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CVS commit: pkgsrc/biology
Module Name: pkgsrc
Committed By: rillig
Date: Sat Nov 2 22:09:01 UTC 2019
Modified Files:
pkgsrc/biology/bcftools: Makefile
pkgsrc/biology/bioperl: Makefile
pkgsrc/biology/bwa: Makefile
pkgsrc/biology/gnome-chemistry-utils: Makefile
pkgsrc/biology/gromacs: Makefile options.mk
pkgsrc/biology/mpqc: Makefile
pkgsrc/biology/ncbi-blast+: Makefile
pkgsrc/biology/phylip: Makefile
pkgsrc/biology/puzzle: Makefile
Log Message:
biology: align variable assignments
pkglint -Wall -F --only aligned --only indent -r
To generate a diff of this commit:
cvs rdiff -u -r1.4 -r1.5 pkgsrc/biology/bcftools/Makefile
cvs rdiff -u -r1.37 -r1.38 pkgsrc/biology/bioperl/Makefile
cvs rdiff -u -r1.8 -r1.9 pkgsrc/biology/bwa/Makefile
cvs rdiff -u -r1.40 -r1.41 pkgsrc/biology/gnome-chemistry-utils/Makefile
cvs rdiff -u -r1.18 -r1.19 pkgsrc/biology/gromacs/Makefile
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/gromacs/options.mk
cvs rdiff -u -r1.15 -r1.16 pkgsrc/biology/mpqc/Makefile
cvs rdiff -u -r1.11 -r1.12 pkgsrc/biology/ncbi-blast+/Makefile
cvs rdiff -u -r1.24 -r1.25 pkgsrc/biology/phylip/Makefile
cvs rdiff -u -r1.14 -r1.15 pkgsrc/biology/puzzle/Makefile
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
Modified files:
Index: pkgsrc/biology/bcftools/Makefile
diff -u pkgsrc/biology/bcftools/Makefile:1.4 pkgsrc/biology/bcftools/Makefile:1.5
--- pkgsrc/biology/bcftools/Makefile:1.4 Sun Aug 11 13:17:59 2019
+++ pkgsrc/biology/bcftools/Makefile Sat Nov 2 22:09:00 2019
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.4 2019/08/11 13:17:59 wiz Exp $
+# $NetBSD: Makefile,v 1.5 2019/11/02 22:09:00 rillig Exp $
DISTNAME= bcftools-1.9
PKGREVISION= 2
@@ -17,7 +17,7 @@ GNU_CONFIGURE= yes
CONFIGURE_ARGS+= --with-htslib=system
TEST_TARGET= test
-BUILDLINK_TRANSFORM+= opt:-ldl:${BUILDLINK_LDADD.dl:M*}
+BUILDLINK_TRANSFORM+= opt:-ldl:${BUILDLINK_LDADD.dl:M*}
REPLACE_PERL+= misc/*.pl
REPLACE_PERL+= misc/plot-vcfstats
Index: pkgsrc/biology/bioperl/Makefile
diff -u pkgsrc/biology/bioperl/Makefile:1.37 pkgsrc/biology/bioperl/Makefile:1.38
--- pkgsrc/biology/bioperl/Makefile:1.37 Sun Aug 11 13:17:59 2019
+++ pkgsrc/biology/bioperl/Makefile Sat Nov 2 22:09:00 2019
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.37 2019/08/11 13:17:59 wiz Exp $
+# $NetBSD: Makefile,v 1.38 2019/11/02 22:09:00 rillig Exp $
DISTNAME= BioPerl-1.007002
PKGNAME= ${DISTNAME:tl}
@@ -12,7 +12,7 @@ COMMENT= Perl tools for computational mo
LICENSE= ${PERL5_LICENSE}
#BUILD_DEPENDS+= {perl>=5.19.6,p5-Module-Build>0.42}:../../devel/p5-Module-Build
-BUILD_DEPENDS+= p5-Test-Most-[0-9]*:../../devel/p5-Test-Most
+BUILD_DEPENDS+= p5-Test-Most-[0-9]*:../../devel/p5-Test-Most
DEPENDS+= p5-Algorithm-Munkres-[0-9]*:../../math/p5-Algorithm-Munkres
DEPENDS+= p5-Array-Compare-[0-9]*:../../devel/p5-Array-Compare
Index: pkgsrc/biology/bwa/Makefile
diff -u pkgsrc/biology/bwa/Makefile:1.8 pkgsrc/biology/bwa/Makefile:1.9
--- pkgsrc/biology/bwa/Makefile:1.8 Sun Aug 11 13:17:59 2019
+++ pkgsrc/biology/bwa/Makefile Sat Nov 2 22:09:00 2019
@@ -1,9 +1,9 @@
-# $NetBSD: Makefile,v 1.8 2019/08/11 13:17:59 wiz Exp $
+# $NetBSD: Makefile,v 1.9 2019/11/02 22:09:00 rillig Exp $
DISTNAME= bwa-0.7.17
CATEGORIES= biology
PKGREVISION= 3
-GITHUB_TAG= v${PKGVERSION_NOREV}
+GITHUB_TAG= v${PKGVERSION_NOREV}
MASTER_SITES= ${MASTER_SITE_GITHUB:=lh3/}
MAINTAINER= bacon%NetBSD.org@localhost
Index: pkgsrc/biology/gnome-chemistry-utils/Makefile
diff -u pkgsrc/biology/gnome-chemistry-utils/Makefile:1.40 pkgsrc/biology/gnome-chemistry-utils/Makefile:1.41
--- pkgsrc/biology/gnome-chemistry-utils/Makefile:1.40 Sun Aug 11 13:18:00 2019
+++ pkgsrc/biology/gnome-chemistry-utils/Makefile Sat Nov 2 22:09:00 2019
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.40 2019/08/11 13:18:00 wiz Exp $
+# $NetBSD: Makefile,v 1.41 2019/11/02 22:09:00 rillig Exp $
#
DISTNAME= gnome-chemistry-utils-0.12.13
@@ -22,8 +22,8 @@ GCONF_SCHEMAS+= gchempaint-arrows.schema
GCONF_SCHEMAS+= gcrystal.schemas
GCONF_SCHEMAS+= gchempaint.schemas
-BUILDLINK_TRANSFORM+=rm:-DGTK_DISABLE_DEPRECATED
-BUILDLINK_TRANSFORM+=rm:-ldl
+BUILDLINK_TRANSFORM+= rm:-DGTK_DISABLE_DEPRECATED
+BUILDLINK_TRANSFORM+= rm:-ldl
CONFIGURE_ARGS+= --disable-update-databases
Index: pkgsrc/biology/gromacs/Makefile
diff -u pkgsrc/biology/gromacs/Makefile:1.18 pkgsrc/biology/gromacs/Makefile:1.19
--- pkgsrc/biology/gromacs/Makefile:1.18 Sun Aug 11 13:18:00 2019
+++ pkgsrc/biology/gromacs/Makefile Sat Nov 2 22:09:00 2019
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.18 2019/08/11 13:18:00 wiz Exp $
+# $NetBSD: Makefile,v 1.19 2019/11/02 22:09:00 rillig Exp $
#
DISTNAME= gromacs-4.5.5
@@ -28,7 +28,7 @@ CONFIGURE_ARGS+= --disable-gcc41-check
USE_TOOLS+= perl:run
REPLACE_PERL= scripts/demux.pl scripts/xplor2gmx.pl
-CHECK_INTERPRETER_SKIP+= share/gromacs/tutor/gmxdemo/demo
+CHECK_INTERPRETER_SKIP+= share/gromacs/tutor/gmxdemo/demo
.include "../../mk/bsd.prefs.mk"
Index: pkgsrc/biology/gromacs/options.mk
diff -u pkgsrc/biology/gromacs/options.mk:1.2 pkgsrc/biology/gromacs/options.mk:1.3
--- pkgsrc/biology/gromacs/options.mk:1.2 Sun May 16 12:04:03 2010
+++ pkgsrc/biology/gromacs/options.mk Sat Nov 2 22:09:00 2019
@@ -1,4 +1,4 @@
-# $NetBSD: options.mk,v 1.2 2010/05/16 12:04:03 asau Exp $
+# $NetBSD: options.mk,v 1.3 2019/11/02 22:09:00 rillig Exp $
PKG_OPTIONS_VAR= PKG_OPTIONS.gromacs
PKG_SUPPORTED_OPTIONS+= mpi x11
@@ -20,7 +20,7 @@ PLIST_SUBST+= MPI=
# X support:
.if !empty(PKG_OPTIONS:Mx11)
CONFIGURE_ARGS+= --with-x
-PLIST.x11= yes
+PLIST.x11= yes
.include "../../x11/libX11/buildlink3.mk"
.include "../../x11/libICE/buildlink3.mk"
Index: pkgsrc/biology/mpqc/Makefile
diff -u pkgsrc/biology/mpqc/Makefile:1.15 pkgsrc/biology/mpqc/Makefile:1.16
--- pkgsrc/biology/mpqc/Makefile:1.15 Sun Aug 11 13:18:00 2019
+++ pkgsrc/biology/mpqc/Makefile Sat Nov 2 22:09:00 2019
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.15 2019/08/11 13:18:00 wiz Exp $
+# $NetBSD: Makefile,v 1.16 2019/11/02 22:09:00 rillig Exp $
DISTNAME= mpqc-2.3.1
PKGREVISION= 8
@@ -10,14 +10,14 @@ MAINTAINER= asau%inbox.ru@localhost
HOMEPAGE= http://www.mpqc.org/
COMMENT= The Massively Parallel Quantum Chemistry Program
-USE_LANGUAGES= c c++ fortran77
-PKGSRC_FORTRAN= f2c # XXX force f2c for now
-GNU_CONFIGURE= yes
+USE_LANGUAGES= c c++ fortran77
+PKGSRC_FORTRAN= f2c # XXX force f2c for now
+GNU_CONFIGURE= yes
CONFIGURE_ARGS+= --with-libdirs="-L${PREFIX}/lib ${COMPILER_RPATH_FLAG}${PREFIX}/lib" # fixme
#CONFIGURE_ARGS= -without-f77 # this doesn't work out of the box
-CONFIGURE_ENV= ac_cv_prog_WISH=${REPLACE.wish.new}
-USE_TOOLS+= perl:run
-USE_LIBTOOL= yes
+CONFIGURE_ENV= ac_cv_prog_WISH=${REPLACE.wish.new}
+USE_TOOLS+= perl:run
+USE_LIBTOOL= yes
USE_TOOLS+= gmake
BUILD_TARGET= default
@@ -28,7 +28,7 @@ INSTALL_MAKE_FLAGS= installroot=${DESTDI
REPLACE_PERL= src/bin/mpqc/ccarun.in src/bin/mpqc/mpqcrun.in
# Don't introduce Tk dependency for minor things, just leave a hook:
-REPLACE_WISH= src/bin/molrender/tkmolrender.in
+REPLACE_WISH= src/bin/molrender/tkmolrender.in
CHECK_INTERPRETER_SKIP= bin/tkmolrender
# optional:
Index: pkgsrc/biology/ncbi-blast+/Makefile
diff -u pkgsrc/biology/ncbi-blast+/Makefile:1.11 pkgsrc/biology/ncbi-blast+/Makefile:1.12
--- pkgsrc/biology/ncbi-blast+/Makefile:1.11 Sun Aug 11 13:18:00 2019
+++ pkgsrc/biology/ncbi-blast+/Makefile Sat Nov 2 22:09:00 2019
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.11 2019/08/11 13:18:00 wiz Exp $
+# $NetBSD: Makefile,v 1.12 2019/11/02 22:09:00 rillig Exp $
DISTNAME= ncbi-blast-2.8.1+-src
PKGNAME= ${DISTNAME:S/+-src//:S/blast/blast+/}
@@ -21,14 +21,14 @@ SUBST_SED.configure+= -e '/--infodir=DIR
SUBST_SED.configure+= -e '/--mandir=DIR/d'
SUBST_FILES.configure+= ${WRKSRC}/src/build-system/configure
-USE_TOOLS+= bash gmake perl
-USE_LANGUAGES= c c++
-GNU_CONFIGURE= yes
+USE_TOOLS+= bash gmake perl
+USE_LANGUAGES= c c++
+GNU_CONFIGURE= yes
GNU_CONFIGURE_STRICT= no # doesn't know --enable-option-checking
-REPLACE_BASH= scripts/common/impl/define_random_macros.sh
-REPLACE_BASH+= src/app/blast/get_species_taxids.sh
-REPLACE_PERL= src/app/blast/legacy_blast.pl src/app/blast/update_blastdb.pl
-REPLACE_PYTHON= src/app/winmasker/windowmasker_2.2.22_adapter.py
+REPLACE_BASH= scripts/common/impl/define_random_macros.sh
+REPLACE_BASH+= src/app/blast/get_species_taxids.sh
+REPLACE_PERL= src/app/blast/legacy_blast.pl src/app/blast/update_blastdb.pl
+REPLACE_PYTHON= src/app/winmasker/windowmasker_2.2.22_adapter.py
# The test for amq can hang, but amq is not needed so just avoid the test
# configure chooses /usr/local/bin/ar with no flags
Index: pkgsrc/biology/phylip/Makefile
diff -u pkgsrc/biology/phylip/Makefile:1.24 pkgsrc/biology/phylip/Makefile:1.25
--- pkgsrc/biology/phylip/Makefile:1.24 Tue Sep 11 20:32:13 2012
+++ pkgsrc/biology/phylip/Makefile Sat Nov 2 22:09:01 2019
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.24 2012/09/11 20:32:13 asau Exp $
+# $NetBSD: Makefile,v 1.25 2019/11/02 22:09:01 rillig Exp $
DISTNAME= phylip-3.69
CATEGORIES= biology
@@ -7,7 +7,7 @@ MASTER_SITES= ftp://evolution.genetics.w
MAINTAINER= babafou%babafou.eu.org@localhost
HOMEPAGE= http://evolution.genetics.washington.edu/phylip.html
COMMENT= Phylogeny Inference Package
-LICENSE= phylip-license
+LICENSE= phylip-license
RESTRICTED= Distribution permitted only if no fee is charged.
NO_SRC_ON_CDROM= ${RESTRICTED}
Index: pkgsrc/biology/puzzle/Makefile
diff -u pkgsrc/biology/puzzle/Makefile:1.14 pkgsrc/biology/puzzle/Makefile:1.15
--- pkgsrc/biology/puzzle/Makefile:1.14 Mon Apr 1 08:56:43 2013
+++ pkgsrc/biology/puzzle/Makefile Sat Nov 2 22:09:01 2019
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.14 2013/04/01 08:56:43 sbd Exp $
+# $NetBSD: Makefile,v 1.15 2019/11/02 22:09:01 rillig Exp $
DISTNAME= tree-puzzle-5.2
PKGNAME= ${DISTNAME:S/^tree-//}
@@ -11,7 +11,7 @@ COMMENT= Maximum likelihood analysis of
LICENSE= gnu-gpl-v2
GNU_CONFIGURE= yes
-MAKE_JOBS_SAFE= no
+MAKE_JOBS_SAFE= no
INSTALLATION_DIRS= share/doc/puzzle \
share/examples/puzzle
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