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wip/t*: fix pkglint indentation warnings
Module Name: pkgsrc-wip
Committed By: Roland Illig <roland.illig%gmx.de@localhost>
Pushed By: rillig
Date: Sat Jan 27 23:53:06 2018 +0000
Changeset: 8e888c6b3c9eb44361abe956a0983067c5253614
Modified Files:
tamago-anthy/Makefile
tardy/options.mk
taskd/Makefile
tasks/PLIST
tc-git/Makefile
tc-git/options.mk
tc-hasida-table/Makefile
tcc/Makefile
tcmplex-panteltje/PLIST
tctool/Makefile
tde/Makefile
teco/PLIST
telepathy-butterfly/Makefile
telepathy-logger/Makefile
telepathy-logger/buildlink3.mk
tendra.org-sid/PLIST
teng/Makefile
testssl/Makefile
tex-arabxtex/Makefile
tex-breqn-doc/Makefile
tex-lineno-doc/Makefile
tex-mathtools-doc/Makefile
tex-relsize-doc/Makefile
tex-setspace-doc/Makefile
texlive-bin/Makefile
texlive2013/Makefile
texlive2013/options.mk
tftp-hpa/Makefile
thabit-ttf/Makefile
thawab/Makefile
thepeg/Makefile
tilda/Makefile
tinycobol/Makefile
tinycobol/PLIST
tk-tkimg/Makefile
tme/Makefile
tme/PLIST
tmuni-ttf/Makefile
tmw/Makefile
todotxt-git/Makefile
tophat/PLIST
tor-dev/Makefile
tor-dev/PLIST
torsocks-git/Makefile
toxcore-git/Makefile
toxcore/Makefile
toxic-git/Makefile
toxic-git/options.mk
tpl/Makefile
tqsllib/Makefile
tr2latex/Makefile
trac-plugins-GraphViz-svn/Makefile
trac-plugins-MasterTickets-svn/Makefile
trac-plugins-SensitiveTickets-svn/Makefile
trac-plugins-TimingAndEstimation-svn/Makefile
trac-plugins-spamfilter-svn/Makefile
translate-toolkit/options.mk
triangle/Makefile
trinity/Makefile
trinity/PLIST
tripwire2/Makefile
truecrypt/Makefile
tsh/Makefile
tsm/PLIST
tsm62/Makefile
tsm62/options.mk
ttf-indic-fonts/PLIST
ttysnoop/Makefile
ttysnoop/PLIST
tuareg-mode/Makefile
tuxanci-server/Makefile
tuxanci/Makefile
tuxanci/PLIST
tuxguitar/Makefile
twemproxy/Makefile
twitmail/Makefile
txt2tags/Makefile
typespeed/Makefile
Log Message:
wip/t*: fix pkglint indentation warnings
pkglint -Wall -F -o aligned t*/
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=8e888c6b3c9eb44361abe956a0983067c5253614
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
tamago-anthy/Makefile | 4 +-
tardy/options.mk | 4 +-
taskd/Makefile | 10 +-
tasks/PLIST | 2 +-
tc-git/Makefile | 12 +-
tc-git/options.mk | 6 +-
tc-hasida-table/Makefile | 12 +-
tcc/Makefile | 4 +-
tcmplex-panteltje/PLIST | 4 +-
tctool/Makefile | 8 +-
tde/Makefile | 2 +-
teco/PLIST | 34 +--
telepathy-butterfly/Makefile | 2 +-
telepathy-logger/Makefile | 2 +-
telepathy-logger/buildlink3.mk | 2 +-
tendra.org-sid/PLIST | 6 +-
teng/Makefile | 2 +-
testssl/Makefile | 4 +-
tex-arabxtex/Makefile | 2 +-
tex-breqn-doc/Makefile | 6 +-
tex-lineno-doc/Makefile | 6 +-
tex-mathtools-doc/Makefile | 6 +-
tex-relsize-doc/Makefile | 6 +-
tex-setspace-doc/Makefile | 6 +-
texlive-bin/Makefile | 24 +-
texlive2013/Makefile | 2 +-
texlive2013/options.mk | 4 +-
tftp-hpa/Makefile | 2 +-
thabit-ttf/Makefile | 4 +-
thawab/Makefile | 4 +-
thepeg/Makefile | 12 +-
tilda/Makefile | 2 +-
tinycobol/Makefile | 2 +-
tinycobol/PLIST | 10 +-
tk-tkimg/Makefile | 6 +-
tme/Makefile | 2 +-
tme/PLIST | 16 +-
tmuni-ttf/Makefile | 6 +-
tmw/Makefile | 6 +-
todotxt-git/Makefile | 6 +-
tophat/PLIST | 2 +-
tor-dev/Makefile | 4 +-
tor-dev/PLIST | 2 +-
torsocks-git/Makefile | 6 +-
toxcore-git/Makefile | 2 +-
toxcore/Makefile | 6 +-
toxic-git/Makefile | 4 +-
toxic-git/options.mk | 4 +-
tpl/Makefile | 2 +-
tqsllib/Makefile | 2 +-
tr2latex/Makefile | 6 +-
trac-plugins-GraphViz-svn/Makefile | 12 +-
trac-plugins-MasterTickets-svn/Makefile | 10 +-
trac-plugins-SensitiveTickets-svn/Makefile | 8 +-
trac-plugins-TimingAndEstimation-svn/Makefile | 2 +-
trac-plugins-spamfilter-svn/Makefile | 6 +-
translate-toolkit/options.mk | 6 +-
triangle/Makefile | 2 +-
trinity/Makefile | 2 +-
trinity/PLIST | 306 +++++++++++++-------------
tripwire2/Makefile | 14 +-
truecrypt/Makefile | 14 +-
tsh/Makefile | 2 +-
tsm/PLIST | 2 +-
tsm62/Makefile | 2 +-
tsm62/options.mk | 6 +-
ttf-indic-fonts/PLIST | 84 +++----
ttysnoop/Makefile | 16 +-
ttysnoop/PLIST | 2 +-
tuareg-mode/Makefile | 18 +-
tuxanci-server/Makefile | 10 +-
tuxanci/Makefile | 14 +-
tuxanci/PLIST | 18 +-
tuxguitar/Makefile | 6 +-
twemproxy/Makefile | 10 +-
twitmail/Makefile | 2 +-
txt2tags/Makefile | 10 +-
typespeed/Makefile | 8 +-
78 files changed, 446 insertions(+), 446 deletions(-)
diffs:
diff --git a/tamago-anthy/Makefile b/tamago-anthy/Makefile
index c62379e54a..5f2020dcbd 100644
--- a/tamago-anthy/Makefile
+++ b/tamago-anthy/Makefile
@@ -1,7 +1,7 @@
# $NetBSD: Makefile,v 1.12 2014/06/18 09:45:35 makoto Exp $
# the version number is for pkglint only
DISTNAME= tamago-anthy-4.0
-PKGREVISION= ${_GIT_PKGVERSION:S/.//g}
+PKGREVISION= ${_GIT_PKGVERSION:S/.//g}
LICENSE= gnu-gpl-v2
# See ../../inputmethod/anthy/Makefile.common
@@ -35,7 +35,7 @@ GIT_REPO.master= git://git.debian.org/git/pkg-anthy/egg.git
GIT_DEEP_CLONE.master= yes # defined
GNU_CONFIGURE= yes
-WRKSRC= ${WRKDIR}/egg
+WRKSRC= ${WRKDIR}/egg
.include "../../editors/emacs/modules.mk"
diff --git a/tardy/options.mk b/tardy/options.mk
index 2c1b7643e4..118a08f6f4 100644
--- a/tardy/options.mk
+++ b/tardy/options.mk
@@ -1,7 +1,7 @@
# $NetBSD: options.mk,v 1.1 2009/06/09 17:19:16 marko_schuetz Exp $
-PKG_OPTIONS_VAR= PKG_OPTIONS.tardy
-PKG_SUPPORTED_OPTIONS= testing
+PKG_OPTIONS_VAR= PKG_OPTIONS.tardy
+PKG_SUPPORTED_OPTIONS= testing
PKG_SUGGESTED_OPTIONS=
.include "../../mk/bsd.prefs.mk"
diff --git a/taskd/Makefile b/taskd/Makefile
index 8937002d95..30b7cbc79e 100644
--- a/taskd/Makefile
+++ b/taskd/Makefile
@@ -33,17 +33,17 @@ FILES_SUBST+= TASKD_USER=${TASKD_USER} TASKD_GROUP=${TASKD_GROUP} \
TASKD_DATA=${TASKD_DATA}
MESSAGE_SUBST+= TASKD_DATA=${TASKD_DATA}
-EGDIR= ${PREFIX}/share/examples/taskd
-EGFILES+= pki/README pki/generate pki/generate.ca \
- pki/generate.client pki/generate.crl \
- pki/generate.server pki/vars
+EGDIR= ${PREFIX}/share/examples/taskd
+EGFILES+= pki/README pki/generate pki/generate.ca \
+ pki/generate.client pki/generate.crl \
+ pki/generate.server pki/vars
INSTALLATION_DIRS+= ${EGDIR}/pki
BUILD_DEFS+= TASKD_USER TASKD_GROUP TASKD_DATA VARBASE
REPLACE_SH= src/taskdctl
-MAKE_DIRS=+ ${TASKD_DATA}
+MAKE_DIRS= + ${TASKD_DATA}
OWN_DIRS_PERMS+= ${TASKD_DATA} ${TASKD_USER} ${TASKD_GROUP} 0750
RCD_SCRIPTS= taskd
diff --git a/tasks/PLIST b/tasks/PLIST
index 936f9d3853..c686cf678a 100644
--- a/tasks/PLIST
+++ b/tasks/PLIST
@@ -12,8 +12,8 @@ share/icons/hicolor/scalable/apps/tasks.svg
share/locale/ar/LC_MESSAGES/tasks.mo
share/locale/ast/LC_MESSAGES/tasks.mo
share/locale/bg/LC_MESSAGES/tasks.mo
-share/locale/ca@valencia/LC_MESSAGES/tasks.mo
share/locale/ca/LC_MESSAGES/tasks.mo
+share/locale/ca@valencia/LC_MESSAGES/tasks.mo
share/locale/cs/LC_MESSAGES/tasks.mo
share/locale/cy/LC_MESSAGES/tasks.mo
share/locale/da/LC_MESSAGES/tasks.mo
diff --git a/tc-git/Makefile b/tc-git/Makefile
index 4707aba43f..901ab25486 100644
--- a/tc-git/Makefile
+++ b/tc-git/Makefile
@@ -32,7 +32,7 @@ GIT_REPOSITORIES= tc
GIT_REPO.tc= http://github.com/kanchoku/tc.git
# fatal: unable to access 'http://github.com/kanchoku/tc.git/': SSL certificate problem: unable to get local issuer certificate
# Add "-c http.sslVerify=false" to git command or,
-PKGSRC_SETENV= GIT_SSL_NO_VERIFY=true
+PKGSRC_SETENV= GIT_SSL_NO_VERIFY=true
## With some condition, it pauses waiting for interaction:
## Saving file /WRKOBJDIR/wip/tc-git/work/tc/etc/bushu.rev...
@@ -64,11 +64,11 @@ SUBST_FILES.texinfo= doc/Makefile
SUBST_SED.texinfo= -e '/if $$\(MAKEINFO\) $$\(AM_MAKEINFOFLAGS\) $$\(MAKEINFOFLAGS\) -I $$\(srcdir\)/s/ -I ./tc.texinfo/'
# string-to-int to string-to-number
-SUBST_CLASSES+= s2i
-SUBST_MESSAGE.s2i= string-to-int is an obsolete function; use `string-to-number' instead
-SUBST_STAGE.s2i= post-patch
-SUBST_FILES.s2i= lisp/eelll.el lisp/tc-is22.el lisp/tc-is20.el lisp/tc-is19.el lisp/tc-pre.el
-SUBST_SED.s2i= -e s/string-to-int/string-to-number/g
+SUBST_CLASSES+= s2i
+SUBST_MESSAGE.s2i= string-to-int is an obsolete function; use `string-to-number' instead
+SUBST_STAGE.s2i= post-patch
+SUBST_FILES.s2i= lisp/eelll.el lisp/tc-is22.el lisp/tc-is20.el lisp/tc-is19.el lisp/tc-pre.el
+SUBST_SED.s2i= -e s/string-to-int/string-to-number/g
.include "options.mk"
diff --git a/tc-git/options.mk b/tc-git/options.mk
index cfc8457fd4..31d9995c60 100644
--- a/tc-git/options.mk
+++ b/tc-git/options.mk
@@ -1,7 +1,7 @@
# $NetBSD: options.mk,v 1.1 2013/01/22 13:54:22 makoto Exp $
-PKG_OPTIONS_VAR= PKG_OPTIONS.tc
-PKG_SUPPORTED_OPTIONS= enable-symbol-rev
+PKG_OPTIONS_VAR= PKG_OPTIONS.tc
+PKG_SUPPORTED_OPTIONS= enable-symbol-rev
PKG_SUGGESTED_OPTIONS=
.include "../../mk/bsd.options.mk"
@@ -9,5 +9,5 @@ PKG_SUGGESTED_OPTIONS=
.if !empty(PKG_OPTIONS:Menable-symbol-rev)
# enable symbol.rev to be included in bushu.rev
# This will get, for example, upper arrow with UE(up) + YA(arrow)
-CONFIGURE_ARGS+= --enable-symbol-rev
+CONFIGURE_ARGS+= --enable-symbol-rev
.endif
diff --git a/tc-hasida-table/Makefile b/tc-hasida-table/Makefile
index 78bc0e38eb..f4d914b4dd 100644
--- a/tc-hasida-table/Makefile
+++ b/tc-hasida-table/Makefile
@@ -2,15 +2,15 @@
DISTNAME= hasida-table-0.8
-CATEGORIES= inputmethod
-MASTER_SITES= ftp://ftp.ki.nu/pub/
+CATEGORIES= inputmethod
+MASTER_SITES= ftp://ftp.ki.nu/pub/
LICENSE= 2-clause-bsd
-MAINTAINER= makoto%ki.nu@localhost
-HOMEPAGE= http://www.ki.nu/~makoto/tcode/
-COMMENT= Kanji table for t-code input (PostScript and PDF)
+MAINTAINER= makoto%ki.nu@localhost
+HOMEPAGE= http://www.ki.nu/~makoto/tcode/
+COMMENT= Kanji table for t-code input (PostScript and PDF)
-USE_TOOLS+= perl
+USE_TOOLS+= perl
REPLACE_PERL= hasida-table
# BUILD_DEPENDS+= ghostscript-cidfonts-ryumin-[0-9]*:../../fonts/ghostscript-cidfonts-ryumin
# BUILD_ENV+= PKG_OPTIONS.ghostscript+=disable-compile-inits
diff --git a/tcc/Makefile b/tcc/Makefile
index c48454843d..c710d5cf0a 100644
--- a/tcc/Makefile
+++ b/tcc/Makefile
@@ -13,8 +13,8 @@ ONLY_FOR_PLATFORM= *-*-i386
NOT_FOR_PLATFORM= NetBSD-1.6.2-*
-USE_TOOLS+= gmake
-HAS_CONFIGURE= yes
+USE_TOOLS+= gmake
+HAS_CONFIGURE= yes
CHECK_PORTABILITY_SKIP= gcctestsuite.sh
.include "../../mk/bsd.prefs.mk"
diff --git a/tcmplex-panteltje/PLIST b/tcmplex-panteltje/PLIST
index 38025cd222..b59440d46f 100644
--- a/tcmplex-panteltje/PLIST
+++ b/tcmplex-panteltje/PLIST
@@ -1,6 +1,6 @@
@comment $NetBSD: PLIST,v 1.2 2009/10/11 10:45:21 thomasklausner Exp $
bin/tcmplex-panteltje
-share/doc/tcmplex-panteltje/README
+share/doc/tcmplex-panteltje/CHANGES
share/doc/tcmplex-panteltje/COPYRIGHT
share/doc/tcmplex-panteltje/LICENSE
-share/doc/tcmplex-panteltje/CHANGES
+share/doc/tcmplex-panteltje/README
diff --git a/tctool/Makefile b/tctool/Makefile
index 5e9a6bfa78..7a3194b7d7 100644
--- a/tctool/Makefile
+++ b/tctool/Makefile
@@ -13,10 +13,10 @@ HOMEPAGE= http://speedmodem50b.berlios.de/
COMMENT= Speed Modem 50B/50B+/200/Cellpipe CELL 19A-BX utility
LICENSE= gnu-gpl-v2
-WRKSRC= ${WRKDIR}/${PKGBASE}/src
-NO_CONFIGURE= YES
-USE_TOOLS+= gmake
-USE_LANGUAGES= c++
+WRKSRC= ${WRKDIR}/${PKGBASE}/src
+NO_CONFIGURE= YES
+USE_TOOLS+= gmake
+USE_LANGUAGES= c++
INSTALLATION_DIRS= bin
CXXFLAGS.Linux+= -DCSTDLIB
diff --git a/tde/Makefile b/tde/Makefile
index ba12c3cf10..a3a1458088 100644
--- a/tde/Makefile
+++ b/tde/Makefile
@@ -17,7 +17,7 @@ SUBST_CLASSES+= prefix
SUBST_FILES.prefix= makefile
SUBST_MESSAGE.prefix= Fixing PREFIX path.
SUBST_SED.prefix= -e "s|/usr/local|${PREFIX}|g"
-SUBST_STAGE.prefix= post-patch
+SUBST_STAGE.prefix= post-patch
INSTALLATION_DIRS+= bin
diff --git a/teco/PLIST b/teco/PLIST
index a0188c4598..95ae2c4693 100644
--- a/teco/PLIST
+++ b/teco/PLIST
@@ -1,35 +1,35 @@
@comment $NetBSD: PLIST,v 1.2 2009/10/11 10:45:21 thomasklausner Exp $
bin/tecoc
-share/teco/upcase.tec
-share/teco/change.tes
-share/teco/date.tes
-share/teco/detab.tes
-share/teco/dir.tes
-share/teco/makprnt.tes
-share/teco/squ.tes
-share/teco/unsqu.tes
+share/doc/teco/aaout.txt
+share/doc/teco/changes.txt
+share/doc/teco/problems.txt
+share/doc/teco/readme.1st
+share/doc/teco/readme.lnx
+share/doc/teco/teco.doc
+share/doc/teco/video.txt
+share/doc/teco/wchart.txt
share/teco/change.tec
+share/teco/change.tes
share/teco/checkqr.tec
share/teco/date.tec
+share/teco/date.tes
share/teco/detab.tec
+share/teco/detab.tes
share/teco/dir.tec
+share/teco/dir.tes
share/teco/lowcase.tec
share/teco/makprnt.tec
+share/teco/makprnt.tes
share/teco/squ.tec
+share/teco/squ.tes
share/teco/sub.tec
+share/teco/tst.tec
share/teco/tstbsl.tec
share/teco/tstcss.tec
share/teco/tstequ.tec
share/teco/tsto.tec
share/teco/tstqr.tec
share/teco/tstsrc.tec
-share/teco/tst.tec
share/teco/unsqu.tec
-share/doc/teco/readme.1st
-share/doc/teco/readme.lnx
-share/doc/teco/changes.txt
-share/doc/teco/aaout.txt
-share/doc/teco/problems.txt
-share/doc/teco/video.txt
-share/doc/teco/teco.doc
-share/doc/teco/wchart.txt
+share/teco/unsqu.tes
+share/teco/upcase.tec
diff --git a/telepathy-butterfly/Makefile b/telepathy-butterfly/Makefile
index 9633ce690e..e4b11e2cd2 100644
--- a/telepathy-butterfly/Makefile
+++ b/telepathy-butterfly/Makefile
@@ -18,7 +18,7 @@ USE_LANGUAGES= # none
PY_PATCHPLIST= yes
-REPLACE_PYTHON+= waf telepathy-butterfly
+REPLACE_PYTHON+= waf telepathy-butterfly
PYTHON_VERSIONS_INCOMPATIBLE= 34 35 36 # py-gobject, py-papyon
.include "../../devel/py-gobject/buildlink3.mk"
diff --git a/telepathy-logger/Makefile b/telepathy-logger/Makefile
index 72b82250b4..dcd5e2eb94 100644
--- a/telepathy-logger/Makefile
+++ b/telepathy-logger/Makefile
@@ -21,7 +21,7 @@ PKGCONFIG_OVERRIDE+= telepathy-logger/telepathy-logger-0.1.pc.in
BUILD_DEPENDS= ${PYPKGPREFIX}-expat-[0-9]*:../../textproc/py-expat
-PYTHON_FOR_BUILD_ONLY= yes
+PYTHON_FOR_BUILD_ONLY= yes
PYTHON_VERSIONS_INCOMPATIBLE= 34 35 36 # not yet ported as of 0.2.7
.include "../../devel/gettext-lib/buildlink3.mk"
diff --git a/telepathy-logger/buildlink3.mk b/telepathy-logger/buildlink3.mk
index 57389e0f90..e6d1885c28 100644
--- a/telepathy-logger/buildlink3.mk
+++ b/telepathy-logger/buildlink3.mk
@@ -7,7 +7,7 @@ TELEPATHY_LOGGER_BUILDLINK3_MK:=
BUILDLINK_API_DEPENDS.telepathy-logger+= telepathy-logger>=0.1.4
BUILDLINK_ABI_DEPENDS.telepathy-logger+= telepathy-logger>=0.8.2
-BUILDLINK_PKGSRCDIR.telepathy-logger?= ../../wip/telepathy-logger
+BUILDLINK_PKGSRCDIR.telepathy-logger?= ../../wip/telepathy-logger
.include "../../devel/glib2/buildlink3.mk"
.include "../../devel/GConf/buildlink3.mk"
diff --git a/tendra.org-sid/PLIST b/tendra.org-sid/PLIST
index f9980a5381..32ef4cd73b 100644
--- a/tendra.org-sid/PLIST
+++ b/tendra.org-sid/PLIST
@@ -1,6 +1,9 @@
@comment $NetBSD: PLIST,v 1.2 2009/10/11 10:45:21 thomasklausner Exp $
bin/sid
man/man1/sid.1
+share/doc/sid/changelog-single/common.css
+share/doc/sid/changelog-single/docbook.css
+share/doc/sid/changelog-single/index.html
share/doc/sid/guide-single/common.css
share/doc/sid/guide-single/docbook.css
share/doc/sid/guide-single/index.html
@@ -19,9 +22,6 @@ share/doc/sid/guide/ch12.html
share/doc/sid/guide/common.css
share/doc/sid/guide/docbook.css
share/doc/sid/guide/index.html
-share/doc/sid/changelog-single/common.css
-share/doc/sid/changelog-single/docbook.css
-share/doc/sid/changelog-single/index.html
share/doc/sid/sid.1-single/common.css
share/doc/sid/sid.1-single/docbook.css
share/doc/sid/sid.1-single/index.html
diff --git a/teng/Makefile b/teng/Makefile
index 07b9849d86..ba0d09438c 100644
--- a/teng/Makefile
+++ b/teng/Makefile
@@ -15,7 +15,7 @@ GNU_CONFIGURE= yes
USE_LIBTOOL= yes
USE_LANGUAGES= c c++
-USE_TOOLS+= aclocal autoconf automake bison
+USE_TOOLS+= aclocal autoconf automake bison
pre-configure:
cd ${WRKSRC} && aclocal && libtoolize --force && automake --add-missing && autoconf
diff --git a/testssl/Makefile b/testssl/Makefile
index 60e6ec8c7f..de93fff726 100644
--- a/testssl/Makefile
+++ b/testssl/Makefile
@@ -15,8 +15,8 @@ GITHUB_TAG= v${PKGVERSION_NOREV}
DEPENDS+= bash-[0-9]*:../../shells/bash
-NO_BUILD= yes
-INSTALLATION_DIRS=bin share/doc/${PKGBASE}
+NO_BUILD= yes
+INSTALLATION_DIRS= bin share/doc/${PKGBASE}
REPLACE_INTERPRETER+= envbash
REPLACE.envbash.old= '/usr/bin/env\ bash'
diff --git a/tex-arabxtex/Makefile b/tex-arabxtex/Makefile
index 01aa315bb2..a3b1b3f1a5 100644
--- a/tex-arabxtex/Makefile
+++ b/tex-arabxtex/Makefile
@@ -3,7 +3,7 @@
DISTNAME= arabxetex
PKGNAME= tex-${DISTNAME}-1.1.4
-TEXLIVE_REV= 17470
+TEXLIVE_REV= 17470
MAINTAINER= kamelderouiche%yahoo.com@localhost
COMMENT= ArabTeX-like interface for XeLaTeX
diff --git a/tex-breqn-doc/Makefile b/tex-breqn-doc/Makefile
index 25b844d639..794cfa1150 100644
--- a/tex-breqn-doc/Makefile
+++ b/tex-breqn-doc/Makefile
@@ -1,8 +1,8 @@
# $NetBSD$
-DISTNAME= breqn.doc
-PKGNAME= tex-${DISTNAME:S/./-/}-0.98c
-TEXLIVE_REV= 38099
+DISTNAME= breqn.doc
+PKGNAME= tex-${DISTNAME:S/./-/}-0.98c
+TEXLIVE_REV= 38099
TEXLIVE_USE_CTAN= yes
MAINTAINER= pkgsrc-users%NetBSD.org@localhost
diff --git a/tex-lineno-doc/Makefile b/tex-lineno-doc/Makefile
index b21fb3673f..871004eb51 100644
--- a/tex-lineno-doc/Makefile
+++ b/tex-lineno-doc/Makefile
@@ -1,8 +1,8 @@
# $NetBSD$
-DISTNAME= lineno.doc
-PKGNAME= tex-${DISTNAME:S/./-/}-4.41
-TEXLIVE_REV= 21442
+DISTNAME= lineno.doc
+PKGNAME= tex-${DISTNAME:S/./-/}-4.41
+TEXLIVE_REV= 21442
TEXLIVE_USE_CTAN= yes
MAINTAINER= pkgsrc-users%NetBSD.org@localhost
diff --git a/tex-mathtools-doc/Makefile b/tex-mathtools-doc/Makefile
index 08bbc83705..da88857208 100644
--- a/tex-mathtools-doc/Makefile
+++ b/tex-mathtools-doc/Makefile
@@ -1,8 +1,8 @@
# $NetBSD$
-DISTNAME= mathtools.doc
-PKGNAME= tex-${DISTNAME:S/./-/}-${TEXLIVE_REV}
-TEXLIVE_REV= 38833
+DISTNAME= mathtools.doc
+PKGNAME= tex-${DISTNAME:S/./-/}-${TEXLIVE_REV}
+TEXLIVE_REV= 38833
TEXLIVE_USE_CTAN= yes
MAINTAINER= pkgsrc-users%NetBSD.org@localhost
diff --git a/tex-relsize-doc/Makefile b/tex-relsize-doc/Makefile
index d721854f1e..cb4c88b7d2 100644
--- a/tex-relsize-doc/Makefile
+++ b/tex-relsize-doc/Makefile
@@ -1,8 +1,8 @@
# $NetBSD$
-DISTNAME= relsize.doc
-PKGNAME= tex-${DISTNAME:S/./-/}-4.1
-TEXLIVE_REV= 30707
+DISTNAME= relsize.doc
+PKGNAME= tex-${DISTNAME:S/./-/}-4.1
+TEXLIVE_REV= 30707
TEXLIVE_USE_CTAN= yes
MAINTAINER= pkgsrc-users%NetBSD.org@localhost
diff --git a/tex-setspace-doc/Makefile b/tex-setspace-doc/Makefile
index 8930eb8f81..eeb0f1a59a 100644
--- a/tex-setspace-doc/Makefile
+++ b/tex-setspace-doc/Makefile
@@ -1,8 +1,8 @@
# $NetBSD$
-DISTNAME= setspace.doc
-PKGNAME= tex-${DISTNAME:S/./-/}-6.7a
-TEXLIVE_REV= 24881
+DISTNAME= setspace.doc
+PKGNAME= tex-${DISTNAME:S/./-/}-6.7a
+TEXLIVE_REV= 24881
TEXLIVE_USE_CTAN= yes
MAINTAINER= pkgsrc-users%NetBSD.org@localhost
diff --git a/texlive-bin/Makefile b/texlive-bin/Makefile
index a64b482028..cb3d706551 100644
--- a/texlive-bin/Makefile
+++ b/texlive-bin/Makefile
@@ -27,21 +27,21 @@ DEPENDS+= t1utils-[0-9]*:../../fonts/t1utils
DEPENDS+= psutils-[0-9]*:../../print/psutils
# Use pkgsrc versions instead of the ones shipped with livetex
-CONFIGURE_ARGS+=--with-system-freetype2
-CONFIGURE_ARGS+=--with-system-ncurses
-CONFIGURE_ARGS+=--with-system-pnglib
-CONFIGURE_ARGS+=--with-system-zlib
-CONFIGURE_ARGS+=--with-system-t1lib
-CONFIGURE_ARGS+=--with-system-gd
-CONFIGURE_ARGS+=--without-t1utils
-CONFIGURE_ARGS+=--without-psutils
+CONFIGURE_ARGS+= --with-system-freetype2
+CONFIGURE_ARGS+= --with-system-ncurses
+CONFIGURE_ARGS+= --with-system-pnglib
+CONFIGURE_ARGS+= --with-system-zlib
+CONFIGURE_ARGS+= --with-system-t1lib
+CONFIGURE_ARGS+= --with-system-gd
+CONFIGURE_ARGS+= --without-t1utils
+CONFIGURE_ARGS+= --without-psutils
# We still need to use icu from texlive for now
-CONFIGURE_ARGS+=--with-fontconfig=${BUILDLINK_PREFIX.fontconfig}
+CONFIGURE_ARGS+= --with-fontconfig=${BUILDLINK_PREFIX.fontconfig}
-CONFIGURE_ARGS+=--without-texinfo
-CONFIGURE_ARGS+=--without-texi2html
-CONFIGURE_ARGS+=--disable-multiplatform
+CONFIGURE_ARGS+= --without-texinfo
+CONFIGURE_ARGS+= --without-texi2html
+CONFIGURE_ARGS+= --disable-multiplatform
.include "../../wip/texlive/Makefile.common"
.include "options.mk"
diff --git a/texlive2013/Makefile b/texlive2013/Makefile
index 38047782f1..defdab3ad5 100644
--- a/texlive2013/Makefile
+++ b/texlive2013/Makefile
@@ -7,7 +7,7 @@ PKGNAME= texlive2013-0.2
#BROKEN= Still getting ERROR: [check-interpreter.mk], and NOT fixed yet.
CATEGORIES= print
-MASTER_SITES= ${MASTER_SITE_TEX_CTAN:=systems/texlive/Source/}
+MASTER_SITES= ${MASTER_SITE_TEX_CTAN:=systems/texlive/Source/}
MASTER_SITES+= ftp://tug.org/texlive/historic/2013/
EXTRACT_SUFX= .tar.xz
diff --git a/texlive2013/options.mk b/texlive2013/options.mk
index 87fb78b7e6..fe007e7d23 100644
--- a/texlive2013/options.mk
+++ b/texlive2013/options.mk
@@ -1,7 +1,7 @@
# $NetBSD: options.mk,v 1.1 2013/11/02 13:01:38 makoto Exp $
### Set options
-PKG_OPTIONS_VAR= PKG_OPTIONS.texlive
-PKG_SUPPORTED_OPTIONS= bundle-lib
+PKG_OPTIONS_VAR= PKG_OPTIONS.texlive
+PKG_SUPPORTED_OPTIONS= bundle-lib
# deleting bundle-lib results unable to define FT_Library
PKG_SUGGESTED_OPTIONS= bundle-lib
diff --git a/tftp-hpa/Makefile b/tftp-hpa/Makefile
index 0525b53591..ae80585afb 100644
--- a/tftp-hpa/Makefile
+++ b/tftp-hpa/Makefile
@@ -24,7 +24,7 @@ MAKE_ENV+= INSTALLROOT="${DESTDIR}"
.if !empty(PKG_OPTIONS:Minet6)
# the following is needed at least on MacOS 10.11
# and should not hurt on earlier versions
-CFLAGS.Darwin+= -D__APPLE_USE_RFC_3542
+CFLAGS.Darwin+= -D__APPLE_USE_RFC_3542
.endif
INSTALLATION_DIRS= bin sbin ${PKGMANDIR}/man1 ${PKGMANDIR}/man8
diff --git a/thabit-ttf/Makefile b/thabit-ttf/Makefile
index 82259d4a44..ca4eb21cb0 100644
--- a/thabit-ttf/Makefile
+++ b/thabit-ttf/Makefile
@@ -11,8 +11,8 @@ HOMEPAGE= https://www.arabeyes.org/project.php?proj=Khotot
COMMENT= Thabit (from Arabic:fixed) is a fixed width OpenType font family
LICENSE= ofl-v1.1
-NO_CONFIGURE= yes
-NO_BUILD= yes
+NO_CONFIGURE= yes
+NO_BUILD= yes
USE_LANGUAGES= # none
FONTS_DIRS.ttf= lib/X11/fonts/TTF
diff --git a/thawab/Makefile b/thawab/Makefile
index 3645da5af3..68fcf075d0 100644
--- a/thawab/Makefile
+++ b/thawab/Makefile
@@ -19,8 +19,8 @@ DEPENDS+= ${PYPKGPREFIX}-Paste>=1.7.5.1:../../www/py-paste
WRKSRC= ${WRKDIR}/thawab-3.0.13
USE_PKGLOCALEDIR= yes
-USE_TOOLS+= intltool msgfmt
-USE_LANGUAGES= # none
+USE_TOOLS+= intltool msgfmt
+USE_LANGUAGES= # none
PYDISTUTILSPKG= yes
PYTHON_VERSIONS_INCOMPATIBLE= 34 35 36 # py-gtk2
diff --git a/thepeg/Makefile b/thepeg/Makefile
index 7a426b3056..3d30406a13 100644
--- a/thepeg/Makefile
+++ b/thepeg/Makefile
@@ -12,13 +12,13 @@ HOMEPAGE= http://home.thep.lu.se/~leif/ThePEG/
COMMENT= Toolkit for High Energy Physics Event Generation
LICENSE= gnu-gpl-v2
-CHECK_PORTABILITY_SKIP= configure
+CHECK_PORTABILITY_SKIP= configure
-GNU_CONFIGURE= yes
-USE_LIBTOOL= yes
-USE_TOOLS+= gmake perl
-USE_GNU_READLINE= yes
-USE_LANGUAGES= c c++
+GNU_CONFIGURE= yes
+USE_LIBTOOL= yes
+USE_TOOLS+= gmake perl
+USE_GNU_READLINE= yes
+USE_LANGUAGES= c c++
.include "../../mk/bsd.prefs.mk"
diff --git a/tilda/Makefile b/tilda/Makefile
index 8b68e89c2a..aacdbb626b 100644
--- a/tilda/Makefile
+++ b/tilda/Makefile
@@ -13,7 +13,7 @@ COMMENT= Terminal like the classic first-person-shooter games
GNU_CONFIGURE= yes
USE_TOOLS+= pkg-config intltool msgfmt gmake flex
USE_PKGLOCALEDIR= yes
-USE_DIRS+= xdg-1.4
+USE_DIRS+= xdg-1.4
.include "../../devel/confuse/buildlink3.mk"
.include "../../devel/libglade/buildlink3.mk"
diff --git a/tinycobol/Makefile b/tinycobol/Makefile
index 099832b62b..3d4077832c 100644
--- a/tinycobol/Makefile
+++ b/tinycobol/Makefile
@@ -13,7 +13,7 @@ COMMENT= Tiny COBOL compiler for IA32 platforms
CONFIGURE_ARGS+= --with-libdb=2
-ONLY_FOR_PLATFORM= *-*-i386
+ONLY_FOR_PLATFORM= *-*-i386
USE_TOOLS+= gmake bison
diff --git a/tinycobol/PLIST b/tinycobol/PLIST
index f36f318492..4da119b2ed 100644
--- a/tinycobol/PLIST
+++ b/tinycobol/PLIST
@@ -1,11 +1,11 @@
@comment $NetBSD: PLIST,v 1.1.1.1 2004/07/29 21:34:21 lrfurtado Exp $
bin/htcobol
-share/htcobol/htcobolrc
-lib/libhtcobol.so.0.61.0
lib/libhtcobol.so
lib/libhtcobol.so.0
-share/htcobol/htcobolpp
-share/htcobol/copybooks/screen.cpy
-man/man1/htcobol.1
+lib/libhtcobol.so.0.61.0
man/man1/htcobf2f.1
+man/man1/htcobol.1
man/man1/htcobolpp.1
+share/htcobol/copybooks/screen.cpy
+share/htcobol/htcobolpp
+share/htcobol/htcobolrc
diff --git a/tk-tkimg/Makefile b/tk-tkimg/Makefile
index 82b461be3a..9a2388145f 100644
--- a/tk-tkimg/Makefile
+++ b/tk-tkimg/Makefile
@@ -10,9 +10,9 @@ HOMEPAGE= http://www.flightlab.com/~joe/downloads/
COMMENT= Add support for several image formats to Tk
LICENSE= 2-clause-bsd # XXX ? Same as Tcl
-WRKSRC= ${WRKDIR}/tkimg-1.3
-GNU_CONFIGURE= yes
-TEST_TARGET= test
+WRKSRC= ${WRKDIR}/tkimg-1.3
+GNU_CONFIGURE= yes
+TEST_TARGET= test
INSTALLATION_DIRS+= lib/Img${PKGVERSION}.9
.include "options.mk"
diff --git a/tme/Makefile b/tme/Makefile
index 57c5136260..c24980caaa 100644
--- a/tme/Makefile
+++ b/tme/Makefile
@@ -3,7 +3,7 @@
DISTNAME= tme-0.10
CATEGORIES= emulators
MASTER_SITES= http://phabrics.com/
-EXTRACT_SUFX= .tar.xz
+EXTRACT_SUFX= .tar.xz
MAINTAINER= phabrics%phabrics.com@localhost
diff --git a/tme/PLIST b/tme/PLIST
index 84a682ab0d..0d73bddd57 100644
--- a/tme/PLIST
+++ b/tme/PLIST
@@ -1,7 +1,7 @@
@comment $NetBSD: PLIST,v 1.3 2015/04/19 22:11:33 phabrics Exp $
-bin/tmesh
bin/tme-sun-eeprom
bin/tme-sun-idprom
+bin/tmesh
include/tme/bus/upa.h
include/tme/common.h
include/tme/completion.h
@@ -26,8 +26,8 @@ include/tme/ic/am9513.h
include/tme/ic/bt458.h
include/tme/ic/i825x6.h
include/tme/ic/ieee754-auto.h
-include/tme/ic/ieee754.h
include/tme/ic/ieee754-ops-auto.h
+include/tme/ic/ieee754.h
include/tme/ic/isil7170.h
include/tme/ic/m68k.h
include/tme/ic/mk48txx.h
@@ -50,18 +50,19 @@ include/tme/scsi/scsi-disk.h
include/tme/scsi/scsi-msg.h
include/tme/scsi/scsi-tape.h
include/tme/threads-glib.h
-include/tme/threads.h
include/tme/threads-posix.h
include/tme/threads-sjlj.h
+include/tme/threads.h
include/tme/tme.h
include/tme/tmesh.h
include/tme/token.h
lib/libtme-generic.la
lib/libtme-host-eth.la
lib/libtme-ieee754.la
-lib/libtme.la
lib/libtme-machine-sun.la
+lib/libtme.la
lib/libtmesh.la
+lib/tme/tme-plugins.txt
lib/tme/tme_bus_multibus.la
lib/tme/tme_bus_sbus.la
lib/tme/tme_generic.la
@@ -90,15 +91,14 @@ lib/tme/tme_ic_z8530.la
lib/tme/tme_machine_sun2.la
lib/tme/tme_machine_sun3.la
lib/tme/tme_machine_sun4.la
-lib/tme/tme-plugins.txt
lib/tme/tme_scsi.la
lib/tme/tme_serial_kb.la
-share/examples/tme/my-sun-macros.txt
+share/examples/tme/SUN-ULTRA-1
share/examples/tme/SUN2-MULTIBUS
share/examples/tme/SUN3-CARRERA
-share/examples/tme/sun3-carrera-eeprom.txt
share/examples/tme/SUN4-75
+share/examples/tme/my-sun-macros.txt
share/examples/tme/sun-keyboards.txt
-share/examples/tme/SUN-ULTRA-1
+share/examples/tme/sun3-carrera-eeprom.txt
share/tme/tmeconfig.h
share/tme/tmememory.h
diff --git a/tmuni-ttf/Makefile b/tmuni-ttf/Makefile
index 8eda9d15d9..2d430e00c2 100644
--- a/tmuni-ttf/Makefile
+++ b/tmuni-ttf/Makefile
@@ -4,7 +4,7 @@
DISTNAME= ttf-tmuni_1.901b.orig
PKGNAME= tmuni-ttf-1.901b
CATEGORIES= fonts
-MASTER_SITES= ${MASTER_SITE_DEBIAN:=pool/main/t/ttf-tmuni/}
+MASTER_SITES= ${MASTER_SITE_DEBIAN:=pool/main/t/ttf-tmuni/}
MAINTAINER= pho%cielonegro.org@localhost
HOMEPAGE= http://www.thlib.org/tools/scripts/wiki/tibetan%20machine%20uni.html
@@ -13,12 +13,12 @@ LICENSE= gnu-gpl-v2
WRKSRC= ${WRKDIR}/${DISTNAME:S/_/-/}
NO_BUILD= YES
-NO_CONFIGURE= YES
+NO_CONFIGURE= YES
FONTS_DIRS.ttf= ${PREFIX}/lib/X11/fonts/TTF
INSTALLATION_DIRS+= ${FONTS_DIRS.ttf}
-DOCDIR= ${PREFIX}/share/doc/${PKGNAME}
+DOCDIR= ${PREFIX}/share/doc/${PKGNAME}
INSTALLATION_DIRS+= ${DOCDIR}
do-install:
diff --git a/tmw/Makefile b/tmw/Makefile
index e4ac3d67c9..dd0e0e7716 100644
--- a/tmw/Makefile
+++ b/tmw/Makefile
@@ -11,10 +11,10 @@ HOMEPAGE= http://themanaworld.sourceforge.net/
COMMENT= Free open source 2D MMORPG in development
-GNU_CONFIGURE= yes
-USE_LANGUAGES= c c++
+GNU_CONFIGURE= yes
+USE_LANGUAGES= c c++
CONFIGURE_ARGS+= --with-opengl
-USE_TOOLS+= pkg-config
+USE_TOOLS+= pkg-config
.include "../../sysutils/desktop-file-utils/desktopdb.mk"
diff --git a/todotxt-git/Makefile b/todotxt-git/Makefile
index 1607aedaf6..78c8eabcd2 100644
--- a/todotxt-git/Makefile
+++ b/todotxt-git/Makefile
@@ -14,8 +14,8 @@ MAINTAINER= pkgsrc-users%NetBSD.org@localhost
HOMEPAGE= http://todotxt.com/
PKG_DESTDIR_SUPPORT= user-destdir
-DEPENDS= bash>=4.3:../../shells/bash
-DEPENDS+= bash-completion>=2.1:../../shells/bash-completion
+DEPENDS= bash>=4.3:../../shells/bash
+DEPENDS+= bash-completion>=2.1:../../shells/bash-completion
WRKSRC= ${WRKDIR}/todo.txt-cli
@@ -34,7 +34,7 @@ NO_BUILD= yes
EGDIR= share/examples/todotxt
DOCDIR= share/doc/todotxt
-INSTALLATION_DIRS= bin ${DOCDIR} ${EGDIR}
+INSTALLATION_DIRS= bin ${DOCDIR} ${EGDIR}
do-install:
${INSTALL_SCRIPT} ${WRKSRC}/todo.sh ${DESTDIR}${PREFIX}/bin
diff --git a/tophat/PLIST b/tophat/PLIST
index 96f3f27ee6..7f15ee3d67 100644
--- a/tophat/PLIST
+++ b/tophat/PLIST
@@ -24,6 +24,6 @@ bin/sortedcontainers/sortedlistwithkey.py
bin/sortedcontainers/sortedset.py
bin/sra_to_solid
bin/tophat
-bin/tophat2
bin/tophat-fusion-post
+bin/tophat2
bin/tophat_reports
diff --git a/tor-dev/Makefile b/tor-dev/Makefile
index 27960b7b8b..55184af901 100644
--- a/tor-dev/Makefile
+++ b/tor-dev/Makefile
@@ -34,7 +34,7 @@ PKG_SYSCONFSUBDIR= tordev
PKG_GROUPS_VARS+= TOR_GROUP
PKG_USERS_VARS= TOR_USER
-RCD_SCRIPTS= tordev
+RCD_SCRIPTS= tordev
RCD_SCRIPT_SRC.tordev= ${FILESDIR}/tordev.in
PKG_GROUPS= ${TOR_GROUP}
PKG_USERS= ${TOR_USER}:${TOR_GROUP}
@@ -55,7 +55,7 @@ FILES_SUBST+= TOR_USER=${TOR_USER} TOR_GROUP=${TOR_GROUP}
INSTALL_MAKE_FLAGS+= sysconfdir=${PREFIX}/share/examples
-CHECK_PORTABILITY_SKIP+=contrib/*
+CHECK_PORTABILITY_SKIP+= contrib/*
.include "../../mk/bsd.prefs.mk"
diff --git a/tor-dev/PLIST b/tor-dev/PLIST
index d55baf3643..45782eb57c 100644
--- a/tor-dev/PLIST
+++ b/tor-dev/PLIST
@@ -3,9 +3,9 @@ bin/tor-dev
bin/tor-gencert-dev
bin/tor-resolve-dev
bin/torify-dev
+${PLIST.doc}man/man1/tor-dev.1
${PLIST.doc}man/man1/tor-gencert-dev.1
${PLIST.doc}man/man1/tor-resolve-dev.1
-${PLIST.doc}man/man1/tor-dev.1
${PLIST.doc}man/man1/torify-dev.1
${PLIST.doc}share/doc/tordev/tor-gencert.html
${PLIST.doc}share/doc/tordev/tor-resolve.html
diff --git a/torsocks-git/Makefile b/torsocks-git/Makefile
index b89ee7c4b5..87d4e7a26b 100644
--- a/torsocks-git/Makefile
+++ b/torsocks-git/Makefile
@@ -9,9 +9,9 @@ COMMENT= Library to torify applications
LICENSE= gnu-gpl-v2
-GIT_REPOSITORIES= master
-GIT_REPO.master= https://git.torproject.org/torsocks.git
-GIT_MODULE.master= torsocks
+GIT_REPOSITORIES= master
+GIT_REPO.master= https://git.torproject.org/torsocks.git
+GIT_MODULE.master= torsocks
DIST_SUBDIR= torsocks
diff --git a/toxcore-git/Makefile b/toxcore-git/Makefile
index 8f767ff197..56ff4dcd95 100644
--- a/toxcore-git/Makefile
+++ b/toxcore-git/Makefile
@@ -6,7 +6,7 @@ MASTER_SITES= ${MASTER_SITE_GITHUB:=toktok/}
GIT_REPOSITORIES= c-toxcore
GIT_REPO.c-toxcore= http://github.com/toktok/c-toxcore.git
-WRKSRC= ${WRKDIR}/c-toxcore
+WRKSRC= ${WRKDIR}/c-toxcore
MAINTAINER= pkgsrc-users%NetBSD.org@localhost
HOMEPAGE= https://tox.chat/
diff --git a/toxcore/Makefile b/toxcore/Makefile
index 3afa6240f0..227fd2b825 100644
--- a/toxcore/Makefile
+++ b/toxcore/Makefile
@@ -7,9 +7,9 @@ MASTER_SITES= ${MASTER_SITE_GITHUB:=TokTok/}
GITHUB_RELEASE= v0.1.11
MAINTAINER= root%zta.lk@localhost
-HOMEPAGE= https://tox.chat/
-COMMENT= Tox protocol library
-LICENSE= gnu-gpl-v3
+HOMEPAGE= https://tox.chat/
+COMMENT= Tox protocol library
+LICENSE= gnu-gpl-v3
GNU_CONFIGURE= yes
USE_CMAKE= yes
diff --git a/toxic-git/Makefile b/toxic-git/Makefile
index aaab7f4b3b..110617ebc6 100644
--- a/toxic-git/Makefile
+++ b/toxic-git/Makefile
@@ -5,8 +5,8 @@ CATEGORIES= chat
MASTER_SITES= ${MASTER_SITE_GITHUB:=JFreegman/}
GIT_REPOSITORIES= toxic
-GIT_REPO.toxic= https://github.com/JFreegman/toxic.git
-WRKSRC= ${WRKDIR}/toxic
+GIT_REPO.toxic= https://github.com/JFreegman/toxic.git
+WRKSRC= ${WRKDIR}/toxic
MAINTAINER= pkgsrc-users%NetBSD.org@localhost
HOMEPAGE= https://wiki.tox.chat/clients/toxic
diff --git a/toxic-git/options.mk b/toxic-git/options.mk
index ec5c397bdd..91a490979a 100644
--- a/toxic-git/options.mk
+++ b/toxic-git/options.mk
@@ -1,8 +1,8 @@
# $NetBSD$
PKG_OPTIONS_VAR= PKG_OPTIONS.toxic
-PKG_SUPPORTED_OPTIONS+= notify x11
-PKG_SUGGESTED_OPTIONS+= notify x11
+PKG_SUPPORTED_OPTIONS+= notify x11
+PKG_SUGGESTED_OPTIONS+= notify x11
.include "../../mk/bsd.options.mk"
diff --git a/tpl/Makefile b/tpl/Makefile
index 30e466b3d4..6214bef5e2 100644
--- a/tpl/Makefile
+++ b/tpl/Makefile
@@ -10,7 +10,7 @@ HOMEPAGE= https://github.com/troydhanson/tpl/
COMMENT= Store and reload your C data
LICENSE= 2-clause-bsd
-GNU_CONFIGURE= yes
+GNU_CONFIGURE= yes
USE_LIBTOOL= yes
USE_TOOLS+= automake autoconf aclocal
USE_LANGUAGES= c c++
diff --git a/tqsllib/Makefile b/tqsllib/Makefile
index 81e8179fb1..20e04cdb5a 100644
--- a/tqsllib/Makefile
+++ b/tqsllib/Makefile
@@ -20,7 +20,7 @@ USE_LIBTOOL= yes
WRKSRC= ${WRKDIR}/${PKGNAME_NOREV}
# There is a failure to find tqsllib.la; this fixed it (situation not clear).
-MAKE_JOBS_SAFE= no
+MAKE_JOBS_SAFE= no
# The configure script is broken and looks in explicit paths, instead
# of just trying to link.
CONFIGURE_ARGS+= --with-expat=${BUILDLINK_PREFIX.expat}
diff --git a/tr2latex/Makefile b/tr2latex/Makefile
index 4e8b962d74..65e535be91 100644
--- a/tr2latex/Makefile
+++ b/tr2latex/Makefile
@@ -25,9 +25,9 @@ DIST_SUBDIR= ${PKGNAME_NOREV}
# also tar ball has windows executable?
# todo: maybe patch Makefile.unix for CC and CFLAGS not overwritten
-MAKE_FILE= Makefile.unix
-BUILD_TARGET= tr2latex
-PKGMANDIR?= man # until in pkgsrc
+MAKE_FILE= Makefile.unix
+BUILD_TARGET= tr2latex
+PKGMANDIR?= man # until in pkgsrc
INSTALLATION_DIRS= bin ${PKGMANDIR}/man1 share/texmf-dist/tex/latex/misc
do-install:
diff --git a/trac-plugins-GraphViz-svn/Makefile b/trac-plugins-GraphViz-svn/Makefile
index 62b8938aa4..5bbbd58fa3 100644
--- a/trac-plugins-GraphViz-svn/Makefile
+++ b/trac-plugins-GraphViz-svn/Makefile
@@ -2,13 +2,13 @@
SVNVERSION= 13275
UPSTREAM_VERSION= 0.7.7
-VERSION= ${UPSTREAM_VERSION}.${SVNVERSION}
-DISTNAME= TracGraphViz-${VERSION}
-PKGNAME= trac-plugins-GraphViz-${VERSION}
+VERSION= ${UPSTREAM_VERSION}.${SVNVERSION}
+DISTNAME= TracGraphViz-${VERSION}
+PKGNAME= trac-plugins-GraphViz-${VERSION}
# Empty to avoid default setting.
-PKGREVISION= 1
-CATEGORIES= www
-MASTER_SITES= # not defined
+PKGREVISION= 1
+CATEGORIES= www
+MASTER_SITES= # not defined
MAINTAINER= pkgsrc-users%netbsd.org@localhost
HOMEPAGE= https://trac-hacks.org/wiki/GraphVizPlugin
diff --git a/trac-plugins-MasterTickets-svn/Makefile b/trac-plugins-MasterTickets-svn/Makefile
index 830c4e7020..051ef1b8a8 100644
--- a/trac-plugins-MasterTickets-svn/Makefile
+++ b/trac-plugins-MasterTickets-svn/Makefile
@@ -1,13 +1,13 @@
# $NetBSD: Makefile,v 1.14 2015/08/04 20:04:16 thomasklausner Exp $
UPSTREAM_VERSION= 3.90
-DISTNAME= TracMasterTickets-${UPSTREAM_VERSION}
-VERSION= ${UPSTREAM_VERSION}.${SVN_TAG.mastertickets}
-PKGNAME= trac-plugins-MasterTickets-${VERSION}
+DISTNAME= TracMasterTickets-${UPSTREAM_VERSION}
+VERSION= ${UPSTREAM_VERSION}.${SVN_TAG.mastertickets}
+PKGNAME= trac-plugins-MasterTickets-${VERSION}
# PKGREVISION must exist for svn, or else it will get a date
PKGREVISION=
-CATEGORIES= www
-MASTER_SITES= # not defined
+CATEGORIES= www
+MASTER_SITES= # not defined
MAINTAINER= gdt%NetBSD.org@localhost
HOMEPAGE= https://trac-hacks.org/wiki/MasterTicketsPlugin
diff --git a/trac-plugins-SensitiveTickets-svn/Makefile b/trac-plugins-SensitiveTickets-svn/Makefile
index 7c701a7e74..2bb1ae688a 100644
--- a/trac-plugins-SensitiveTickets-svn/Makefile
+++ b/trac-plugins-SensitiveTickets-svn/Makefile
@@ -1,8 +1,8 @@
# $NetBSD: Makefile,v 1.10 2015/08/04 20:04:16 thomasklausner Exp $
UPSTREAM_VERSION= 0.22
-VERSION= ${UPSTREAM_VERSION}.${SVN_VERSION}
-SVN_VERSION= 12834
+VERSION= ${UPSTREAM_VERSION}.${SVN_VERSION}
+SVN_VERSION= 12834
DISTNAME= TracSensitiveTickets-${VERSION}
PKGNAME= trac-plugins-SensitiveTickets-${VERSION}
@@ -22,10 +22,10 @@ DEPENDS+= trac>=0.11:../../www/trac
EGG_NAME= sensitivetickets-${UPSTREAM_VERSION}
-SVN_REPOSITORIES= sensitivetickets
+SVN_REPOSITORIES= sensitivetickets
SVN_REPO.sensitivetickets= https://trac-hacks.org/svn/sensitiveticketsplugin/trunk
SVN_REVISION.sensitivetickets= ${SVN_VERSION}
-WRKSRC= ${WRKDIR}/sensitivetickets
+WRKSRC= ${WRKDIR}/sensitivetickets
NO_CHECKSUM= yes
diff --git a/trac-plugins-TimingAndEstimation-svn/Makefile b/trac-plugins-TimingAndEstimation-svn/Makefile
index 5bf3acaec9..9759a9f6ff 100644
--- a/trac-plugins-TimingAndEstimation-svn/Makefile
+++ b/trac-plugins-TimingAndEstimation-svn/Makefile
@@ -22,7 +22,7 @@ PYTHON_VERSIONS_INCOMPATIBLE= 34 35 36 # not yet ported as of 1.2.8/11739
SVN_REPOSITORIES= plugin
SVN_REPO.plugin= https://trac-hacks.org/svn/timingandestimationplugin/branches/trac0.12
-SVN_REVISION.plugin= ${SVNVERSION}
+SVN_REVISION.plugin= ${SVNVERSION}
NO_CHECKSUM= yes
diff --git a/trac-plugins-spamfilter-svn/Makefile b/trac-plugins-spamfilter-svn/Makefile
index 8b43a6bb88..383ad6fa0c 100644
--- a/trac-plugins-spamfilter-svn/Makefile
+++ b/trac-plugins-spamfilter-svn/Makefile
@@ -16,9 +16,9 @@ DEPENDS+= ${PYPKGPREFIX}-dns-[0-9]*:../../net/py-dns
PYTHON_VERSIONS_INCOMPATIBLE= 34 35 36 # not yet ported as of 0.3.2dev/9935
-SVN_REPOSITORIES= spamfilter
-SVN_REPO.spamfilter= https://svn.edgewall.org/repos/trac/plugins/0.12/spam-filter-captcha
-SVN_REVISION.spamfilter=${SVNREV}
+SVN_REPOSITORIES= spamfilter
+SVN_REPO.spamfilter= https://svn.edgewall.org/repos/trac/plugins/0.12/spam-filter-captcha
+SVN_REVISION.spamfilter= ${SVNREV}
NO_CHECKSUM= yes
diff --git a/translate-toolkit/options.mk b/translate-toolkit/options.mk
index 782b5dbbf8..8f02bf9275 100644
--- a/translate-toolkit/options.mk
+++ b/translate-toolkit/options.mk
@@ -13,7 +13,7 @@ DEPENDS+= ${PYPKGPREFIX}-lxml>=3.5:../../textproc/py-lxml
.endif
.if !empty(PKG_OPTIONS:Mlevenshtein)
-DEPENDS+= ${PYPKGPREFIX}-Levenshtein>=0.12:../../textproc/py-Levenshtein
+DEPENDS+= ${PYPKGPREFIX}-Levenshtein>=0.12:../../textproc/py-Levenshtein
.endif
.if !empty(PKG_OPTIONS:Mchardet)
@@ -29,14 +29,14 @@ DEPENDS+= ${PYPKGPREFIX}-beautifulsoup4>=4.3:../../www/py-beautifulsoup4
.endif
.if !empty(PKG_OPTIONS:Mdoc)
-BUILD_DEPENDS+= ${PYPKGPREFIX}-sphinx>=1.6.3.:../../textproc/py-sphinx
+BUILD_DEPENDS+= ${PYPKGPREFIX}-sphinx>=1.6.3.:../../textproc/py-sphinx
SUBST_CLASSES+= sphinx
SUBST_SED.sphinx+= -e "s,sphinx-build,sphinx-build${PYVERSSUFFIX},"
SUBST_FILES.sphinx+= docs/Makefile
SUBST_STAGE.sphinx= pre-configure
SUBST_MESSAGE.sphinx= Fix sphinx command names.
INSTALLATION_DIRS+= ${PKGMANDIR}/man1
-PLIST.doc= yes
+PLIST.doc= yes
pre-build:
cd ${WRKSRC}/docs && ${MAKE} man
diff --git a/triangle/Makefile b/triangle/Makefile
index 959dac0a7c..03274d8676 100644
--- a/triangle/Makefile
+++ b/triangle/Makefile
@@ -16,7 +16,7 @@ WRKSRC= ${WRKDIR}
VERSION= 1.6
MAKE_FILE= makefile
-INSTALLATION_DIRS= bin
+INSTALLATION_DIRS= bin
do-install:
${INSTALL_PROGRAM} ${WRKSRC}/${DISTNAME} ${DESTDIR}${PREFIX}/bin
diff --git a/trinity/Makefile b/trinity/Makefile
index 6f422ef92f..4ec9e0cafb 100644
--- a/trinity/Makefile
+++ b/trinity/Makefile
@@ -56,7 +56,7 @@ LICENSE= modified-bsd
# Test and change if necessary.
# MAKE_JOBS_SAFE= no
-ONLY_FOR_PLATFORM= *-*-x86_64
+ONLY_FOR_PLATFORM= *-*-x86_64
SUBST_CLASSES+= env
SUBST_STAGE.env= post-patch
diff --git a/trinity/PLIST b/trinity/PLIST
index 4775fad716..2494e2479f 100644
--- a/trinity/PLIST
+++ b/trinity/PLIST
@@ -2,7 +2,6 @@
bin/Trinity
libexec/trinity/Butterfly/Butterfly.jar
libexec/trinity/Chrysalis/BreakTransByPairs
-libexec/trinity/Chrysalis/checkLock
libexec/trinity/Chrysalis/Chrysalis
libexec/trinity/Chrysalis/CreateIwormFastaBundle
libexec/trinity/Chrysalis/GraphFromFasta
@@ -16,15 +15,15 @@ libexec/trinity/Chrysalis/ReadsToTranscripts_MPI
libexec/trinity/Chrysalis/ReadsToTranscripts_MPI_chang
libexec/trinity/Chrysalis/RunButterfly
libexec/trinity/Chrysalis/TranscriptomeFromVaryK
-libexec/trinity/Inchworm/bin/cigar_tweaker
+libexec/trinity/Chrysalis/checkLock
libexec/trinity/Inchworm/bin/FastaToDeBruijn
+libexec/trinity/Inchworm/bin/cigar_tweaker
libexec/trinity/Inchworm/bin/fastaToKmerCoverageStats
libexec/trinity/Inchworm/bin/inchworm
libexec/trinity/Inchworm/bin/pull_reads_with_kmers
libexec/trinity/PerlLib/Ascii_genome_illustrator.pm
libexec/trinity/PerlLib/BED_utils.pm
libexec/trinity/PerlLib/BHStats.pm
-libexec/trinity/PerlLib/CanvasXpress/Heatmap.pm
libexec/trinity/PerlLib/CDNA/Alignment_segment.pm
libexec/trinity/PerlLib/CDNA/Alternative_splice_comparer.pm
libexec/trinity/PerlLib/CDNA/CDNA_alignment.pm
@@ -37,20 +36,21 @@ libexec/trinity/PerlLib/CDNA/PASA_alignment_assembler.pm
libexec/trinity/PerlLib/CDNA/Splice_graph_assembler.pm
libexec/trinity/PerlLib/CIGAR.pm
libexec/trinity/PerlLib/CMD_processor.pm
-libexec/trinity/PerlLib/ColorGradient.pm
libexec/trinity/PerlLib/COMMON.pm
+libexec/trinity/PerlLib/CanvasXpress/Heatmap.pm
+libexec/trinity/PerlLib/ColorGradient.pm
libexec/trinity/PerlLib/EM.pm
libexec/trinity/PerlLib/Exons_to_geneobj.pm
libexec/trinity/PerlLib/Fasta_reader.pm
libexec/trinity/PerlLib/Fasta_retriever.pm
libexec/trinity/PerlLib/Fastq_reader.pm
-libexec/trinity/PerlLib/Gene_obj_indexer.pm
-libexec/trinity/PerlLib/Gene_obj.pm
libexec/trinity/PerlLib/GFF3_alignment_utils.pm
libexec/trinity/PerlLib/GFF3_utils.pm
libexec/trinity/PerlLib/GFF_maker.pm
libexec/trinity/PerlLib/GTF.pm
libexec/trinity/PerlLib/GTF_utils.pm
+libexec/trinity/PerlLib/Gene_obj.pm
+libexec/trinity/PerlLib/Gene_obj_indexer.pm
libexec/trinity/PerlLib/HPC/Base_handler.pm
libexec/trinity/PerlLib/HPC/FarmIt.pm
libexec/trinity/PerlLib/HPC/GridRunner.pm
@@ -78,26 +78,29 @@ libexec/trinity/PerlLib/Longest_orf.pm
libexec/trinity/PerlLib/Nuc_translator.pm
libexec/trinity/PerlLib/Overlap_info.pm
libexec/trinity/PerlLib/Overlap_piler.pm
-libexec/trinity/PerlLib/overlapping_nucs.ph
+libexec/trinity/PerlLib/PSL_parser.pm
libexec/trinity/PerlLib/Pipeliner.pm
libexec/trinity/PerlLib/Process_cmd.pm
-libexec/trinity/PerlLib/PSL_parser.pm
libexec/trinity/PerlLib/SAM_entry.pm
libexec/trinity/PerlLib/SAM_reader.pm
libexec/trinity/PerlLib/Simulate/Uniform_Read_Generator.pm
libexec/trinity/PerlLib/SingleLinkageClusterer.pm
-libexec/trinity/PerlLib/test_Fasta_retriever.pl
-libexec/trinity/PerlLib/test_htc_gridrunner_LSF.pl
-libexec/trinity/PerlLib/test_htc_gridrunner_SGE.pl
libexec/trinity/PerlLib/Thread_helper.pm
libexec/trinity/PerlLib/TiedHash.pm
libexec/trinity/PerlLib/VCF_parser.pm
libexec/trinity/PerlLib/WigParser.pm
+libexec/trinity/PerlLib/overlapping_nucs.ph
+libexec/trinity/PerlLib/test_Fasta_retriever.pl
+libexec/trinity/PerlLib/test_htc_gridrunner_LSF.pl
+libexec/trinity/PerlLib/test_htc_gridrunner_SGE.pl
+libexec/trinity/trinity-plugins/GAL_0.2.1/README
+libexec/trinity/trinity-plugins/GAL_0.2.1/fasta_tool
+libexec/trinity/trinity-plugins/collectl/bin/UNINSTALL
libexec/trinity/trinity-plugins/collectl/bin/client.pl
libexec/trinity/trinity-plugins/collectl/bin/col2tlviz.pl
libexec/trinity/trinity-plugins/collectl/bin/collectl
-libexec/trinity/trinity-plugins/collectl/bin/collectl2html
libexec/trinity/trinity-plugins/collectl/bin/collectl.conf
+libexec/trinity/trinity-plugins/collectl/bin/collectl2html
libexec/trinity/trinity-plugins/collectl/bin/envrules.std
libexec/trinity/trinity-plugins/collectl/bin/formatit.ph
libexec/trinity/trinity-plugins/collectl/bin/gexpr.ph
@@ -109,15 +112,38 @@ libexec/trinity/trinity-plugins/collectl/bin/misc.ph
libexec/trinity/trinity-plugins/collectl/bin/plot.py
libexec/trinity/trinity-plugins/collectl/bin/proctree.ph
libexec/trinity/trinity-plugins/collectl/bin/timetable.py
-libexec/trinity/trinity-plugins/collectl/bin/UNINSTALL
libexec/trinity/trinity-plugins/collectl/bin/vmstat.ph
-libexec/trinity/trinity-plugins/GAL_0.2.1/fasta_tool
-libexec/trinity/trinity-plugins/GAL_0.2.1/README
libexec/trinity/trinity-plugins/scaffold_iworm_contigs/scaffold_iworm_contigs
+libexec/trinity/util/PBS/N50stats.pl
+libexec/trinity/util/PBS/README
+libexec/trinity/util/PBS/TRINITY.CONFIG.template
+libexec/trinity/util/PBS/pbs_check.pl
+libexec/trinity/util/PBS/trinity_kill.pl
+libexec/trinity/util/PBS/trinity_kill.sh
+libexec/trinity/util/PBS/trinity_pbs.cont
+libexec/trinity/util/PBS/trinity_pbs.header
+libexec/trinity/util/PBS/trinity_pbs.p1
+libexec/trinity/util/PBS/trinity_pbs.p2
+libexec/trinity/util/PBS/trinity_pbs.p3
+libexec/trinity/util/PBS/trinity_pbs.p4a
+libexec/trinity/util/PBS/trinity_pbs.p4b
+libexec/trinity/util/PBS/trinity_pbs.p5b
+libexec/trinity/util/PBS/trinity_pbs.sh
+libexec/trinity/util/R/expression_analysis_lib.R
+libexec/trinity/util/R/get_Poisson_conf_intervals.R
+libexec/trinity/util/R/noiseq.r
+libexec/trinity/util/SAM_nameSorted_to_uniq_count_stats.pl
+libexec/trinity/util/TrinityStats.pl
libexec/trinity/util/abundance_estimates_to_matrix.pl
libexec/trinity/util/align_and_estimate_abundance.pl
libexec/trinity/util/analyze_blastPlus_topHit_coverage.pl
libexec/trinity/util/bowtie_PE_separate_then_join.pl
+libexec/trinity/util/deprecated/PairPathsToGraphDot.pl
+libexec/trinity/util/deprecated/RSEM_util/Nx_rsem_to_table.pl
+libexec/trinity/util/deprecated/RSEM_util/merge_RSEM_counts_and_labels_single_table.pl
+libexec/trinity/util/deprecated/RSEM_util/merge_RSEM_frag_counts_single_table.pl
+libexec/trinity/util/deprecated/RSEM_util/merge_RSEM_output_to_matrix.pl
+libexec/trinity/util/deprecated/RSEM_util/run_RSEM_align_n_estimate.pl
libexec/trinity/util/deprecated/alignReads.pl
libexec/trinity/util/deprecated/annot_genome_SAM_to_transcript_FPKM_simple.pl
libexec/trinity/util/deprecated/annot_genome_SAM_to_transcriptome_SAM.pl
@@ -132,19 +158,35 @@ libexec/trinity/util/deprecated/eXpress_util/run_eXpress_align_n_estimate.pl
libexec/trinity/util/deprecated/eXpress_util/usage.txt
libexec/trinity/util/deprecated/eXpress_util/use_express.py
libexec/trinity/util/deprecated/fasta_to_deBruijn_graph.pl
-libexec/trinity/util/deprecated/PairPathsToGraphDot.pl
libexec/trinity/util/deprecated/purge_dir.pl
-libexec/trinity/util/deprecated/RSEM_util/merge_RSEM_counts_and_labels_single_table.pl
-libexec/trinity/util/deprecated/RSEM_util/merge_RSEM_frag_counts_single_table.pl
-libexec/trinity/util/deprecated/RSEM_util/merge_RSEM_output_to_matrix.pl
-libexec/trinity/util/deprecated/RSEM_util/Nx_rsem_to_table.pl
-libexec/trinity/util/deprecated/RSEM_util/run_RSEM_align_n_estimate.pl
libexec/trinity/util/deprecated/run_AllpathsLG_error_correction.pl
libexec/trinity/util/deprecated/sort_fasta.sh
libexec/trinity/util/deprecated/write_inchworm_cmds.pl
libexec/trinity/util/fasta_tool
libexec/trinity/util/filter_fasta_by_rsem_values.pl
libexec/trinity/util/insilico_read_normalization.pl
+libexec/trinity/util/misc/Artemis/join_multi_wig_to_graph_plot.pl
+libexec/trinity/util/misc/BLAT_to_SAM.pl
+libexec/trinity/util/misc/ButterflyFastaToGraphDot.pl
+libexec/trinity/util/misc/HiCpipe_nameSortedSam_to_raw.pl
+libexec/trinity/util/misc/Monarch
+libexec/trinity/util/misc/Monarch_util/generate_gene_alt_splicing_graphs.pl
+libexec/trinity/util/misc/Monarch_util/generate_trans_graphs.pl
+libexec/trinity/util/misc/N50.pl
+libexec/trinity/util/misc/PerlLib/SegmentGraph.pm
+libexec/trinity/util/misc/SAM_coordsorted_max_reads_per_position.pl
+libexec/trinity/util/misc/SAM_intron_extractor.pl
+libexec/trinity/util/misc/SAM_pair_to_bed.pl
+libexec/trinity/util/misc/SAM_show_alignment.pl
+libexec/trinity/util/misc/SAM_show_alignment.summarize_stats.pl
+libexec/trinity/util/misc/SAM_sortAny_to_count_stats.pl
+libexec/trinity/util/misc/SAM_toString.pl
+libexec/trinity/util/misc/SAM_to_bed.pl
+libexec/trinity/util/misc/SAM_to_fasta.pl
+libexec/trinity/util/misc/SRA_to_fastq.notes
+libexec/trinity/util/misc/SRA_to_fastq.pl
+libexec/trinity/util/misc/TEST_SUPPORT/BFLY_TESTING/graph_out_to_bfly_cmd.pl
+libexec/trinity/util/misc/TophatCufflinksWrapper.pl
libexec/trinity/util/misc/acc_list_to_fasta_entries.pl
libexec/trinity/util/misc/alexie_analyze_blast.pl
libexec/trinity/util/misc/allele_simulator.pl
@@ -153,25 +195,22 @@ libexec/trinity/util/misc/analyze_blastPlus_topHit_coverage.annotate_details_w_F
libexec/trinity/util/misc/analyze_blastPlus_topHit_coverage.by_prioritized_compreh_category.pl
libexec/trinity/util/misc/analyze_blastPlus_topHit_coverage.extract_OS.pl
libexec/trinity/util/misc/analyze_blastPlus_topHit_coverage.org_matrix.pl
-libexec/trinity/util/misc/Artemis/join_multi_wig_to_graph_plot.pl
libexec/trinity/util/misc/average.pl
libexec/trinity/util/misc/bam_gene_tests/extract_bam_reads_per_target_gene.pl
libexec/trinity/util/misc/bam_gene_tests/extract_bam_reads_per_target_transcript.pl
libexec/trinity/util/misc/bam_gene_tests/harvest_transcripts.pl
libexec/trinity/util/misc/bam_gene_tests/write_trin_cmds.pl
-libexec/trinity/util/misc/blastn_wrapper.pl
libexec/trinity/util/misc/blast_outfmt6_group_segments.pl
libexec/trinity/util/misc/blast_outfmt6_group_segments.to_Markov_Clustering.pl
libexec/trinity/util/misc/blast_outfmt6_group_segments.tophit_coverage.pl
-libexec/trinity/util/misc/BLAT_to_SAM.pl
+libexec/trinity/util/misc/blastn_wrapper.pl
libexec/trinity/util/misc/blat_util/blat_sam_add_reads2.pl
-libexec/trinity/util/misc/blat_util/blat_top_hit_extractor.pl
libexec/trinity/util/misc/blat_util/blat_to_sam.pl
+libexec/trinity/util/misc/blat_util/blat_top_hit_extractor.pl
libexec/trinity/util/misc/blat_util/process_BLAT_alignments.pl
libexec/trinity/util/misc/blat_util/pslx_to_gff3.pl
libexec/trinity/util/misc/blat_util/run_BLAT_shortReads.pl
libexec/trinity/util/misc/blat_util/top_blat_sam_extractor.pl
-libexec/trinity/util/misc/ButterflyFastaToGraphDot.pl
libexec/trinity/util/misc/capture_orig_n_unmapped_reads.pl
libexec/trinity/util/misc/cat_require_newlines.pl
libexec/trinity/util/misc/cdna_fasta_file_to_transcript_gtf.pl
@@ -182,10 +221,10 @@ libexec/trinity/util/misc/compare_bflies.pl
libexec/trinity/util/misc/component_to_graph_dot.pl
libexec/trinity/util/misc/contig_ExN50_statistic.pl
libexec/trinity/util/misc/convert_fasta_identifiers_for_FL_analysis.pl
+libexec/trinity/util/misc/count_N50_given_MIN_FPKM_threshold.pl
libexec/trinity/util/misc/count_features_given_MIN_FPKM_threshold.pl
libexec/trinity/util/misc/count_iso_per_gene_dist.pl
libexec/trinity/util/misc/count_matrix_features_given_MIN_TPM_threshold.pl
-libexec/trinity/util/misc/count_N50_given_MIN_FPKM_threshold.pl
libexec/trinity/util/misc/count_number_fasta_seqs.pl
libexec/trinity/util/misc/count_trans_per_component.pl
libexec/trinity/util/misc/decode_SAM_flag_value.pl
@@ -194,19 +233,19 @@ libexec/trinity/util/misc/examine_iworm_FL_across_threads.pl
libexec/trinity/util/misc/examine_weldmer_halves.pl
libexec/trinity/util/misc/extract_fastQ_pairings.pl
libexec/trinity/util/misc/fan_out_fasta_seqs_to_indiv_files.pl
+libexec/trinity/util/misc/fastQ_append_acc.pl
+libexec/trinity/util/misc/fastQ_rand_subset.pl
+libexec/trinity/util/misc/fastQ_rand_subset.reservoir_sampling_reqiures_high_mem.pl
+libexec/trinity/util/misc/fastQ_top_N_records.pl
libexec/trinity/util/misc/fasta_file_reformatter.pl
libexec/trinity/util/misc/fasta_filter_by_min_length.pl
libexec/trinity/util/misc/fasta_remove_duplicates.pl
libexec/trinity/util/misc/fasta_to_cmd_generator.pl
libexec/trinity/util/misc/fasta_write_sense_n_anti.pl
-libexec/trinity/util/misc/fastQ_append_acc.pl
libexec/trinity/util/misc/fastq_cleaner.pl
libexec/trinity/util/misc/fastq_interleave_pairs.pl
libexec/trinity/util/misc/fastq_merge_sorted_tab_lists.pl
-libexec/trinity/util/misc/fastQ_rand_subset.pl
-libexec/trinity/util/misc/fastQ_rand_subset.reservoir_sampling_reqiures_high_mem.pl
libexec/trinity/util/misc/fastq_stats.pl
-libexec/trinity/util/misc/fastQ_top_N_records.pl
libexec/trinity/util/misc/fastq_unweave_pairs.pl
libexec/trinity/util/misc/frag_boundary_to_wig.pl
libexec/trinity/util/misc/frag_to_bed.pl
@@ -226,12 +265,11 @@ libexec/trinity/util/misc/gmap_gff3_to_percent_length_stats.pl
libexec/trinity/util/misc/gmap_native_to_format_converter.pl
libexec/trinity/util/misc/gtf_to_bed_format.pl
libexec/trinity/util/misc/gtf_to_introns.pl
-libexec/trinity/util/misc/HiCpipe_nameSortedSam_to_raw.pl
libexec/trinity/util/misc/hicpipe_raw_converter.pl
libexec/trinity/util/misc/identify_distal_isoform_variations.pl
libexec/trinity/util/misc/illustrate_ref_comparison.pl
-libexec/trinity/util/misc/insilico_norm_kmer_hists/kmer_histo.all.txt
libexec/trinity/util/misc/insilico_norm_kmer_hists/kmer_histo.NormMaxKCov50.txt
+libexec/trinity/util/misc/insilico_norm_kmer_hists/kmer_histo.all.txt
libexec/trinity/util/misc/insilico_norm_kmer_hists/plot_me.R
libexec/trinity/util/misc/insilico_norm_kmer_hists/result.pdf
libexec/trinity/util/misc/iso_reco_analysis/bam_to_cuff.pl
@@ -239,8 +277,8 @@ libexec/trinity/util/misc/iso_reco_analysis/cuff_gtf_to_bed.pl
libexec/trinity/util/misc/iso_reco_analysis/gene_gff3_to_bed_cmds.pl
libexec/trinity/util/misc/iso_reco_analysis/gmap_to_ref.pl
libexec/trinity/util/misc/iso_reco_analysis/notes
-libexec/trinity/util/misc/iso_reco_analysis/run_trinity_no_LR.pl
libexec/trinity/util/misc/iso_reco_analysis/run_trinity_WITH_LR.pl
+libexec/trinity/util/misc/iso_reco_analysis/run_trinity_no_LR.pl
libexec/trinity/util/misc/iso_reco_analysis/sim_reads.pl
libexec/trinity/util/misc/iso_reco_analysis/trans_gff3_to_bed_cmds.pl
libexec/trinity/util/misc/jaccard_sam_pair_refiner.pl
@@ -250,14 +288,10 @@ libexec/trinity/util/misc/join_expr_vals_single_table.pl
libexec/trinity/util/misc/kmer_counter.pl
libexec/trinity/util/misc/m8_blastclust.pl
libexec/trinity/util/misc/map_gtf_transcripts_to_genome_annots.pl
+libexec/trinity/util/misc/merge_RSEM_output_to_matrix.pl
libexec/trinity/util/misc/merge_blast_n_rsem_results.pl
libexec/trinity/util/misc/merge_rsem_n_express_for_compare.pl
-libexec/trinity/util/misc/merge_RSEM_output_to_matrix.pl
-libexec/trinity/util/misc/Monarch
-libexec/trinity/util/misc/Monarch_util/generate_gene_alt_splicing_graphs.pl
-libexec/trinity/util/misc/Monarch_util/generate_trans_graphs.pl
libexec/trinity/util/misc/mpi_iworm_proc_contigs_to_fa.pl
-libexec/trinity/util/misc/N50.pl
libexec/trinity/util/misc/nameSorted_SAM_to_FastQ.pl
libexec/trinity/util/misc/omp_iworm_thread_contigs_to_fa.pl
libexec/trinity/util/misc/organize_data_table_by_trinity_component.pl
@@ -265,34 +299,24 @@ libexec/trinity/util/misc/pair_up_fastq_files_1_2.pl
libexec/trinity/util/misc/pair_up_fastq_files_LeftRight.pl
libexec/trinity/util/misc/pair_up_fastq_files_R1_R2.pl
libexec/trinity/util/misc/pairwise_kmer_content_comparer.pl
-libexec/trinity/util/misc/PerlLib/SegmentGraph.pm
libexec/trinity/util/misc/plot_expressed_gene_dist.pl
-libexec/trinity/util/misc/print_kmers.pl
libexec/trinity/util/misc/print.pl
+libexec/trinity/util/misc/print_kmers.pl
libexec/trinity/util/misc/process_GMAP_alignments_gff3_chimeras_ok.pl
libexec/trinity/util/misc/prop_pair_sam_refiner.pl
libexec/trinity/util/misc/remove_cntrl_chars.pl
libexec/trinity/util/misc/row_to_column.pl
-libexec/trinity/util/misc/run_bwa.pl
-libexec/trinity/util/misc/run_bwasw_trinity.pl
libexec/trinity/util/misc/run_GSNAP.pl
-libexec/trinity/util/misc/run_HiCpipe_bowtie.pl
libexec/trinity/util/misc/run_HISAT.pl
+libexec/trinity/util/misc/run_HiCpipe_bowtie.pl
+libexec/trinity/util/misc/run_STAR.pl
+libexec/trinity/util/misc/run_TOPHAT.pl
+libexec/trinity/util/misc/run_bwa.pl
+libexec/trinity/util/misc/run_bwasw_trinity.pl
libexec/trinity/util/misc/run_jellyfish.pl
libexec/trinity/util/misc/run_read_simulator_per_fasta_entry.pl
libexec/trinity/util/misc/run_read_simulator_per_gene.pl
-libexec/trinity/util/misc/run_STAR.pl
-libexec/trinity/util/misc/run_TOPHAT.pl
libexec/trinity/util/misc/run_trimmomatic_qual_trimming.pl
-libexec/trinity/util/misc/SAM_coordsorted_max_reads_per_position.pl
-libexec/trinity/util/misc/SAM_intron_extractor.pl
-libexec/trinity/util/misc/SAM_pair_to_bed.pl
-libexec/trinity/util/misc/SAM_show_alignment.pl
-libexec/trinity/util/misc/SAM_show_alignment.summarize_stats.pl
-libexec/trinity/util/misc/SAM_sortAny_to_count_stats.pl
-libexec/trinity/util/misc/SAM_to_bed.pl
-libexec/trinity/util/misc/SAM_to_fasta.pl
-libexec/trinity/util/misc/SAM_toString.pl
libexec/trinity/util/misc/shuffle.pl
libexec/trinity/util/misc/simulate_illuminaPE_from_transcripts.pl
libexec/trinity/util/misc/simulate_reads_sam_and_fa.pl
@@ -302,55 +326,41 @@ libexec/trinity/util/misc/splice_path_analysis/assess_intron_path_sensitivity.pl
libexec/trinity/util/misc/splice_path_analysis/assess_intron_path_sensitivity.summarizer.pl
libexec/trinity/util/misc/splice_path_analysis/diff_splice_paths.pl
libexec/trinity/util/misc/splice_path_analysis/intron_barcharter.pl
-libexec/trinity/util/misc/SRA_to_fastq.notes
-libexec/trinity/util/misc/SRA_to_fastq.pl
libexec/trinity/util/misc/strip_fasta_header.pl
-libexec/trinity/util/misc/tab_to_fasta.pl
libexec/trinity/util/misc/tab_to_fastQ.pl
+libexec/trinity/util/misc/tab_to_fasta.pl
libexec/trinity/util/misc/tblastn_wrapper.pl
-libexec/trinity/util/misc/TEST_SUPPORT/BFLY_TESTING/graph_out_to_bfly_cmd.pl
libexec/trinity/util/misc/testUnlimitStacksize.pl
-libexec/trinity/util/misc/TophatCufflinksWrapper.pl
libexec/trinity/util/misc/transcript_coverage_UTR_trimmer.pl
libexec/trinity/util/misc/transcript_fasta_to_ORF_pics.pl
libexec/trinity/util/misc/transcript_gff3_to_bed.pl
libexec/trinity/util/misc/transdecoder_pep_to_false_fusion_finder.pl
libexec/trinity/util/misc/trinity_component_distribution.pl
-libexec/trinity/util/PBS/N50stats.pl
-libexec/trinity/util/PBS/pbs_check.pl
-libexec/trinity/util/PBS/README
-libexec/trinity/util/PBS/TRINITY.CONFIG.template
-libexec/trinity/util/PBS/trinity_kill.pl
-libexec/trinity/util/PBS/trinity_kill.sh
-libexec/trinity/util/PBS/trinity_pbs.cont
-libexec/trinity/util/PBS/trinity_pbs.header
-libexec/trinity/util/PBS/trinity_pbs.p1
-libexec/trinity/util/PBS/trinity_pbs.p2
-libexec/trinity/util/PBS/trinity_pbs.p3
-libexec/trinity/util/PBS/trinity_pbs.p4a
-libexec/trinity/util/PBS/trinity_pbs.p4b
-libexec/trinity/util/PBS/trinity_pbs.p5b
-libexec/trinity/util/PBS/trinity_pbs.sh
libexec/trinity/util/retrieve_sequences_from_fasta.pl
-libexec/trinity/util/R/expression_analysis_lib.R
-libexec/trinity/util/R/get_Poisson_conf_intervals.R
-libexec/trinity/util/R/noiseq.r
libexec/trinity/util/run_DE_analysis_from_samples_file.pl
libexec/trinity/util/run_RSEM_from_samples_file.pl
libexec/trinity/util/run_Trinity_edgeR_pipeline.pl
libexec/trinity/util/run_Trinity_from_samples_file.pl
-libexec/trinity/util/SAM_nameSorted_to_uniq_count_stats.pl
-libexec/trinity/util/support_scripts/define_coverage_partitions.pl
-libexec/trinity/util/support_scripts/define_SAM_coverage_partitions2.pl
libexec/trinity/util/support_scripts/ExitTester.jar
+libexec/trinity/util/support_scripts/GG_partitioned_trinity_aggregator.pl
+libexec/trinity/util/support_scripts/SAM_coordSorted_fragment_Read_coverage_writer.pl
+libexec/trinity/util/support_scripts/SAM_coordSorted_fragment_coverage_writer2.pl
+libexec/trinity/util/support_scripts/SAM_extract_properly_mapped_pairs.pl
+libexec/trinity/util/support_scripts/SAM_extract_uniquely_mapped_reads.pl
+libexec/trinity/util/support_scripts/SAM_filter_out_unmapped_reads.pl
+libexec/trinity/util/support_scripts/SAM_ordered_pair_jaccard.pl
+libexec/trinity/util/support_scripts/SAM_set_transcribed_orient_info.pl
+libexec/trinity/util/support_scripts/SAM_strand_separator.pl
+libexec/trinity/util/support_scripts/SAM_to_frag_coords.pl
+libexec/trinity/util/support_scripts/define_SAM_coverage_partitions2.pl
+libexec/trinity/util/support_scripts/define_coverage_partitions.pl
libexec/trinity/util/support_scripts/eXpress_trans_to_gene_results.pl
libexec/trinity/util/support_scripts/extract_reads_per_partition.pl
-libexec/trinity/util/support_scripts/fasta_to_tab.pl
libexec/trinity/util/support_scripts/fastQ_to_fastA.pl
libexec/trinity/util/support_scripts/fastQ_to_tab.pl
+libexec/trinity/util/support_scripts/fasta_to_tab.pl
libexec/trinity/util/support_scripts/fragment_coverage_writer.pl
libexec/trinity/util/support_scripts/get_Trinity_gene_to_trans_map.pl
-libexec/trinity/util/support_scripts/GG_partitioned_trinity_aggregator.pl
libexec/trinity/util/support_scripts/inchworm_transcript_splitter.pl
libexec/trinity/util/support_scripts/jaccard_fasta_clipper.pl
libexec/trinity/util/support_scripts/jaccard_wig_clipper.pl
@@ -369,34 +379,19 @@ libexec/trinity/util/support_scripts/process_GMAP_alignments_gff3_chimeras_ok.pl
libexec/trinity/util/support_scripts/revcomp_fasta.pl
libexec/trinity/util/support_scripts/run_TMM_scale_matrix.pl
libexec/trinity/util/support_scripts/run_UpperQuartileNormalization_matrix.pl
-libexec/trinity/util/support_scripts/SAM_coordSorted_fragment_coverage_writer2.pl
-libexec/trinity/util/support_scripts/SAM_coordSorted_fragment_Read_coverage_writer.pl
-libexec/trinity/util/support_scripts/SAM_extract_properly_mapped_pairs.pl
-libexec/trinity/util/support_scripts/SAM_extract_uniquely_mapped_reads.pl
-libexec/trinity/util/support_scripts/SAM_filter_out_unmapped_reads.pl
-libexec/trinity/util/support_scripts/SAM_ordered_pair_jaccard.pl
-libexec/trinity/util/support_scripts/SAM_set_transcribed_orient_info.pl
-libexec/trinity/util/support_scripts/SAM_strand_separator.pl
-libexec/trinity/util/support_scripts/SAM_to_frag_coords.pl
libexec/trinity/util/support_scripts/scaffold_iworm_contigs.pl
libexec/trinity/util/support_scripts/segment_GFF_partitions.pl
-libexec/trinity/util/support_scripts/tests/test_prep.py
libexec/trinity/util/support_scripts/tests/test.py
+libexec/trinity/util/support_scripts/tests/test_prep.py
libexec/trinity/util/support_scripts/tests/tests.py
libexec/trinity/util/support_scripts/trinity_install_tests.sh
libexec/trinity/util/support_scripts/wig_clip_to_bed.pl
libexec/trinity/util/support_scripts/write_partitioned_trinity_cmds.pl
-libexec/trinity/util/TrinityStats.pl
share/examples/trinity/Makefile
share/examples/trinity/__regression_tests/test_GraphFromFasta/both.fa.gz
share/examples/trinity/__regression_tests/test_GraphFromFasta/inchworm.K25.L25.fa.gz
share/examples/trinity/__regression_tests/test_GraphFromFasta/iworm_scaffolds.txt.gz
share/examples/trinity/__regression_tests/test_GraphFromFasta/runMe.sh
-share/examples/trinity/test_align_and_estimate_abundance/align_and_estimate_tester.pl
-share/examples/trinity/test_align_and_estimate_abundance/cleanme.pl
-share/examples/trinity/test_align_and_estimate_abundance/Makefile
-share/examples/trinity/test_align_and_estimate_abundance/plot_paired_comparisons.Rscript
-share/examples/trinity/test_align_and_estimate_abundance/samples.txt
share/examples/trinity/test_DATA/Sp_ds.10k.left.fq.gz
share/examples/trinity/test_DATA/Sp_ds.10k.right.fq.gz
share/examples/trinity/test_DATA/Sp_hs.10k.left.fq.gz
@@ -406,83 +401,80 @@ share/examples/trinity/test_DATA/Sp_log.10k.right.fq.gz
share/examples/trinity/test_DATA/Sp_plat.10k.left.fq.gz
share/examples/trinity/test_DATA/Sp_plat.10k.right.fq.gz
share/examples/trinity/test_DATA/Trinity.fasta
+share/examples/trinity/test_DE_analysis/Makefile
+share/examples/trinity/test_DE_analysis/Trinity_trans.TMM.EXPR.matrix
+share/examples/trinity/test_DE_analysis/Trinity_trans.TPM.not_cross_norm
+share/examples/trinity/test_DE_analysis/Trinity_trans.counts.matrix
+share/examples/trinity/test_DE_analysis/deprecated/example_DESeq2_analysis_pipeline/Makefile
share/examples/trinity/test_DE_analysis/deprecated/example_DESeq2_analysis_pipeline/cleanme.pl
share/examples/trinity/test_DE_analysis/deprecated/example_DESeq2_analysis_pipeline/counts.matrix
-share/examples/trinity/test_DE_analysis/deprecated/example_DESeq2_analysis_pipeline/Makefile
share/examples/trinity/test_DE_analysis/deprecated/example_DESeq2_analysis_pipeline/run_DESeq2.sh
share/examples/trinity/test_DE_analysis/deprecated/example_DESeq2_analysis_pipeline/samples.txt
-share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/cleanMe.sh
+share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/Makefile
+share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/Trinity.fa.seqLens
+share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/TMM_info.txt
+share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/__tmp_runTMM.R
+share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/__tmp_run_edgeR.1820.R
+share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/__tmp_targets.1820.dat
share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/all_data_files.list
share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/cysts.dat
share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/example.matrix.normalized.FPKM
share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/myc.dat
share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/myc_vs_cysts.eps
share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/myc_vs_cysts.results.txt
-share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/TMM_info.txt
-share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/__tmp_run_edgeR.1820.R
-share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/__tmp_runTMM.R
-share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/__tmp_targets.1820.dat
+share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/cleanMe.sh
share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/example.matrix
-share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/Makefile
share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/runMe.sh
-share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/Trinity.fa.seqLens
+share/examples/trinity/test_DE_analysis/deprecated/testEdgeRfuncs/Makefile
share/examples/trinity/test_DE_analysis/deprecated/testEdgeRfuncs/cleanMe.sh
share/examples/trinity/test_DE_analysis/deprecated/testEdgeRfuncs/dataA.dat
share/examples/trinity/test_DE_analysis/deprecated/testEdgeRfuncs/dataB.dat
-share/examples/trinity/test_DE_analysis/deprecated/testEdgeRfuncs/Makefile
-share/examples/trinity/test_DE_analysis/deprecated/testEdgeRfuncs/run_edgeR_on_sample_data.R
share/examples/trinity/test_DE_analysis/deprecated/testEdgeRfuncs/runMe.sh
+share/examples/trinity/test_DE_analysis/deprecated/testEdgeRfuncs/run_edgeR_on_sample_data.R
share/examples/trinity/test_DE_analysis/deprecated/testEdgeRfuncs/targets.dat
-share/examples/trinity/test_DE_analysis/Makefile
share/examples/trinity/test_DE_analysis/notes
share/examples/trinity/test_DE_analysis/samples.txt
-share/examples/trinity/test_DE_analysis/Trinity_trans.counts.matrix
-share/examples/trinity/test_DE_analysis/Trinity_trans.TMM.EXPR.matrix
-share/examples/trinity/test_DE_analysis/Trinity_trans.TPM.not_cross_norm
-share/examples/trinity/test_full_edgeR_pipeline/cleanme.pl
-share/examples/trinity/test_full_edgeR_pipeline/Makefile
-share/examples/trinity/test_full_edgeR_pipeline/runMe.sh
-share/examples/trinity/test_full_edgeR_pipeline/samples_n_reads_decribed.txt
-share/examples/trinity/test_GenomeGuidedTrinity/cleanme.pl
+share/examples/trinity/test_GOSeq_trinotate_pipe/Spombe/Trinity.seq_lengths
+share/examples/trinity/test_GOSeq_trinotate_pipe/Spombe/Trinotate_report.xls
+share/examples/trinity/test_GOSeq_trinotate_pipe/Spombe/Trinotate_report.xls.trans.gene_ontology
+share/examples/trinity/test_GOSeq_trinotate_pipe/Spombe/cleanme.pl
+share/examples/trinity/test_GOSeq_trinotate_pipe/Spombe/ds_induced_vs_log.accs.lab
+share/examples/trinity/test_GOSeq_trinotate_pipe/Spombe/ds_induced_vs_log.factors
+share/examples/trinity/test_GOSeq_trinotate_pipe/Spombe/hs_induced_vs_log.accs.lab
+share/examples/trinity/test_GOSeq_trinotate_pipe/Spombe/hs_induced_vs_log.factors
+share/examples/trinity/test_GOSeq_trinotate_pipe/Spombe/runMe.sh
+share/examples/trinity/test_GOSeq_trinotate_pipe/from_enrichnet.org/Cancer_genes_Futreal2004.ids
+share/examples/trinity/test_GOSeq_trinotate_pipe/from_enrichnet.org/Parkinsons_disease_Phenopedia2011.ids
share/examples/trinity/test_GenomeGuidedTrinity/Makefile
+share/examples/trinity/test_GenomeGuidedTrinity/SP2.annot.bed.gz
+share/examples/trinity/test_GenomeGuidedTrinity/SP2.chr.SE.sam.gz
+share/examples/trinity/test_GenomeGuidedTrinity/SP2.chr.bam
+share/examples/trinity/test_GenomeGuidedTrinity/SP2.chr.fa.gz
+share/examples/trinity/test_GenomeGuidedTrinity/cleanme.pl
share/examples/trinity/test_GenomeGuidedTrinity/mm9chr17.annotation.bed.gz
share/examples/trinity/test_GenomeGuidedTrinity/mm9chr17.fasta.gz
share/examples/trinity/test_GenomeGuidedTrinity/mm9chr17.tophat.bam
-share/examples/trinity/test_GenomeGuidedTrinity/old/run_genome-guided_Trinity.sh
share/examples/trinity/test_GenomeGuidedTrinity/old/__run_genome-guided_Trinity_use_existing_bam.use_LSF.sh
share/examples/trinity/test_GenomeGuidedTrinity/old/__run_genome-guided_Trinity_use_existing_bam.use_PBS.sh
share/examples/trinity/test_GenomeGuidedTrinity/old/__run_genome-guided_Trinity_use_existing_bam.use_SGE.sh
-share/examples/trinity/test_GenomeGuidedTrinity/old/run_mouse_TrinityGG.sh
share/examples/trinity/test_GenomeGuidedTrinity/old/run_Schizo_TrinityGG.SE.sh
share/examples/trinity/test_GenomeGuidedTrinity/old/run_Schizo_TrinityGG.sh
-share/examples/trinity/test_GenomeGuidedTrinity/run_genome-guided_Trinity_use_existing_bam.sh
+share/examples/trinity/test_GenomeGuidedTrinity/old/run_genome-guided_Trinity.sh
+share/examples/trinity/test_GenomeGuidedTrinity/old/run_mouse_TrinityGG.sh
share/examples/trinity/test_GenomeGuidedTrinity/run_Schizo_TrinityGG_jaccard_clip.sh
-share/examples/trinity/test_GenomeGuidedTrinity/SP2.annot.bed.gz
-share/examples/trinity/test_GenomeGuidedTrinity/SP2.chr.bam
-share/examples/trinity/test_GenomeGuidedTrinity/SP2.chr.fa.gz
-share/examples/trinity/test_GenomeGuidedTrinity/SP2.chr.SE.sam.gz
-share/examples/trinity/test_GenomeGuidedTrinity/top100k.genome.gz
+share/examples/trinity/test_GenomeGuidedTrinity/run_genome-guided_Trinity_use_existing_bam.sh
share/examples/trinity/test_GenomeGuidedTrinity/top100k.Left.fq.gz
share/examples/trinity/test_GenomeGuidedTrinity/top100k.Right.fq.gz
-share/examples/trinity/test_GOSeq_trinotate_pipe/from_enrichnet.org/Cancer_genes_Futreal2004.ids
-share/examples/trinity/test_GOSeq_trinotate_pipe/from_enrichnet.org/Parkinsons_disease_Phenopedia2011.ids
-share/examples/trinity/test_GOSeq_trinotate_pipe/Spombe/cleanme.pl
-share/examples/trinity/test_GOSeq_trinotate_pipe/Spombe/ds_induced_vs_log.accs.lab
-share/examples/trinity/test_GOSeq_trinotate_pipe/Spombe/ds_induced_vs_log.factors
-share/examples/trinity/test_GOSeq_trinotate_pipe/Spombe/hs_induced_vs_log.accs.lab
-share/examples/trinity/test_GOSeq_trinotate_pipe/Spombe/hs_induced_vs_log.factors
-share/examples/trinity/test_GOSeq_trinotate_pipe/Spombe/runMe.sh
-share/examples/trinity/test_GOSeq_trinotate_pipe/Spombe/Trinity.seq_lengths
-share/examples/trinity/test_GOSeq_trinotate_pipe/Spombe/Trinotate_report.xls
-share/examples/trinity/test_GOSeq_trinotate_pipe/Spombe/Trinotate_report.xls.trans.gene_ontology
-share/examples/trinity/test_Inchworm/jellyfish.kmers.fa.gz
-share/examples/trinity/test_Inchworm/runMe_MPI.sh
-share/examples/trinity/test_InSilicoReadNormalization/cleanme.pl
+share/examples/trinity/test_GenomeGuidedTrinity/top100k.genome.gz
share/examples/trinity/test_InSilicoReadNormalization/Makefile
+share/examples/trinity/test_InSilicoReadNormalization/cleanme.pl
share/examples/trinity/test_InSilicoReadNormalization/test_PE_normalization.sh
share/examples/trinity/test_InSilicoReadNormalization/test_PE_normalization.w_base_cov_stats.sh
share/examples/trinity/test_InSilicoReadNormalization/test_SE_normalization.sh
-share/examples/trinity/test_Trinity_Assembly/cleanme.pl
+share/examples/trinity/test_Inchworm/jellyfish.kmers.fa.gz
+share/examples/trinity/test_Inchworm/runMe_MPI.sh
+share/examples/trinity/test_Trinity_Assembly/Makefile
+share/examples/trinity/test_Trinity_Assembly/README
share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/align_reads_via_bowtie.sh
share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/bowtie2.sam.aligned.bam
share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex01/ex01.IGV.png
@@ -547,31 +539,39 @@ share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex09/regi
share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex09/region9.sam.adj
share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex09/runMe.sh
share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/refSeqs.fa
+share/examples/trinity/test_Trinity_Assembly/cleanme.pl
share/examples/trinity/test_Trinity_Assembly/longReads.fa
-share/examples/trinity/test_Trinity_Assembly/Makefile
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__run_abundance_estimation_include_antisense.sh
+share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe.diff_kmer_length.sh
+share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_CuffFly.sh
+share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_PasaFly.sh
share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_as_DS.sh
share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_bowtie_components.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_CuffFly.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe.diff_kmer_length.sh
share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_include_long_reads.sh
share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_no_cleanup.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/runMe_no_qualTrim.sh
share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_parallel_iworm_assembly.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_PasaFly.sh
share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_using_Grid_LSF.sh
share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_using_Grid_SGE.sh
+share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_w_monitoring.sh
+share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming.sh
share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming_and_normalization.sh
share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming_and_normalize_libs_separately.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_w_monitoring.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__test_runMe_include_normalization.sh
+share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__run_abundance_estimation_include_antisense.sh
share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__test_runMe.singleFQ.sh
+share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__test_runMe_include_normalization.sh
share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__test_runMe_with_jaccard_clip.sh
-share/examples/trinity/test_Trinity_Assembly/README
-share/examples/trinity/test_Trinity_Assembly/reads2.left.fq.gz
-share/examples/trinity/test_Trinity_Assembly/reads2.right.fq.gz
+share/examples/trinity/test_Trinity_Assembly/misc_run_tests/runMe_no_qualTrim.sh
share/examples/trinity/test_Trinity_Assembly/reads.left.fq.gz
share/examples/trinity/test_Trinity_Assembly/reads.right.fq.gz
+share/examples/trinity/test_Trinity_Assembly/reads2.left.fq.gz
+share/examples/trinity/test_Trinity_Assembly/reads2.right.fq.gz
share/examples/trinity/test_Trinity_Assembly/runMe.sh
share/examples/trinity/test_Trinity_Assembly/test_FL.sh
+share/examples/trinity/test_align_and_estimate_abundance/Makefile
+share/examples/trinity/test_align_and_estimate_abundance/align_and_estimate_tester.pl
+share/examples/trinity/test_align_and_estimate_abundance/cleanme.pl
+share/examples/trinity/test_align_and_estimate_abundance/plot_paired_comparisons.Rscript
+share/examples/trinity/test_align_and_estimate_abundance/samples.txt
+share/examples/trinity/test_full_edgeR_pipeline/Makefile
+share/examples/trinity/test_full_edgeR_pipeline/cleanme.pl
+share/examples/trinity/test_full_edgeR_pipeline/runMe.sh
+share/examples/trinity/test_full_edgeR_pipeline/samples_n_reads_decribed.txt
diff --git a/tripwire2/Makefile b/tripwire2/Makefile
index 03b4d1c1ff..2b21ddecc9 100644
--- a/tripwire2/Makefile
+++ b/tripwire2/Makefile
@@ -9,19 +9,19 @@ MAINTAINER= pkgsrc-users%NetBSD.org@localhost
HOMEPAGE= http://sourceforge.net/projects/tripwire/
COMMENT= File and directory integrity checker
-WRKSRC= ${WRKDIR}/${DISTNAME}/src/
-CONFLICTS+= tripwire-1*
-BUILD_TARGET= release
-USE_TOOLS+= gmake
-ONLY_FOR_PLATFORM= Linux-*-* OpenBSD-*-* FreeBSD-*-*
+WRKSRC= ${WRKDIR}/${DISTNAME}/src/
+CONFLICTS+= tripwire-1*
+BUILD_TARGET= release
+USE_TOOLS+= gmake
+ONLY_FOR_PLATFORM= Linux-*-* OpenBSD-*-* FreeBSD-*-*
.include "../../mk/bsd.prefs.mk"
.if (${OPSYS} == "OpenBSD")
-SYSPRE=i386-unknown-openbsd
+SYSPRE= i386-unknown-openbsd
.endif
.if (${OPSYS} == "FreeBSD")
-SYSPRE=i386-unknown-freebsd
+SYSPRE= i386-unknown-freebsd
.endif
MAKE_ENV+= SYSPRE=${SYSPRE:Q}
diff --git a/truecrypt/Makefile b/truecrypt/Makefile
index 6beb1d01eb..1ca2222a35 100644
--- a/truecrypt/Makefile
+++ b/truecrypt/Makefile
@@ -19,13 +19,13 @@ NO_CONFIGURE= yes
USE_LANGUAGES= c c++
GCC_REQD= 4.0
-ONLY_FOR_PLATFORM= Linux-*-* # maybe: Darwin-*-*
+ONLY_FOR_PLATFORM= Linux-*-* # maybe: Darwin-*-*
-RESTRICTED= Unclear license
-NO_SRC_ON_CDROM=${RESTRICTED}
-NO_SRC_ON_FTP= ${RESTRICTED}
-NO_BIN_ON_CDROM=${RESTRICTED}
-NO_BIN_ON_FTP= ${RESTRICTED}
+RESTRICTED= Unclear license
+NO_SRC_ON_CDROM= ${RESTRICTED}
+NO_SRC_ON_FTP= ${RESTRICTED}
+NO_BIN_ON_CDROM= ${RESTRICTED}
+NO_BIN_ON_FTP= ${RESTRICTED}
FETCH_MESSAGE = " The file ${DISTNAME}${EXTRACT_SUFX} must be fetched"
FETCH_MESSAGE+= " from ${DOWNLOAD}"
@@ -37,7 +37,7 @@ FETCH_MESSAGE+= " and click download."
BUILD_TARGET=
MAKE_ENV+= PKCS11=1
-INSTALLATION_DIRS+= bin
+INSTALLATION_DIRS+= bin
do-install:
${INSTALL_PROGRAM} ${WRKSRC}/Main/truecrypt ${DESTDIR}${PREFIX}/bin/
diff --git a/tsh/Makefile b/tsh/Makefile
index e05c628d95..94906ab516 100644
--- a/tsh/Makefile
+++ b/tsh/Makefile
@@ -11,7 +11,7 @@ HOMEPAGE= http://www.cr0.net:8040/code/network/
COMMENT= Lightweight remote shel wity 128AES and file transfers
-BUILD_TARGET=${LOWER_OPSYS}
+BUILD_TARGET= ${LOWER_OPSYS}
INSTALLATION_DIRS= bin sbin
diff --git a/tsm/PLIST b/tsm/PLIST
index 04d7849387..036724230f 100644
--- a/tsm/PLIST
+++ b/tsm/PLIST
@@ -1,8 +1,8 @@
@comment $NetBSD: PLIST,v 1.5 2011/03/18 16:46:42 hfath Exp $
share/examples/tsm/dsm.opt.smp
share/examples/tsm/dsm.sys.smp
-share/examples/tsm/tsm_ld_so.conf
share/examples/tsm/tsm_daily.sh
+share/examples/tsm/tsm_ld_so.conf
@exec ${LN} -s ${EMULDIR}/${TSMCLIENTSUBDIR}/ba/bin/en_US/ ${PKG_SYSCONFDIR}/en_US
@exec ${LN} -s ${EMULDIR}/${TSMCLIENTSUBDIR}/ba/bin/en_US/ ${PKG_SYSCONFDIR}/EN_US
@exec ${EMULDIR}/sbin/ldconfig
diff --git a/tsm62/Makefile b/tsm62/Makefile
index ebf6bf1f67..4d1297c90e 100644
--- a/tsm62/Makefile
+++ b/tsm62/Makefile
@@ -60,7 +60,7 @@ RPMFILES+= ${WRKDIR}/TIVsm-API64.i386.rpm \
${WRKDIR}/gskssl64-8.0.14.6.linux.x86_64.rpm
# Make sure suse pkg version equals the above
-DEPENDS+= suse32_base-[0-9]*:../../emulators/suse121_32_base
+DEPENDS+= suse32_base-[0-9]*:../../emulators/suse121_32_base
EMUL32DIR= ${PREFIX}${_OPSYS_EMULDIR.linux32}
PLIST_SUBST+= EMUL32DIR=${EMUL32DIR:Q}
diff --git a/tsm62/options.mk b/tsm62/options.mk
index bc3e63e2ec..8e4b69d285 100644
--- a/tsm62/options.mk
+++ b/tsm62/options.mk
@@ -1,7 +1,7 @@
# $NetBSD: options.mk,v 1.1 2013/03/25 15:52:51 hfath Exp $
#
-PKG_OPTIONS_VAR= PKG_OPTIONS.tsm
-PKG_SUPPORTED_OPTIONS= java
+PKG_OPTIONS_VAR= PKG_OPTIONS.tsm
+PKG_SUPPORTED_OPTIONS= java
.include "../../mk/bsd.options.mk"
@@ -11,7 +11,7 @@ PLIST_VARS+= java
USE_TOOLS+= bash:run
-SUBST_CLASSES+= bash_path
+SUBST_CLASSES+= bash_path
SUBST_STAGE.bash_path= post-install
SUBST_FILES.bash_path= .destdir/usr/pkg/emul/linux/opt/tivoli/tsm/client/ba/bin/dsmj
SUBST_SED.bash_path= -e "s|/.*/bash|${TOOLS_PATH.bash}|g"
diff --git a/ttf-indic-fonts/PLIST b/ttf-indic-fonts/PLIST
index e2fc0e431d..ffe729af04 100644
--- a/ttf-indic-fonts/PLIST
+++ b/ttf-indic-fonts/PLIST
@@ -1,56 +1,30 @@
@comment $NetBSD: PLIST,v 1.1.1.1 2009/08/15 03:23:42 prudhvikrishna Exp $
-lib/X11/fonts/TTF/JamrulNormal.ttf
-lib/X11/fonts/TTF/LikhanNormal.ttf
-lib/X11/fonts/TTF/MuktiNarrow.ttf
-lib/X11/fonts/TTF/MuktiNarrowBold.ttf
-lib/X11/fonts/TTF/ani.ttf
-lib/X11/fonts/TTF/lohit_bn.ttf
-lib/X11/fonts/TTF/mitra.ttf
-lib/X11/fonts/TTF/ttf-bengali-fonts.conf
lib/X11/fonts/TTF/AksharYogini.ttf
-lib/X11/fonts/TTF/Samyak-Devanagari.ttf
-lib/X11/fonts/TTF/Sarai_07.ttf
-lib/X11/fonts/TTF/chandas1-2.ttf
-lib/X11/fonts/TTF/gargi.ttf
-lib/X11/fonts/TTF/kalimati.ttf
-lib/X11/fonts/TTF/lohit_hi.ttf
-lib/X11/fonts/TTF/nakula.ttf
-lib/X11/fonts/TTF/sahadeva.ttf
-lib/X11/fonts/TTF/samanata.ttf
-lib/X11/fonts/TTF/ttf-devanagari-fonts.conf
-lib/X11/fonts/TTF/Rekha.ttf
-lib/X11/fonts/TTF/Samyak-Gujarati.ttf
-lib/X11/fonts/TTF/aakar-medium.ttf
-lib/X11/fonts/TTF/lohit_gu.ttf
-lib/X11/fonts/TTF/padmaa-Bold.1.1.ttf
-lib/X11/fonts/TTF/padmaa-Medium-0.5.ttf
-lib/X11/fonts/TTF/padmaa.ttf
-lib/X11/fonts/TTF/ttf-gujarati-fonts.conf
+lib/X11/fonts/TTF/AnjaliOldLipi.ttf
+lib/X11/fonts/TTF/Dyuthi3.ttf
+lib/X11/fonts/TTF/JamrulNormal.ttf
+lib/X11/fonts/TTF/Kalyani121.ttf
lib/X11/fonts/TTF/Kedage-b.ttf
lib/X11/fonts/TTF/Kedage-i.ttf
lib/X11/fonts/TTF/Kedage-n.ttf
lib/X11/fonts/TTF/Kedage-t.ttf
+lib/X11/fonts/TTF/LikhanNormal.ttf
lib/X11/fonts/TTF/Malige-b.ttf
lib/X11/fonts/TTF/Malige-i.ttf
lib/X11/fonts/TTF/Malige-n.ttf
lib/X11/fonts/TTF/Malige-t.ttf
-lib/X11/fonts/TTF/lohit_kn.ttf
-lib/X11/fonts/TTF/ttf-kannada-fonts.conf
-lib/X11/fonts/TTF/AnjaliOldLipi.ttf
-lib/X11/fonts/TTF/Dyuthi3.ttf
-lib/X11/fonts/TTF/Kalyani121.ttf
lib/X11/fonts/TTF/Meera_04.ttf
+lib/X11/fonts/TTF/MuktiNarrow.ttf
+lib/X11/fonts/TTF/MuktiNarrowBold.ttf
+lib/X11/fonts/TTF/Pothana2000.ttf
lib/X11/fonts/TTF/Rachana_04.ttf
lib/X11/fonts/TTF/RaghuMalayalamSans2.ttf
-lib/X11/fonts/TTF/suruma2.ttf
-lib/X11/fonts/TTF/ttf-malayalam-fonts.conf
-lib/X11/fonts/TTF/Samyak-Oriya.ttf
-lib/X11/fonts/TTF/lohit_or.ttf
-lib/X11/fonts/TTF/ttf-oriya-fonts.conf
-lib/X11/fonts/TTF/utkal.ttf
+lib/X11/fonts/TTF/Rekha.ttf
lib/X11/fonts/TTF/Saab.ttf
-lib/X11/fonts/TTF/lohit_pa.ttf
-lib/X11/fonts/TTF/ttf-punjabi-fonts.conf
+lib/X11/fonts/TTF/Samyak-Devanagari.ttf
+lib/X11/fonts/TTF/Samyak-Gujarati.ttf
+lib/X11/fonts/TTF/Samyak-Oriya.ttf
+lib/X11/fonts/TTF/Sarai_07.ttf
lib/X11/fonts/TTF/TAMu_Kadampari.ttf
lib/X11/fonts/TTF/TAMu_Kalyani.ttf
lib/X11/fonts/TTF/TAMu_Maduram.ttf
@@ -59,9 +33,35 @@ lib/X11/fonts/TTF/TSCu_Paranar.ttf
lib/X11/fonts/TTF/TSCu_Times.ttf
lib/X11/fonts/TTF/TSCu_paranarb.ttf
lib/X11/fonts/TTF/TSCu_paranari.ttf
-lib/X11/fonts/TTF/lohit_ta.ttf
-lib/X11/fonts/TTF/ttf-tamil-fonts.conf
-lib/X11/fonts/TTF/Pothana2000.ttf
lib/X11/fonts/TTF/Vemana.ttf
+lib/X11/fonts/TTF/aakar-medium.ttf
+lib/X11/fonts/TTF/ani.ttf
+lib/X11/fonts/TTF/chandas1-2.ttf
+lib/X11/fonts/TTF/gargi.ttf
+lib/X11/fonts/TTF/kalimati.ttf
+lib/X11/fonts/TTF/lohit_bn.ttf
+lib/X11/fonts/TTF/lohit_gu.ttf
+lib/X11/fonts/TTF/lohit_hi.ttf
+lib/X11/fonts/TTF/lohit_kn.ttf
+lib/X11/fonts/TTF/lohit_or.ttf
+lib/X11/fonts/TTF/lohit_pa.ttf
+lib/X11/fonts/TTF/lohit_ta.ttf
lib/X11/fonts/TTF/lohit_te.ttf
+lib/X11/fonts/TTF/mitra.ttf
+lib/X11/fonts/TTF/nakula.ttf
+lib/X11/fonts/TTF/padmaa-Bold.1.1.ttf
+lib/X11/fonts/TTF/padmaa-Medium-0.5.ttf
+lib/X11/fonts/TTF/padmaa.ttf
+lib/X11/fonts/TTF/sahadeva.ttf
+lib/X11/fonts/TTF/samanata.ttf
+lib/X11/fonts/TTF/suruma2.ttf
+lib/X11/fonts/TTF/ttf-bengali-fonts.conf
+lib/X11/fonts/TTF/ttf-devanagari-fonts.conf
+lib/X11/fonts/TTF/ttf-gujarati-fonts.conf
+lib/X11/fonts/TTF/ttf-kannada-fonts.conf
+lib/X11/fonts/TTF/ttf-malayalam-fonts.conf
+lib/X11/fonts/TTF/ttf-oriya-fonts.conf
+lib/X11/fonts/TTF/ttf-punjabi-fonts.conf
+lib/X11/fonts/TTF/ttf-tamil-fonts.conf
lib/X11/fonts/TTF/ttf-telugu-fonts.conf
+lib/X11/fonts/TTF/utkal.ttf
diff --git a/ttysnoop/Makefile b/ttysnoop/Makefile
index 70d9ef744e..4b3c46092d 100644
--- a/ttysnoop/Makefile
+++ b/ttysnoop/Makefile
@@ -3,7 +3,7 @@
# TODO : wrong name ?
DISTNAME= ttysnoop-0.12d.k26
-PKGREVISION= 2
+PKGREVISION= 2
CATEGORIES= sysutils
MASTER_SITES= http://grad.icmc.usp.br/~duker/ttysnoop/
@@ -11,20 +11,20 @@ MAINTAINER= pkgsrc-users%NetBSD.org@localhost
HOMEPAGE= http://grad.icmc.usp.br/~duker/ttysnoop/
COMMENT= Snoop TTYs on Linux for kernels 2.6
-SUBST_CLASSES+=etc
-SUBST_FILES.etc=config.h
-SUBST_STAGE.etc=configure
-SUBST_SED.etc=-e 's,/var/,${VARBASE}/,'
-SUBST_SED.etc+=-e 's,/etc,${PKG_SYSCONFDIR},'
+SUBST_CLASSES+= etc
+SUBST_FILES.etc= config.h
+SUBST_STAGE.etc= configure
+SUBST_SED.etc= -e 's,/var/,${VARBASE}/,'
+SUBST_SED.etc+= -e 's,/etc,${PKG_SYSCONFDIR},'
INSTALLATION_DIRS= sbin ${PKGMANDIR}/man8
+ONLY_FOR_PLATFORM= Linux-*-*
+
do-install:
${INSTALL_PROGRAM} ${WRKSRC}/ttysnoop ${DESTDIR}${PREFIX}/sbin
${INSTALL_PROGRAM} ${WRKSRC}/ttysnoops ${DESTDIR}${PREFIX}/sbin
${INSTALL_MAN} ${WRKSRC}/ttysnoop.8 ${DESTDIR}${PREFIX}/${PKGMANDIR}/man8/
${INSTALL_DATA_DIR} ${DESTDIR}${VARBASE}/spool/ttysnoop
-ONLY_FOR_PLATFORM= Linux-*-*
-
.include "../../mk/bsd.pkg.mk"
diff --git a/ttysnoop/PLIST b/ttysnoop/PLIST
index dcf59021a5..c2e7895588 100644
--- a/ttysnoop/PLIST
+++ b/ttysnoop/PLIST
@@ -1,4 +1,4 @@
@comment $NetBSD: PLIST,v 1.2 2005/11/02 02:35:31 poppnk Exp $
+man/man8/ttysnoop.8
sbin/ttysnoop
sbin/ttysnoops
-man/man8/ttysnoop.8
diff --git a/tuareg-mode/Makefile b/tuareg-mode/Makefile
index 36f3cbdfb4..f24f8f9816 100644
--- a/tuareg-mode/Makefile
+++ b/tuareg-mode/Makefile
@@ -1,17 +1,17 @@
# $NetBSD: Makefile,v 1.12 2012/10/07 17:11:34 asau Exp $
-DISTNAME= tuareg-mode-1.46.2
-PKGNAME= ${EMACS_PKGNAME_PREFIX}${DISTNAME}
-CATEGORIES= devel editors
-MASTER_SITES= http://www-rocq.inria.fr/~acohen/tuareg/mode/
+DISTNAME= tuareg-mode-1.46.2
+PKGNAME= ${EMACS_PKGNAME_PREFIX}${DISTNAME}
+CATEGORIES= devel editors
+MASTER_SITES= http://www-rocq.inria.fr/~acohen/tuareg/mode/
-MAINTAINER= tonio%NetBSD.org@localhost
-HOMEPAGE= http://www-rocq.inria.fr/~acohen/tuareg/
-COMMENT= GNU Emacs/XEmacs major mode for editing Caml and OCaml programs
+MAINTAINER= tonio%NetBSD.org@localhost
+HOMEPAGE= http://www-rocq.inria.fr/~acohen/tuareg/
+COMMENT= GNU Emacs/XEmacs major mode for editing Caml and OCaml programs
-NO_BUILD= yes
+NO_BUILD= yes
-SRCS= camldebug.el sym-lock.el tuareg.el
+SRCS= camldebug.el sym-lock.el tuareg.el
do-install:
${INSTALL_DATA_DIR} ${DESTDIR}${EMACS_LISPPREFIX}/
diff --git a/tuxanci-server/Makefile b/tuxanci-server/Makefile
index 9fa1f78d91..8e6dc5d3fe 100644
--- a/tuxanci-server/Makefile
+++ b/tuxanci-server/Makefile
@@ -14,7 +14,7 @@ COMMENT= Server of Czechoslovak multiplatform action game like Bulanci
WRKSRC= ${WRKDIR}/pkgs/tuxanci-0.20.0-src
-USE_CMAKE= yes
+USE_CMAKE= yes
USE_LANGUAGES+= c c++
EGDIR= ${PREFIX}/share/examples
@@ -22,9 +22,9 @@ MAKE_ENV+= EGDIR=${EGDIR}
MAKE_DIRS+= ${PKG_SYSCONFDIR}/tuxanci-server
CONF_FILES+= ${EGDIR}/tuxanci-server/server.conf ${PKG_SYSCONFDIR}/tuxanci-server/server.conf
-CMAKE_ARGS+= -DServer=1 \
- -DPREFIX=\\\"${PREFIX}/\\\" \
- -DCMAKE_INSTALL_PREFIX:PATH=${PREFIX} \
- -DEGDIR=${EGDIR}
+CMAKE_ARGS+= -DServer=1 \
+ -DPREFIX=\\\"${PREFIX}/\\\" \
+ -DCMAKE_INSTALL_PREFIX:PATH=${PREFIX} \
+ -DEGDIR=${EGDIR}
.include "../../mk/bsd.pkg.mk"
diff --git a/tuxanci/Makefile b/tuxanci/Makefile
index e7c81230ae..983719b7dd 100644
--- a/tuxanci/Makefile
+++ b/tuxanci/Makefile
@@ -15,15 +15,15 @@ COMMENT= Czechoslovak multiplatform action game like Bulanci
WRKSRC= ${WRKDIR}/pkgs/tuxanci-0.20.0-src
-USE_CMAKE= yes
+USE_CMAKE= yes
USE_LANGUAGES+= c c++
-CMAKE_ARGS+= -DPREFIX=\\\"${PREFIX}/\\\" \
- -DCMAKE_INSTALL_PREFIX:PATH=${PREFIX} \
- -DSDL_INCLUDE_DIR=${PREFIX}/include/SDL \
- -DSDLIMAGE_INCLUDE_DIR=${PREFIX}/include/SDL \
- -DSDLMIXER_INCLUDE_DIR=${PREFIX}/include/SDL \
- -DSDLTTF_INCLUDE_DIR=${PREFIX}/include/SDL
+CMAKE_ARGS+= -DPREFIX=\\\"${PREFIX}/\\\" \
+ -DCMAKE_INSTALL_PREFIX:PATH=${PREFIX} \
+ -DSDL_INCLUDE_DIR=${PREFIX}/include/SDL \
+ -DSDLIMAGE_INCLUDE_DIR=${PREFIX}/include/SDL \
+ -DSDLMIXER_INCLUDE_DIR=${PREFIX}/include/SDL \
+ -DSDLTTF_INCLUDE_DIR=${PREFIX}/include/SDL
.include "../../graphics/SDL_image/buildlink3.mk"
.include "../../audio/SDL_mixer/buildlink3.mk"
diff --git a/tuxanci/PLIST b/tuxanci/PLIST
index 00253ce017..4c6f9f1e82 100644
--- a/tuxanci/PLIST
+++ b/tuxanci/PLIST
@@ -22,19 +22,19 @@ share/tuxanci/image/big-explosion.png
share/tuxanci/image/bombball.png
share/tuxanci/image/button0.png
share/tuxanci/image/button1.png
+share/tuxanci/image/chat.png
+share/tuxanci/image/check.png
share/tuxanci/image/construction_site.png
share/tuxanci/image/cross.png
share/tuxanci/image/explosion.png
share/tuxanci/image/for_a_good_night.png
share/tuxanci/image/graf.bonus.png
-share/tuxanci/image/chat.png
-share/tuxanci/image/check.png
+share/tuxanci/image/icon.bonus.4x.png
share/tuxanci/image/icon.bonus.ghost.png
share/tuxanci/image/icon.bonus.hidden.png
share/tuxanci/image/icon.bonus.shot.png
share/tuxanci/image/icon.bonus.speed.png
share/tuxanci/image/icon.bonus.teleport.png
-share/tuxanci/image/icon.bonus.4x.png
share/tuxanci/image/icon.gun.bombball.png
share/tuxanci/image/icon.gun.dual.simple.png
share/tuxanci/image/icon.gun.lasser.png
@@ -44,20 +44,17 @@ share/tuxanci/image/icon.gun.simple.png
share/tuxanci/image/icon.gun.tommy.png
share/tuxanci/image/in_a_captivity_of_8-bit.png
share/tuxanci/image/item.bombball.png
+share/tuxanci/image/item.bonus.4x.png
share/tuxanci/image/item.bonus.ghost.png
share/tuxanci/image/item.bonus.hidden.png
share/tuxanci/image/item.bonus.shot.png
share/tuxanci/image/item.bonus.speed.png
share/tuxanci/image/item.bonus.teleport.png
-share/tuxanci/image/item.bonus.4x.png
share/tuxanci/image/item.dual.png
share/tuxanci/image/item.lasser.png
share/tuxanci/image/item.mine.png
share/tuxanci/image/item.scatter.png
share/tuxanci/image/item.tommy.png
-share/tuxanci/image/lasserX.png
-share/tuxanci/image/lasserY.png
-share/tuxanci/image/level4.png
share/tuxanci/image/l1.grow.png
share/tuxanci/image/l1.hut.png
share/tuxanci/image/l1.peduncle.png
@@ -85,6 +82,9 @@ share/tuxanci/image/l4.palety.png
share/tuxanci/image/l4.pozadi.png
share/tuxanci/image/l4.pytle.png
share/tuxanci/image/l4.tvarnice.png
+share/tuxanci/image/lasserX.png
+share/tuxanci/image/lasserY.png
+share/tuxanci/image/level4.png
share/tuxanci/image/mine.png
share/tuxanci/image/naboj.png
share/tuxanci/image/night_workshift.png
@@ -97,11 +97,11 @@ share/tuxanci/image/screen_table.png
share/tuxanci/image/shot.png
share/tuxanci/image/textfield0.png
share/tuxanci/image/textfield1.png
-share/tuxanci/image/tuxanci.png
share/tuxanci/image/tux2.png
share/tuxanci/image/tux4.png
share/tuxanci/image/tux6.png
share/tuxanci/image/tux8.png
+share/tuxanci/image/tuxanci.png
share/tuxanci/lang/cs.lang
share/tuxanci/lang/en.lang
share/tuxanci/lang/fr.lang
@@ -113,11 +113,11 @@ share/tuxanci/music/night_workshift.ogg
share/tuxanci/sound/dead.ogg
share/tuxanci/sound/end.ogg
share/tuxanci/sound/explozion.ogg
+share/tuxanci/sound/gun2.ogg
share/tuxanci/sound/gun_lasser.ogg
share/tuxanci/sound/gun_revolver.ogg
share/tuxanci/sound/gun_scatter.ogg
share/tuxanci/sound/gun_tommy.ogg
-share/tuxanci/sound/gun2.ogg
share/tuxanci/sound/item_bonus.ogg
share/tuxanci/sound/item_gun.ogg
share/tuxanci/sound/odraz-gun.ogg
diff --git a/tuxguitar/Makefile b/tuxguitar/Makefile
index 1134cd2be2..10c34ca63d 100644
--- a/tuxguitar/Makefile
+++ b/tuxguitar/Makefile
@@ -16,13 +16,13 @@ USE_LANGUAGES= c c++
USE_JAVA2= yes
BUILD_DEPENDS+= apache-ant-[0-9]*:../../devel/apache-ant
-MAKE_PROGRAM=ant
-MAKE_FILE=build.xml
+MAKE_PROGRAM= ant
+MAKE_FILE= build.xml
.include "../../mk/bsd.prefs.mk"
.include "options.mk"
-NO_CONFIGURE=yes
+NO_CONFIGURE= yes
do-build:
.for optn in ${PKG_OPTIONS}
diff --git a/twemproxy/Makefile b/twemproxy/Makefile
index 3b21faeb8c..fee8b919dc 100644
--- a/twemproxy/Makefile
+++ b/twemproxy/Makefile
@@ -12,13 +12,13 @@ HOMEPAGE= https://github.com/twitter/twemproxy/
COMMENT= Fast, light-weight proxy for memcached and redis
LICENSE= apache-2.0
-EGFILES= conf/nutcracker.yml
-EGFILES+= conf/nutcracker.leaf.yml conf/nutcracker.root.yml
-EGDIR= share/examples/twemproxy
+EGFILES= conf/nutcracker.yml
+EGFILES+= conf/nutcracker.leaf.yml conf/nutcracker.root.yml
+EGDIR= share/examples/twemproxy
INSTALLATION_DIRS= ${EGDIR}
-GNU_CONFIGURE= YES
-USE_LIBTOOL= yes
+GNU_CONFIGURE= YES
+USE_LIBTOOL= yes
USE_TOOLS+= autoreconf automake m4
WRKSRC= ${WRKDIR}/twemproxy-0.4.1
diff --git a/twitmail/Makefile b/twitmail/Makefile
index 30e822bf48..27aac283a7 100644
--- a/twitmail/Makefile
+++ b/twitmail/Makefile
@@ -19,7 +19,7 @@ DEPENDS+= p5-Net-Twitter>=0:../../net/p5-Net-Twitter
DEPENDS+= p5-TimeDate>=0:../../time/p5-TimeDate
DEPENDS+= p5-Getopt-GUI-Long>=0:../../wip/p5-Getopt-GUI-Long
-PERL5_PACKLIST= auto/twitmail/.packlist
+PERL5_PACKLIST= auto/twitmail/.packlist
USE_LANGUAGES= # none
.include "../../lang/perl5/module.mk"
diff --git a/txt2tags/Makefile b/txt2tags/Makefile
index bcbb11b1ce..73f12ef6fd 100644
--- a/txt2tags/Makefile
+++ b/txt2tags/Makefile
@@ -2,7 +2,7 @@
#
DISTNAME= txt2tags-2.5
-CATEGORIES= textproc
+CATEGORIES= textproc
MASTER_SITES= http://txt2tags.googlecode.com/files/
EXTRACT_SUFX= .tgz
@@ -13,13 +13,13 @@ COMMENT= Text formatting and conversion tool
REPLACE_PYTHON= txt2tags
USE_PKGLOCALEDIR= yes
-NO_BUILD= yes
-USE_LANGUAGES= # none
+NO_BUILD= yes
+USE_LANGUAGES= # none
DOC_DIR= ${PREFIX}/share/doc/${PKGBASE}
SAMPLES_DIR= ${PREFIX}/share/examples/${PKGBASE}
-INSTALLATION_DIRS+= ${DOC_DIR} ${SAMPLES_DIR}
-INSTALLATION_DIRS+= bin ${PKGMANDIR}/man1
+INSTALLATION_DIRS+= ${DOC_DIR} ${SAMPLES_DIR}
+INSTALLATION_DIRS+= bin ${PKGMANDIR}/man1
do-install:
${INSTALL_DATA_DIR} ${DOC_DIR} ${SAMPLES_DIR} ${DESTDIR}${SAMPLES_DIR}/img
diff --git a/typespeed/Makefile b/typespeed/Makefile
index 295e05ea2d..aec23fb871 100644
--- a/typespeed/Makefile
+++ b/typespeed/Makefile
@@ -23,10 +23,10 @@ CONF_FILES_PERMS+= ${EGDIR}/typespeedrc ${PREFIX}/etc/typespeedrc \
CONF_FILES_PERMS+= /dev/null ${SCORE_PATH}/typespeed.score ${GAMEOWN} \
games 664
-SUBST_CLASSES+= man-paths
-SUBST_STAGE.man-paths= pre-patch
-SUBST_FILES.man-paths= man/typespeed.6
-SUBST_SED.man-paths= -e 's|/etc/|${PREFIX}/etc/|g'
+SUBST_CLASSES+= man-paths
+SUBST_STAGE.man-paths= pre-patch
+SUBST_FILES.man-paths= man/typespeed.6
+SUBST_SED.man-paths= -e 's|/etc/|${PREFIX}/etc/|g'
SUBST_MESSAGE.man-paths= Adjusting path in the game's man page
post-install:
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