Date: Mon, 6 Sep 2021 14:24:32 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: fa2e0b8c66d4 - main - biology/emboss: Add emboss-shell: Run subshell with proper PATH Message-ID: <202109061424.186EOWm6046144@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=fa2e0b8c66d459b05b1a6624cd482950f9ea3376 commit fa2e0b8c66d459b05b1a6624cd482950f9ea3376 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2021-09-06 14:21:44 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2021-09-06 14:21:44 +0000 biology/emboss: Add emboss-shell: Run subshell with proper PATH Also silence portlint and stage-qa warnings PR: 258316 Approved by: wen --- biology/emboss/Makefile | 10 +++++---- biology/emboss/distinfo | 1 + biology/emboss/files/emboss-shell.in | 26 ++++++++++++++++++++++ biology/emboss/files/patch-Makefile.in | 16 ++++++------- biology/emboss/files/patch-emboss-Makefile.in | 6 ++--- ...mplate => patch-emboss_emboss.default.template} | 4 ++-- biology/emboss/pkg-plist | 1 + 7 files changed, 47 insertions(+), 17 deletions(-) diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile index 3fd93f959e77..aa966ad37b6d 100644 --- a/biology/emboss/Makefile +++ b/biology/emboss/Makefile @@ -2,7 +2,7 @@ PORTNAME= emboss PORTVERSION= 6.6.0 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= biology MASTER_SITES= ftp://emboss.open-bio.org/pub/EMBOSS/ DISTNAME= ${PORTNAME:tu}-${PORTVERSION} @@ -18,15 +18,16 @@ BUILD_DEPENDS= clustalw:biology/clustalw \ LIB_DEPENDS= libgd.so:graphics/gd \ libpng.so:graphics/png +USES= gmake libtool iconv mysql pgsql ssl +USE_SUBMAKE= yes + CONFLICTS= qmail-ldap-[0-9]* digest-[0-9]* PREFIX?= ${LOCALBASE}/emboss NO_MTREE= yes -USES= gmake libtool iconv -USE_SUBMAKE= yes GNU_CONFIGURE= yes USE_LDCONFIG= yes -SUB_FILES= pkg-message +SUB_FILES= pkg-message emboss-shell SUB_LIST= PREFIX=${PREFIX} DATADIR=${DATADIR} LDFLAGS+= -L${LOCALBASE}/lib CONFIGURE_ARGS+=${ICONV_CONFIGURE_ARG} @@ -54,5 +55,6 @@ pre-install: post-install: ${INSTALL_DATA} ${CONFIG_FILE} ${STAGEDIR}${DATADIR} + ${INSTALL_SCRIPT} ${WRKDIR}/emboss-shell ${STAGEDIR}${PREFIX}/bin .include <bsd.port.mk> diff --git a/biology/emboss/distinfo b/biology/emboss/distinfo index ed69bf264b49..d36d2d7c9e0b 100644 --- a/biology/emboss/distinfo +++ b/biology/emboss/distinfo @@ -1,2 +1,3 @@ +TIMESTAMP = 1630936830 SHA256 (emboss/EMBOSS-6.6.0.tar.gz) = 7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e SIZE (emboss/EMBOSS-6.6.0.tar.gz) = 117962028 diff --git a/biology/emboss/files/emboss-shell.in b/biology/emboss/files/emboss-shell.in new file mode 100755 index 000000000000..525b04bcc397 --- /dev/null +++ b/biology/emboss/files/emboss-shell.in @@ -0,0 +1,26 @@ +#!/bin/sh -e + +emboss_bin=%%PREFIX%%/bin +cat << EOM + +Prefixing \$PATH with $emboss_bin. + +Emboss contains commands that conflict with other tools, including at least +"charge", "cons", "garnier", "prophet", and "tcode". + +The other commands with these names may serve entirely different functions +and will not be accessible while running this shell unless you refer to them +by their absolute path name (e.g. %%LOCALBASE%%/bin/garnier), which is not +portable, BTW, so don't hard-code such paths into your scripts. + +Type "exit" or "Ctrl+D" to return to your normal shell. + +EOM + +export PATH=${emboss_bin}:$PATH + +# Invoke the user's chosen shell +if echo $SHELL | grep -q '/t?csh'; then + args='-f' +fi +exec $SHELL $args diff --git a/biology/emboss/files/patch-Makefile.in b/biology/emboss/files/patch-Makefile.in index b79dd7233e0f..469f8acfc64e 100644 --- a/biology/emboss/files/patch-Makefile.in +++ b/biology/emboss/files/patch-Makefile.in @@ -1,6 +1,6 @@ ---- Makefile.in.orig 2014-05-29 03:27:28.070199330 +0600 -+++ Makefile.in 2014-05-29 03:28:00.167196553 +0600 -@@ -756,7 +756,7 @@ +--- Makefile.in.orig 2013-07-15 21:27:28 UTC ++++ Makefile.in +@@ -756,7 +756,7 @@ install-dvi-am: install-exec-am: @$(NORMAL_INSTALL) @@ -9,7 +9,7 @@ install-html: install-html-recursive install-html-am: -@@ -810,7 +810,7 @@ +@@ -810,7 +810,7 @@ uninstall-am: distclean-libtool distclean-tags distcleancheck distdir \ distuninstallcheck dvi dvi-am html html-am info info-am \ install install-am install-data install-data-am install-dvi \ @@ -18,13 +18,13 @@ install-html install-html-am install-info install-info-am \ install-man install-pdf install-pdf-am install-ps \ install-ps-am install-strip installcheck installcheck-am \ -@@ -832,9 +832,6 @@ +@@ -831,9 +831,6 @@ dist-hook: + ### tar cBf - plplot/lib | ( cd $(distdir); tar xBf - ; find plplot -name CVS | xargs rm -rf ) tar cBf - doc | ( cd $(distdir); tar xBf - ; find doc -name CVS | xargs rm -rf; ) tar cBf - jemboss | ( cd $(distdir); tar xBf - ; find jemboss -name CVS | xargs rm -rf; find jemboss -name Makefile | xargs rm -rf; find jemboss -name .cvsignore | xargs rm -rf ) - +- -install-exec-hook: - $(bindir)/embossupdate -- + # Tell versions [3.59,3.63) of GNU make to not export all variables. # Otherwise a system limit (for SysV at least) may be exceeded. - .NOEXPORT: diff --git a/biology/emboss/files/patch-emboss-Makefile.in b/biology/emboss/files/patch-emboss-Makefile.in index 8ee767984aa5..f6278c64dded 100644 --- a/biology/emboss/files/patch-emboss-Makefile.in +++ b/biology/emboss/files/patch-emboss-Makefile.in @@ -1,6 +1,6 @@ ---- emboss/Makefile.in.orig 2014-05-29 14:42:20.540406535 +0600 -+++ emboss/Makefile.in 2014-05-29 14:42:42.364404204 +0600 -@@ -3216,7 +3216,6 @@ +--- emboss/Makefile.in.orig 2013-07-15 21:27:30 UTC ++++ emboss/Makefile.in +@@ -3216,7 +3216,6 @@ LDADD = ../nucleus/libnucleus.la ../ajax/acd/libacd.la $(am__append_3) ../ajax/pcre/libepcre.la \ ../plplot/libeplplot.la $(XLIB) dist_pkgdata_DATA = \ diff --git a/biology/emboss/files/patch-emboss.default.template b/biology/emboss/files/patch-emboss_emboss.default.template similarity index 85% rename from biology/emboss/files/patch-emboss.default.template rename to biology/emboss/files/patch-emboss_emboss.default.template index 04ee586b4bfb..0f06201f5f80 100644 --- a/biology/emboss/files/patch-emboss.default.template +++ b/biology/emboss/files/patch-emboss_emboss.default.template @@ -1,5 +1,5 @@ ---- emboss/emboss.default.template.orig Wed Feb 8 00:43:42 2006 -+++ emboss/emboss.default.template Wed Feb 8 00:40:34 2006 +--- emboss/emboss.default.template.orig 2011-03-11 09:04:31 UTC ++++ emboss/emboss.default.template @@ -4,7 +4,7 @@ # By default this is /usr/local/share/EMBOSS/test but the directory can # be changed with --prefix when you configure EMBOSS. diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist index c8161feb85cc..7ab1e1f9b74b 100644 --- a/biology/emboss/pkg-plist +++ b/biology/emboss/pkg-plist @@ -77,6 +77,7 @@ bin/edamisid bin/edamname bin/edialign bin/einverted +bin/emboss-shell bin/embossdata bin/embossupdate bin/embossversion
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