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[pkgsrc/trunk]: pkgsrc/biology biology: align variable assignments



details:   https://anonhg.NetBSD.org/pkgsrc/rev/7fd0fba0be2e
branches:  trunk
changeset: 343349:7fd0fba0be2e
user:      rillig <rillig%pkgsrc.org@localhost>
date:      Sat Nov 02 22:09:00 2019 +0000

description:
biology: align variable assignments

pkglint -Wall -F --only aligned --only indent -r

diffstat:

 biology/bcftools/Makefile              |   4 ++--
 biology/bioperl/Makefile               |   4 ++--
 biology/bwa/Makefile                   |   4 ++--
 biology/gnome-chemistry-utils/Makefile |   6 +++---
 biology/gromacs/Makefile               |   4 ++--
 biology/gromacs/options.mk             |   4 ++--
 biology/mpqc/Makefile                  |  16 ++++++++--------
 biology/ncbi-blast+/Makefile           |  16 ++++++++--------
 biology/phylip/Makefile                |   4 ++--
 biology/puzzle/Makefile                |   4 ++--
 10 files changed, 33 insertions(+), 33 deletions(-)

diffs (213 lines):

diff -r 930fac329786 -r 7fd0fba0be2e biology/bcftools/Makefile
--- a/biology/bcftools/Makefile Sat Nov 02 21:31:14 2019 +0000
+++ b/biology/bcftools/Makefile Sat Nov 02 22:09:00 2019 +0000
@@ -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 @@
 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
diff -r 930fac329786 -r 7fd0fba0be2e biology/bioperl/Makefile
--- a/biology/bioperl/Makefile  Sat Nov 02 21:31:14 2019 +0000
+++ b/biology/bioperl/Makefile  Sat Nov 02 22:09:00 2019 +0000
@@ -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 @@
 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
diff -r 930fac329786 -r 7fd0fba0be2e biology/bwa/Makefile
--- a/biology/bwa/Makefile      Sat Nov 02 21:31:14 2019 +0000
+++ b/biology/bwa/Makefile      Sat Nov 02 22:09:00 2019 +0000
@@ -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
diff -r 930fac329786 -r 7fd0fba0be2e biology/gnome-chemistry-utils/Makefile
--- a/biology/gnome-chemistry-utils/Makefile    Sat Nov 02 21:31:14 2019 +0000
+++ b/biology/gnome-chemistry-utils/Makefile    Sat Nov 02 22:09:00 2019 +0000
@@ -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+=        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
 
diff -r 930fac329786 -r 7fd0fba0be2e biology/gromacs/Makefile
--- a/biology/gromacs/Makefile  Sat Nov 02 21:31:14 2019 +0000
+++ b/biology/gromacs/Makefile  Sat Nov 02 22:09:00 2019 +0000
@@ -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 @@
 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"
 
diff -r 930fac329786 -r 7fd0fba0be2e biology/gromacs/options.mk
--- a/biology/gromacs/options.mk        Sat Nov 02 21:31:14 2019 +0000
+++ b/biology/gromacs/options.mk        Sat Nov 02 22:09:00 2019 +0000
@@ -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 @@
 # 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"
diff -r 930fac329786 -r 7fd0fba0be2e biology/mpqc/Makefile
--- a/biology/mpqc/Makefile     Sat Nov 02 21:31:14 2019 +0000
+++ b/biology/mpqc/Makefile     Sat Nov 02 22:09:00 2019 +0000
@@ -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 @@
 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 @@
 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:
diff -r 930fac329786 -r 7fd0fba0be2e biology/ncbi-blast+/Makefile
--- a/biology/ncbi-blast+/Makefile      Sat Nov 02 21:31:14 2019 +0000
+++ b/biology/ncbi-blast+/Makefile      Sat Nov 02 22:09:00 2019 +0000
@@ -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 '/--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
diff -r 930fac329786 -r 7fd0fba0be2e biology/phylip/Makefile
--- a/biology/phylip/Makefile   Sat Nov 02 21:31:14 2019 +0000
+++ b/biology/phylip/Makefile   Sat Nov 02 22:09:00 2019 +0000
@@ -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 @@
 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}
diff -r 930fac329786 -r 7fd0fba0be2e biology/puzzle/Makefile
--- a/biology/puzzle/Makefile   Sat Nov 02 21:31:14 2019 +0000
+++ b/biology/puzzle/Makefile   Sat Nov 02 22:09:00 2019 +0000
@@ -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 @@
 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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