samtools0119: Remove obsolete legacy package

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: samtools0119: Remove obsolete legacy package
From: Jason Bacon <bacon%NetBSD.org@localhost>
Date: Thu, 21 May 2020 18:53:18 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Thu May 21 13:53:18 2020 -0500
Changeset:	c4bc22b0e5d71206a076750ba3884ba008aa71cb

Modified Files:
	Makefile
Removed Files:
	samtools0119/DESCR
	samtools0119/Makefile
	samtools0119/PLIST
	samtools0119/buildlink3.mk
	samtools0119/distinfo
	samtools0119/patches/patch-Makefile
	samtools0119/patches/patch-bcftools_Makefile
	samtools0119/patches/patch-misc_Makefile

Log Message:
samtools0119: Remove obsolete legacy package

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=c4bc22b0e5d71206a076750ba3884ba008aa71cb

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile                                     |  1 -
 samtools0119/DESCR                           |  3 --
 samtools0119/Makefile                        | 63 ----------------------------
 samtools0119/PLIST                           | 47 ---------------------
 samtools0119/buildlink3.mk                   | 12 ------
 samtools0119/distinfo                        |  8 ----
 samtools0119/patches/patch-Makefile          | 60 --------------------------
 samtools0119/patches/patch-bcftools_Makefile | 14 -------
 samtools0119/patches/patch-misc_Makefile     | 42 -------------------
 9 files changed, 250 deletions(-)

diffs:
diff --git a/Makefile b/Makefile
index 9195a4b3c1..36e7c897c6 100644
--- a/Makefile
+++ b/Makefile
@@ -4439,7 +4439,6 @@ SUBDIR+=	sais-demo-data
 SUBDIR+=	salmon
 SUBDIR+=	samhain
 SUBDIR+=	samtools
-SUBDIR+=	samtools0119
 SUBDIR+=	sara
 SUBDIR+=	sarf
 SUBDIR+=	sbc
diff --git a/samtools0119/DESCR b/samtools0119/DESCR
deleted file mode 100644
index dcebc45425..0000000000
--- a/samtools0119/DESCR
+++ /dev/null
@@ -1,3 +0,0 @@
-[description of the port]
-
-WWW: http://port.home.page/
diff --git a/samtools0119/Makefile b/samtools0119/Makefile
deleted file mode 100644
index 6680ba7ea5..0000000000
--- a/samtools0119/Makefile
+++ /dev/null
@@ -1,63 +0,0 @@
-# $NetBSD$
-
-###########################################################
-#               Generated by fbsd2pkg                     #
-###########################################################
-
-DISTNAME=	samtools-${PORTVERSION}
-PKGNAME=	samtools0119-${PORTVERSION}
-CATEGORIES=	biology
-MASTER_SITES=	${MASTER_SITE_SOURCEFORGE:=samtools/}
-EXTRACT_SUFX=	.tar.bz2
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-
-PORTVERSION=	0.1.19
-
-COMMENT=	Generic format for storing large nucleotide sequence alignments
-LICENSE=	mit
-
-USE_TOOLS+=	gmake perl
-USE_ZLIB=	yes
-
-REPLACE_PERL=	misc/export2sam.pl misc/plot-bamcheck
-REPLACE_PYTHON=	misc/varfilter.py
-
-# No REPLACE_LUAJIT available at this time
-SUBST_CLASSES+=		luajit
-SUBST_STAGE.luajit=	post-patch
-SUBST_SED.luajit=	-e 's|/usr/bin/env luajit|${PREFIX}/bin/luajit|g'
-SUBST_FILES.luajit=	misc/r2plot.lua misc/vcfutils.lua
-
-LDFLAGS+=	${COMPILER_RPATH_FLAG}${PREFIX}/lib
-
-SAMPREFIX=	${PREFIX}/samtools0119
-
-do-build:
-	cd ${WRKSRC} && ${MAKE_PROGRAM} LDFLAGS="${LDFLAGS}" all-recur razip
-
-do-install:
-	${MKDIR} ${DESTDIR}${SAMPREFIX}/bin
-	${INSTALL_PROGRAM} ${WRKSRC}/samtools ${DESTDIR}${SAMPREFIX}/bin
-	${INSTALL_PROGRAM} ${WRKSRC}/razip ${DESTDIR}${SAMPREFIX}/bin
-	${INSTALL_PROGRAM} ${WRKSRC}/bcftools/bcftools ${DESTDIR}${SAMPREFIX}/bin
-.for f in ace2sam bamcheck maq2sam-long maq2sam-short md5fa md5sum-lite wgsim
-	${INSTALL_PROGRAM} ${WRKSRC}/misc/${f} ${DESTDIR}${SAMPREFIX}/bin
-.endfor
-	${INSTALL_SCRIPT} ${WRKSRC}/misc/*.pl ${WRKSRC}/misc/plot-bamcheck \
-		${DESTDIR}${SAMPREFIX}/bin
-	${INSTALL_SCRIPT} ${WRKSRC}/misc/*.py ${DESTDIR}${SAMPREFIX}/bin
-	${INSTALL_SCRIPT} ${WRKSRC}/misc/*.lua ${DESTDIR}${SAMPREFIX}/bin
-	${MKDIR} ${DESTDIR}${SAMPREFIX}/lib
-	${INSTALL_DATA} ${WRKSRC}/libbam.a ${DESTDIR}${SAMPREFIX}/lib
-	${MKDIR} ${DESTDIR}${SAMPREFIX}/man/man1
-	${INSTALL_MAN} ${WRKSRC}/samtools.1 ${DESTDIR}${SAMPREFIX}/man/man1
-	${MKDIR} ${DESTDIR}${SAMPREFIX}/include/bam
-	${INSTALL_DATA} ${WRKSRC}/*.h ${DESTDIR}${SAMPREFIX}/include/bam
-
-.include "../../lang/python/application.mk"
-.include "../../lang/lua/application.mk"
-.include "../../lang/LuaJIT2/buildlink3.mk"
-.include "../../devel/zlib/buildlink3.mk"
-.include "../../devel/ncurses/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/samtools0119/PLIST b/samtools0119/PLIST
deleted file mode 100644
index e6691a7b30..0000000000
--- a/samtools0119/PLIST
+++ /dev/null
@@ -1,47 +0,0 @@
-@comment $NetBSD$
-samtools0119/bin/ace2sam
-samtools0119/bin/bamcheck
-samtools0119/bin/bcftools
-samtools0119/bin/blast2sam.pl
-samtools0119/bin/bowtie2sam.pl
-samtools0119/bin/export2sam.pl
-samtools0119/bin/interpolate_sam.pl
-samtools0119/bin/maq2sam-long
-samtools0119/bin/maq2sam-short
-samtools0119/bin/md5fa
-samtools0119/bin/md5sum-lite
-samtools0119/bin/novo2sam.pl
-samtools0119/bin/plot-bamcheck
-samtools0119/bin/psl2sam.pl
-samtools0119/bin/r2plot.lua
-samtools0119/bin/razip
-samtools0119/bin/sam2vcf.pl
-samtools0119/bin/samtools
-samtools0119/bin/samtools.pl
-samtools0119/bin/soap2sam.pl
-samtools0119/bin/varfilter.py
-samtools0119/bin/vcfutils.lua
-samtools0119/bin/wgsim
-samtools0119/bin/wgsim_eval.pl
-samtools0119/bin/zoom2sam.pl
-samtools0119/include/bam/bam.h
-samtools0119/include/bam/bam2bcf.h
-samtools0119/include/bam/bam_endian.h
-samtools0119/include/bam/bam_tview.h
-samtools0119/include/bam/bgzf.h
-samtools0119/include/bam/errmod.h
-samtools0119/include/bam/faidx.h
-samtools0119/include/bam/kaln.h
-samtools0119/include/bam/khash.h
-samtools0119/include/bam/klist.h
-samtools0119/include/bam/knetfile.h
-samtools0119/include/bam/kprobaln.h
-samtools0119/include/bam/kseq.h
-samtools0119/include/bam/ksort.h
-samtools0119/include/bam/kstring.h
-samtools0119/include/bam/razf.h
-samtools0119/include/bam/sam.h
-samtools0119/include/bam/sam_header.h
-samtools0119/include/bam/sample.h
-samtools0119/lib/libbam.a
-samtools0119/man/man1/samtools.1
diff --git a/samtools0119/buildlink3.mk b/samtools0119/buildlink3.mk
deleted file mode 100644
index 1166981617..0000000000
--- a/samtools0119/buildlink3.mk
+++ /dev/null
@@ -1,12 +0,0 @@
-# $NetBSD$
-
-BUILDLINK_TREE+=	samtools01
-
-.if !defined(SAMTOOLS_BUILDLINK3_MK)
-SAMTOOLS_BUILDLINK3_MK:=
-
-BUILDLINK_API_DEPENDS.samtools01+=	samtools01>=0.1.19
-BUILDLINK_PKGSRCDIR.samtools01?=	../../wip/samtools0119
-.endif	# SAMTOOLS_BUILDLINK3_MK
-
-BUILDLINK_TREE+=	-samtools01
diff --git a/samtools0119/distinfo b/samtools0119/distinfo
deleted file mode 100644
index 31fb308761..0000000000
--- a/samtools0119/distinfo
+++ /dev/null
@@ -1,8 +0,0 @@
-$NetBSD$
-
-SHA1 (samtools-0.1.19.tar.bz2) = ff3f4cf40612d4c2ad26e6fcbfa5f8af84cbe881
-RMD160 (samtools-0.1.19.tar.bz2) = 4e74858d3762f785452d1c9507bd127de9791894
-Size (samtools-0.1.19.tar.bz2) = 514507 bytes
-SHA1 (patch-Makefile) = 0eacdb0d29ac3c4864ee59f061c8c7094be415dd
-SHA1 (patch-bcftools_Makefile) = 8a4d19200856962c7adcbf7745a6fe0a74b4550d
-SHA1 (patch-misc_Makefile) = 6150b8e9de04af17077015402e507ee450ab12a2
diff --git a/samtools0119/patches/patch-Makefile b/samtools0119/patches/patch-Makefile
deleted file mode 100644
index c4ab04dbfd..0000000000
--- a/samtools0119/patches/patch-Makefile
+++ /dev/null
@@ -1,60 +0,0 @@
-$NetBSD$
-
-# Respect env
---- Makefile.orig	2013-03-19 07:48:09.000000000 +0000
-+++ Makefile
-@@ -1,6 +1,7 @@
--CC=			gcc
--CFLAGS=		-g -Wall -O2
--#LDFLAGS=		-Wl,-rpath,\$$ORIGIN/../lib
-+CC?=		gcc
-+CFLAGS?=	-g -Wall -O2
-+RANLIB?=	/usr/bin/ranlib
-+#LDFLAGS=	-Wl,-rpath,\$$ORIGIN/../lib
- DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
- KNETFILE_O=	knetfile.o
- LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\
-@@ -14,7 +15,7 @@ AOBJS=		bam_tview.o bam_plcmd.o sam_view
- PROG=		samtools
- INCLUDES=	-I.
- SUBDIRS=	. bcftools misc
--LIBPATH=
-+LIBPATH=	-L${PREFIX}/lib
- LIBCURSES=	-lcurses # -lXCurses
- 
- .SUFFIXES:.c .o
-@@ -41,16 +42,17 @@ all:$(PROG)
- lib:libbam.a
- 
- libbam.a:$(LOBJS)
--		$(AR) -csru $@ $(LOBJS)
-+		$(AR) cr $@ $(LOBJS)
-+		$(RANLIB) $@
- 
- samtools:lib-recur $(AOBJS)
--		$(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
-+		$(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) ${LDFLAGS} -lm -lz -lpthread
- 
- razip:razip.o razf.o $(KNETFILE_O)
--		$(CC) $(CFLAGS) -o $@ $^ -lz
-+		$(CC) $(CFLAGS) -o $@ $^ ${LDFLAGS} -lz
- 
- bgzip:bgzip.o bgzf.o $(KNETFILE_O)
--		$(CC) $(CFLAGS) -o $@ $^ -lz -lpthread
-+		$(CC) $(CFLAGS) -o $@ $^ ${LDFLAGS} -lz -lpthread
- 
- bgzf.o:bgzf.c bgzf.h
- 		$(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@
-@@ -81,10 +83,10 @@ faidx_main.o:faidx.h razf.h
- 
- 
- libbam.1.dylib-local:$(LOBJS)
--		libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz
-+		libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc ${LDFLAGS} -lz
- 
- libbam.so.1-local:$(LOBJS)
--		$(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz
-+		$(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc ${LDFLAGS} -lz
- 
- dylib:
- 		@$(MAKE) cleanlocal; \
diff --git a/samtools0119/patches/patch-bcftools_Makefile b/samtools0119/patches/patch-bcftools_Makefile
deleted file mode 100644
index 6372844b28..0000000000
--- a/samtools0119/patches/patch-bcftools_Makefile
+++ /dev/null
@@ -1,14 +0,0 @@
-$NetBSD$
-
-# Find pkgsrc libs
---- bcftools/Makefile.orig	2017-11-28 19:24:34.616905493 +0000
-+++ bcftools/Makefile
-@@ -31,7 +31,7 @@ libbcf.a:$(LOBJS)
- 		$(AR) -csru $@ $(LOBJS)
- 
- bcftools:lib $(AOBJS)
--		$(CC) $(CFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread
-+		$(CC) $(CFLAGS) -o $@ $(AOBJS) -L. ${LDFLAGS} $(LIBPATH) -lbcf -lm -lz -lpthread
- 
- bcf.o:bcf.h
- vcf.o:bcf.h
diff --git a/samtools0119/patches/patch-misc_Makefile b/samtools0119/patches/patch-misc_Makefile
deleted file mode 100644
index 04f4aa9177..0000000000
--- a/samtools0119/patches/patch-misc_Makefile
+++ /dev/null
@@ -1,42 +0,0 @@
-$NetBSD$
-
-# Find pkgsrc libs
---- misc/Makefile.orig	2017-11-28 19:27:12.519750924 +0000
-+++ misc/Makefile
-@@ -28,19 +28,19 @@ lib-recur all-recur clean-recur cleanloc
- lib:
- 
- bamcheck:bamcheck.o
--		$(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz
-+		$(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread ${LDFLAGS} -lz
- 
- bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h
- 		$(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c
- 
- ace2sam:ace2sam.o
--		$(CC) $(CFLAGS) -o $@ ace2sam.o -lz
-+		$(CC) $(CFLAGS) -o $@ ace2sam.o ${LDFLAGS} -lz
- 
- wgsim:wgsim.o
--		$(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz
-+		$(CC) $(CFLAGS) -o $@ wgsim.o -lm ${LDFLAGS} -lz
- 
- md5fa:md5.o md5fa.o md5.h ../kseq.h
--		$(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz
-+		$(CC) $(CFLAGS) -o $@ md5.o md5fa.o ${LDFLAGS} -lz
- 
- md5sum-lite:md5sum-lite.o
- 		$(CC) $(CFLAGS) -o $@ md5sum-lite.o
-@@ -49,10 +49,10 @@ md5sum-lite.o:md5.c md5.h
- 		$(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c
- 
- maq2sam-short:maq2sam.c
--		$(CC) $(CFLAGS) -o $@ maq2sam.c -lz
-+		$(CC) $(CFLAGS) -o $@ maq2sam.c ${LDFLAGS} -lz
- 
- maq2sam-long:maq2sam.c
--		$(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz
-+		$(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c ${LDFLAGS} -lz
- 
- md5fa.o:md5.h md5fa.c
- 		$(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c
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