## needed for tRNAscan-SE but included for their utility
+@@ -233,16 +231,16 @@
+ 	cp $(UTILS) $(BINDIR)/.
+ 
+ reformat: $(SQUIDOBJ) reformat_main.o
+-	$(CC) $(CFLAGS) $(MDEFS) -o reformat $(SQUIDOBJ) reformat_main.o $(LIBS)
++	$(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o reformat $(SQUIDOBJ) reformat_main.o $(LIBS)
+ 
+ revcomp: $(SQUIDOBJ) revcomp_main.o
+-	$(CC) $(CFLAGS) $(MDEFS) -o revcomp $(SQUIDOBJ) revcomp_main.o $(LIBS)
++	$(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o revcomp $(SQUIDOBJ) revcomp_main.o $(LIBS)
+ 
+ seqstat: $(SQUIDOBJ) seqstat_main.o
+-	$(CC) $(CFLAGS) $(MDEFS) -o seqstat $(SQUIDOBJ) seqstat_main.o $(LIBS)
++	$(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o seqstat $(SQUIDOBJ) seqstat_main.o $(LIBS)
+ 
+ shuffle: $(SQUIDOBJ) shuffle_main.o
+-	$(CC) $(CFLAGS) $(MDEFS) -o shuffle $(SQUIDOBJ) shuffle_main.o $(LIBS)
++	$(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o shuffle $(SQUIDOBJ) shuffle_main.o $(LIBS)
+ 
+ ## other programs in Cove package (below) not needed for
+ ## tRNAscan-SE, but are included for users who wish to apply
+@@ -255,25 +253,25 @@
+ 	cp $(COVE_SUITE) $(BINDIR)/.
+ 
+ covea: $(OBJ) align_main.o
+-	$(CC) $(CFLAGS) $(RFLAGS) -o covea align_main.o $(OBJ) $(LIBS)
++	$(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covea align_main.o $(OBJ) $(LIBS)
+ 
+ coveb: $(OBJ) build_main.o
+-	$(CC) $(CFLAGS) $(RFLAGS) -o coveb build_main.o $(OBJ) $(LIBS)
++	$(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o coveb build_main.o $(OBJ) $(LIBS)
+ 
+ covee: $(OBJ) emit_main.o
+-	$(CC) $(CFLAGS) $(RFLAGS) -o covee emit_main.o $(OBJ) $(LIBS)
++	$(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covee emit_main.o $(OBJ) $(LIBS)
+ 
+ covet: $(OBJ) train_main.o
+-	$(CC) $(CFLAGS) $(RFLAGS) -o covet train_main.o $(OBJ) $(LIBS)
++	$(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covet train_main.o $(OBJ) $(LIBS)
+ 
+ covels:  $(OBJ) scan_main.o
+-	$(CC) $(CFLAGS) $(RFLAGS) -o covels scan_main.o $(OBJ) $(LIBS)
++	$(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covels scan_main.o $(OBJ) $(LIBS)
+ 
+ coves: $(OBJ) score_main.o
+-	$(CC) $(CFLAGS) $(RFLAGS) -o coves score_main.o $(OBJ) $(LIBS)
++	$(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o coves score_main.o $(OBJ) $(LIBS)
+ 
+ structcheck: $(OBJ) structcheck_main.o
+-	$(CC) $(CFLAGS) $(RFLAGS) -o structcheck structcheck_main.o $(OBJ) $(LIBS)
++	$(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o structcheck structcheck_main.o $(OBJ) $(LIBS)
+ 
+ 
+ ## Maspar memory limits
diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-portable-perl-shebangs.patch b/sci-biology/trnascan-se/files/trnascan-se-1.31-portable-perl-shebangs.patch
new file mode 100644
index 000000000000..187705e8b3a0
--- /dev/null
+++ b/sci-biology/trnascan-se/files/trnascan-se-1.31-portable-perl-shebangs.patch
@@ -0,0 +1,32 @@
+--- a/fasta2gsi.pl
++++ b/fasta2gsi.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Usage: fasta2gsi.perl <seqfile>
+ # Creates seqfile.gsi
+--- a/instman.pl
++++ b/instman.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Sean Eddy, Wed Jul 29 15:24:43 1992
+ 
+--- a/sstofa.pl
++++ b/sstofa.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ 
+ if ($#ARGV < 0) {
+--- a/tRNAscan-SE.src
++++ b/tRNAscan-SE.src
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ #
+ # --------------------------------------------------------------------
+ # tRNAscan-SE: a program for improved detection of transfer RNA
diff --git a/sci-biology/trnascan-se/trnascan-se-1.31-r2.ebuild b/sci-biology/trnascan-se/trnascan-se-1.31-r2.ebuild
new file mode 100644
index 000000000000..f35c31b22798
--- /dev/null
+++ b/sci-biology/trnascan-se/trnascan-se-1.31-r2.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit perl-functions toolchain-funcs
+
+DESCRIPTION="tRNA detection in large-scale genome sequences"
+HOMEPAGE="http://lowelab.ucsc.edu/tRNAscan-SE/"
+SRC_URI="http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}"/tRNAscan-SE-1.3.1/
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-lang/perl:="
+BDEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-makefile.patch
+	"${FILESDIR}"/${P}-portable-perl-shebangs.patch
+)
+
+src_configure() {
+	tc-export CC
+}
+
+src_test() {
+	emake PATH="${S}:${PATH}" testrun
+}
+
+src_install() {
+	dobin covels-SE coves-SE eufindtRNA tRNAscan-SE trnascan-1.4
+
+	newman tRNAscan-SE.man tRNAscan-SE.man.1
+	dodoc MANUAL Manual.ps README Release.history
+
+	insinto /usr/share/trnascan-se
+	doins *.cm gcode.* Dsignal TPCsignal
+
+	perl_domodule -r tRNAscanSE
+}
diff --git a/sci-biology/trnascan-se/trnascan-se-1.31.ebuild b/sci-biology/trnascan-se/trnascan-se-1.31.ebuild
deleted file mode 100644
index cd8dc152d6d2..000000000000
--- a/sci-biology/trnascan-se/trnascan-se-1.31.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit perl-functions toolchain-funcs
-
-DESCRIPTION="tRNA detection in large-scale genome sequences"
-HOMEPAGE="http://lowelab.ucsc.edu/tRNAscan-SE/"
-SRC_URI="http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE=""
-
-S="${WORKDIR}"/tRNAscan-SE-1.3.1/
-
-PATCHES=(
-	"${FILESDIR}"/${P}-ldflags.patch
-)
-
-src_prepare() {
-	default
-	sed \
-		-e "s:BINDIR  = \$(HOME)/bin:BINDIR = ${EPREFIX}/usr/bin:" \
-		-e "s:LIBDIR  = \$(HOME)/lib/tRNAscan-SE:LIBDIR = ${EPRFIX}/usr/share/${PN}:" \
-		-e "s:MANDIR  = \$(HOME)/man:MANDIR = ${EPREFIX}/usr/share/man:" \
-		-e "s:CC = gcc:CC = $(tc-getCC):" \
-		-e "s:CFLAGS = -O:CFLAGS = ${CFLAGS}:" \
-		-i Makefile || die
-
-	perl_set_version
-}
-
-src_test() {
-	emake PATH="${S}:${PATH}" testrun
-}
-
-src_install() {
-	dobin covels-SE coves-SE eufindtRNA tRNAscan-SE trnascan-1.4
-
-	newman tRNAscan-SE.man tRNAscan-SE.man.1
-
-	dodoc MANUAL README Release.history
-
-	insinto /usr/share/${PN}/
-	doins *.cm gcode.* Dsignal TPCsignal
-
-	dodoc Manual.ps
-
-	insinto ${VENDOR_LIB}
-	doins -r tRNAscanSE
-}