Add patches from Debian to use system libtool, respect proper directory, and a man page

Package-Manager: portage-2.2.01.22124-prefix/cvs/Linux x86_64
Manifest-Sign-Key: 0x13CB1360

9 files changed, 302 insertions, 5 deletions

diff --git a/sci-astronomy/esorex/ChangeLog b/sci-astronomy/esorex/ChangeLog
index 3e124fd096f8..c8fa37d4af19 100644
--- a/sci-astronomy/esorex/ChangeLog
+++ b/sci-astronomy/esorex/ChangeLog
@@ -1,6 +1,18 @@
 # ChangeLog for sci-astronomy/esorex
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-astronomy/esorex/ChangeLog,v 1.9 2013/06/11 17:43:53 bicatali Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-astronomy/esorex/ChangeLog,v 1.10 2013/07/25 17:26:47 bicatali Exp $
+
+*esorex-3.10-r1 (25 Jul 2013)
+
+  25 Jul 2013; Sébastien Fabbro <bicatali@gentoo.org> +esorex-3.10-r1.ebuild,
+  +files/esorex-3.10-fix-autotools.patch,
+  +files/esorex-3.10-fix_format_strings.patch,
+  +files/esorex-3.10-generate-manpage.patch,
+  +files/esorex-3.10-remove-empty-configdir.patch,
+  +files/esorex-3.10-remove-private-ltdl.patch,
+  +files/esorex-3.10-set-default-plugin-path.patch:
+  Add patches from Debian to use system libtool, respect proper directory, and a
+  man page
 
   11 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> -esorex-3.9.6-r1.ebuild,
   -files/esorex-3.9.6-autoconf-26.patch,
diff --git a/sci-astronomy/esorex/Manifest b/sci-astronomy/esorex/Manifest
index e33f452d745c..9d0a68f26a0b 100644
--- a/sci-astronomy/esorex/Manifest
+++ b/sci-astronomy/esorex/Manifest
@@ -1,15 +1,22 @@
 -----BEGIN PGP SIGNED MESSAGE-----
 Hash: SHA256
 
+AUX esorex-3.10-fix-autotools.patch 299 SHA256 228c524e9dea6296299b41dda11515f5a22373623abb7b7adab3ebf5c738a9f7 SHA512 6044c916ece118c455a69a14e8a4d26bb66a75eb30291dea877f6cac93d919e3b39e9887d695ec153ef50abb1b546f937ae5d0c4d94191e97a1247c18990eda5 WHIRLPOOL 00ca2603e61cc0e4a41253ba1540dd46281ffc3e1317853830f417b9c829aca73fc993df24dee84bfee9dedf4d906345e457c98c8cdb4797f98d0efb643414c1
+AUX esorex-3.10-fix_format_strings.patch 845 SHA256 caf734b4501639f88470043425260b309ca655a32b939cd6ac3935993f8284b0 SHA512 9bcb4cb1ab0eb6ed846df7ec22abd6004d2fd72a8255cfa482f9ecd039255e4d1ccf987fad60265347e17cefcb0dde226f923048fcad15e384a7bd6884aa8541 WHIRLPOOL 6f9c6a0b7116de526fdff9fb626e9fa95670b77af5695e64ef18b7b1e6cd871d8f60b36bc0e98291f24627a36b4a693f6ccdfdadafe268eb306612cf8588572e
+AUX esorex-3.10-generate-manpage.patch 4865 SHA256 ca69cc20e5291dce3fe2bec20ee7ef4929f98c7a635208ff0e2d1a8645eb755c SHA512 5a2aeb18e08f36969d439f999f76933030b6a462b8e10041f20d3ffccefdf04f68daeecaaab7ee1694a0127bfe570cd0db8fbf9ced17a484eac2023929aff2b8 WHIRLPOOL 2314b9a10406d9c7ff695e9626dceade5670597dd7cfabf3a53f9016ae875c6e5263dd9040ce157a2cca88c2c3da5632175a3bdb97b59d36c27ddb5cc75dc9c9
+AUX esorex-3.10-remove-empty-configdir.patch 400 SHA256 03a89a4072b52c85866f5cb601d7f71a51fbe4cda9e5fba07a8e3c76bae37a3f SHA512 24c2893f47c779368f72a01b00088e1dccb830797a7c3c094b48dda833770b37b9d98f8a7068d1d12e0a88182b0649e0418cb24c5f597cfb2467caee9e1d0f14 WHIRLPOOL bc3d5001dfb179d3b494d90620942656b4d6ecf5aaed3dbdb37001286a4852540e882d45aeb6f4d06a0fbace40482a7855de3640c65a233f3660e7a03fd8ea61
+AUX esorex-3.10-remove-private-ltdl.patch 1053 SHA256 d7dd4f889409e28c510b0f11d6d6d1efd75fd5e7fcad96b22700c6be60bd6b4e SHA512 039e6147d6ccb08cbde344ca21628e03bc039bd16ea9edc2cc5d5cea60f5478166f5f82b60b63fcfc71a6bf003510071d11b4882ef0c3cd3ba01c4a7d914d520 WHIRLPOOL 5d3ac2162d067af71e6c9231bd4a07b2eafaf8d96cb7be347b666ed1e12b760844cde4ca3fdbd0272c5fc33248e6a52ec18cc156411710d0d949565b38beb4fd
+AUX esorex-3.10-set-default-plugin-path.patch 951 SHA256 d39d57620e1c38d5167f0003c9ea4b5ce8c870f82a764b2e7d90ed5a69989a2a SHA512 004ebad285f4bc8eac0917ccdd1ab22563f73926b276e5ce2c469e144a6f7d6f2310c098904aeab73e88d57886147dcfae7704ec54a3b5ef86005a58f6f41829 WHIRLPOOL 3255a3a63d315895c0afa07011cc6c4f1d0191a4c39afc8b1c244cf1f868104cd4af9a5f49bb1cd3bba513ebb66f99b34721398bbcce8d0759bec8e53a0030c4
 AUX esorex-3.9.6-use-shared-libs.patch 562 SHA256 1a8922317e93d5840144b79d84e93b7ca329da9aa0e1872ad3493913e6975e90 SHA512 224ddaa94e1d7f105634f53b4238176ff84b2df0ebbfbfe8470fcb30182b4b3aa874ce002d98275488cf38128586e7dc7da0e26729db748e843ce661fa20930c WHIRLPOOL da69698daaf93607e8a4542dc35c2aaeb6b1327139927276bebca72e4788110c53e3b1aa88e7495b23ec4a1ba75fca1ce2efa34f82a4469a1366d7a393b96884
 DIST esorex-3.10.tar.gz 817307 SHA256 72ff1d26a45d7e926b1f4f74f1f286c8feb142dba7b0b5bb717c6286644f9494 SHA512 985a906418488fec46fc939bf64b40330ae829771860a36a40240b703f6f6f89f3da6701ee4ceb8c6d2c0b478004596dce4dbc11389937e75ef02d9ecb4c3d16 WHIRLPOOL ef368d35f5145b5626c88d6d4af7249889cce1ef901c67318d1f06f9baa7a0411c87917969261c0a268a06e5fd0dafd30701f49394cb82671f8c9ce282bc4768
+EBUILD esorex-3.10-r1.ebuild 1104 SHA256 4db98a946c0b784273f21263ee96abda8704ea289def79039b0e59e1cdc0af38 SHA512 c17a3d949e05c4a27118636926b04a072a0e86148e0d1812fcbb8b30cf47a3bf40ddcd8b159d0dde4673981beb100e454e87c408d30b06c560383b204f08e1a1 WHIRLPOOL 3654739586b65b9470da423d2700017597e3cd907896d2e41edbaccbb3e57e5ca367139f7882dd560a85fa877d45ac91ac55e5e6bd6bf58b87adc903e6f51881
 EBUILD esorex-3.10.ebuild 835 SHA256 de89161eaee83613d59567cd9992fd5c307700bddfb4738177436b23dabd633e SHA512 ed635437b918ab69c605297c82d26e23aa0c1ba2345c6349df623d9707310cffa54a89bec6abcdeb95ad9206deff3341e87073970594676e8d80458575fb27e6 WHIRLPOOL 8b4f09748c5dcf09f07a5dae766409295f09a93da9a58e46c1c079b923e5d0d8b8ec6b97123d4834d1f666653dcf5c97d934df2c73d6ff38dbfb69dc09476935
-MISC ChangeLog 2697 SHA256 af09c5298d04af5e529f3e6c6362476c6a7044f85d3b037f694d5032d9f36ebe SHA512 848b06874b22edf4c77b210a57cd4a8c421b6e2b58fb6765bc0f514a89a174c446b4f7dffd63da0e3ffe0b2d7f66d4704f84a166f7a89ffe313a8e5c30bff4e1 WHIRLPOOL 53e4071712b7f510be30f3b9131ddf513274b0821b2087c44f659608798b4e017415b2cccd1c3946e432b5e95ca5e546f2ecbe21d4060f4d50f696972f9516fd
+MISC ChangeLog 3186 SHA256 f81dd4b5ff298df7c5674078b0bb8682f425d81c9de1fb95f7e0c172c553d9e6 SHA512 f913e443107dd84ecbd585343a60fdb73cae39bc02b35bb0d8b8ea8a44ea33adb8b0f50df6847b886e3b945ca6f7a800a877054135b1b0c0789ab80c6669a205 WHIRLPOOL bfcf4ce6280543a9695c8042a6983da80a8de7ee674d18fec19abc93f6883b8a84c2f25074bc5fa3f1282c6c5544521e56a70178281485488a217aea1e648425
 MISC metadata.xml 925 SHA256 9b482343b9d05dbf69ac34df5999fe45f8a8529c6ebd4b57bb0678d37505df3f SHA512 239224d707497e129665879c43149011118e4f74f42a14306e3912d0b4436cbb6ff592a0587e1d4045fa972796e1e2462114f53013667dd15f47841f62b68048 WHIRLPOOL c68578baa7660c905d80977c34834413b7d158258a4a993051376a1f8c2212028365f5269842ff33dc0b6a636ba60fd9588b80204bab4e2743bfad1e2596e845
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diff --git a/sci-astronomy/esorex/esorex-3.10-r1.ebuild b/sci-astronomy/esorex/esorex-3.10-r1.ebuild
new file mode 100644
index 000000000000..b1404021624e
--- /dev/null
+++ b/sci-astronomy/esorex/esorex-3.10-r1.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-astronomy/esorex/esorex-3.10-r1.ebuild,v 1.1 2013/07/25 17:26:47 bicatali Exp $
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=1
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+inherit autotools-utils
+
+DESCRIPTION="ESO Recipe Execution Tool to exec cpl scripts"
+HOMEPAGE="http://www.eso.org/sci/software/cpl/esorex.html"
+SRC_URI="ftp://ftp.eso.org/pub/dfs/pipelines/libraries/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+DEPEND=">=sci-astronomy/cpl-6.3"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-3.9.6-use-shared-libs.patch
+	"${FILESDIR}"/${PN}-3.10-remove-private-ltdl.patch
+	"${FILESDIR}"/${PN}-3.10-fix-autotools.patch
+	"${FILESDIR}"/${PN}-3.10-generate-manpage.patch
+	"${FILESDIR}"/${PN}-3.10-remove-empty-configdir.patch
+	"${FILESDIR}"/${PN}-3.10-set-default-plugin-path.patch
+)
+
+export CPLDIR="${EPREFIX}/usr"
+
+src_install() {
+	autotools-utils_src_install
+	dodoc -r examples
+	docompress -x /usr/share/doc/${PF}/examples
+}
diff --git a/sci-astronomy/esorex/files/esorex-3.10-fix-autotools.patch b/sci-astronomy/esorex/files/esorex-3.10-fix-autotools.patch
new file mode 100644
index 000000000000..44919f54aa9b
--- /dev/null
+++ b/sci-astronomy/esorex/files/esorex-3.10-fix-autotools.patch
@@ -0,0 +1,12 @@
+Author: Ole Streicher <debian@liska.ath.cx>
+Subject: Fix autotools files to allow the current version.
+--- a/configure.ac
++++ b/configure.ac
+@@ -5,6 +5,7 @@
+ 
+ AC_CONFIG_SRCDIR([Makefile.am])
+ AC_CONFIG_AUX_DIR([admin])
++AC_CONFIG_MACRO_DIR([m4])
+ AC_CONFIG_HEADERS([config.h])
+ 
+ AC_CANONICAL_HOST
diff --git a/sci-astronomy/esorex/files/esorex-3.10-fix_format_strings.patch b/sci-astronomy/esorex/files/esorex-3.10-fix_format_strings.patch
new file mode 100644
index 000000000000..fe4d37b3009c
--- /dev/null
+++ b/sci-astronomy/esorex/files/esorex-3.10-fix_format_strings.patch
@@ -0,0 +1,24 @@
+Author: Ole Streicher <debian@liska.ath.cx>
+Description: Fix -Werror=format-security errors
+--- a/src/er_paramutils.c
++++ b/src/er_paramutils.c
+@@ -731,7 +731,7 @@
+             (void) strcat (tmp, " to ");
+             (void) strcat (tmp, er_strutils_dblstr (cpl_parameter_get_range_max_double (p)));
+             (void) strcat (tmp, ".\n");
+-            cpl_msg_error (er_func, tmp);
++            cpl_msg_error (er_func, "%s", tmp);
+ 
+             cpl_free(tmp);
+             return -1;
+--- a/src/er_plugin.c
++++ b/src/er_plugin.c
+@@ -367,7 +367,7 @@
+             if (wer != 0)
+                {
+                (void) snprintf(estr,(size_t)238,"Expansion of %s failed...",xpath);
+-               cpl_msg_error (er_func, estr);
++               cpl_msg_error (er_func, "%s", estr);
+                goto dealloc;
+                }
+             }
diff --git a/sci-astronomy/esorex/files/esorex-3.10-generate-manpage.patch b/sci-astronomy/esorex/files/esorex-3.10-generate-manpage.patch
new file mode 100644
index 000000000000..017eb2c8f776
--- /dev/null
+++ b/sci-astronomy/esorex/files/esorex-3.10-generate-manpage.patch
@@ -0,0 +1,123 @@
+Author: Ole Streicher <debian@liska.ath.cx>
+Subject: Generate a manpage for esorex.
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -62,3 +62,7 @@
+  include $(top_builddir)/Makefile.purify
+ endif
+ 
++esorex.man: esorex
++	sh esorex_create_man.sh
++
++man1_MANS = esorex.man
+--- /dev/null
++++ b/src/esorex_create_man.sh
+@@ -0,0 +1,108 @@
++#!/bin/sh
++
++help2man -N -i $0  ./esorex | sed s/^:\ // | fgrep -v "***" > esorex.man
++<< instrument.
++
++[NAME]
++esorex \- ESO Recipe Execution Tool
++
++[DESCRIPTION]
++EsoRex is the ESO Recipe Execution Tool. It can list, configure and execute
++CPL-based recipes from the command line. 
++
++One of the features provided by the CPL is the ability to create
++data-reduction algorithms that run as plugins (dynamic libraries). These are
++called recipes and are one of the main aspects of the CPL data-reduction
++development environment.
++
++As these recipes are dynamic libraries, it is not possible to run them
++directly from the command line. However, ESO provides several tools to do
++this, thus saving recipe developers the need to write such an application
++themselves. One of these is GASGANO (a GUI-based tool) and the other is 
++ EsoRex (which runs from the command line) and is described here.  
++
++[ENVIRONMENT]
++All options can be set as environment parameters as well. See the previous
++paragraph for details.
++
++[HINTS]
++.TP
++.SH File permissions
++When a recipe is used with the \fB\-\-suppress\-prefix\fR option, and the 
++\fB\-\-output\-dir\fR is set to the current working directory, then the first
++execution of a recipe will work correctly, but subsequent executions may 
++fail. This is due to output products being given \`read-only\' permission 
++(to avoid the potential inadvertant loss of products). The recipe itself 
++is unable to modify the permissions, and thus it fails when attempting to 
++create the file. The solution (other than using a different output directory
++or prefixes) is to change the permission of these output files or delete 
++them prior to any subsequent execution of that recipe. 
++
++This problem is less likely to occur in EsoRex v2+, due to the replacement of
++the \fB\-\-output\-overwrite\fR option with the \fB\-\-output\-readonly\fR 
++(which is disabled by default). However, a determined user can still reach 
++this situation, in which case the non-readable products must have their 
++permissions changed, as described above.
++
++.TP
++.SH Configuration files
++When creating configuration files, if the the recipe is provided on the
++command line, then EsoRex will generate the configuration file for this
++recipe. If no recipe name is given, then EsoRex will generate a configuration
++file for EsoRex itself. All configuration files are written in the
++$HOME/.esorex/ directory.
++
++.TP
++.SH Memory checking
++It is possible to get EsoRex to check for memory leaks in the recipe
++that it is running, by enabling the \fB\-\-mem\-check\fR option. Then, at the
++conclusion of the recipe execution, and after memory deallocation, a list of
++all remaining allocated memory will be printed to screen. If there are no
++memory leaks, then no addition output is displayed.
++
++[FILES]
++.TP
++.SH /etc/esorex.rc $HOME/.esorex/esorex.rc
++Default configuration files
++
++The configuration file contains the EsoRex options, less the \`\-\-\'
++switch, but prefixed with \`esorex.caller.\'. Blank lines are ignored and
++lines beginning with \`#\' are treated as comments.
++
++Here is an example configuration file.
++
++ # Example EsoRex configuration file
++ #
++ esorex.caller.recipe-dir=/home/username/EsoRex/Plugins
++ esorex.caller.log-dir=.
++ esorex.caller.log-file=esorex.log
++ esorex.caller.log-file=esorex.log
++ esorex.caller.output-dir=.
++ esorex.caller.output-prefix=out_
++
++.TP
++.SH filename.sof
++A sof file contains a list of the input data. This data is specified in an sof
++file (which is just a text file), where each input file is specified with its
++associated classification and category. The format of each line in the sof
++file is as follows:
++
++ full-path-to-file  classification
++
++Optionally, a third column may be provided. Permitted values are either RAW or
++CALIB. This is for when a recipe does not identify the type of input file, but
++as all ESO recipes are required to do so, this column is typically not needed.
++
++An example sof file, for the mythological "ZIMOS" instrument, might look like this:
++
++ /data/mos/ZIMOS.03-12-26T01:05:06.fits  MOS_SCIENCE
++ /data/mos/ZIMOS.03-12-26T01:26:00.fits  MOS_SCIENCE
++ /data/mos/ZIMOS.03-12-26T01:47:04.fits  MOS_SCIENCE
++ /data/cal/master_bias4.fits             MASTER_BIAS
++ /data/cal/grs_LR_red.3.tfits            GRISM_TABLE
++ /data/gasgano/extract_table2.fits       EXTRACT_TABLE
++ /data/cal/badpixel.3.tfits              CCD_TABLE
++
++For an concrete example for a specific instrument, check the documentation for that
++instrument.
++
diff --git a/sci-astronomy/esorex/files/esorex-3.10-remove-empty-configdir.patch b/sci-astronomy/esorex/files/esorex-3.10-remove-empty-configdir.patch
new file mode 100644
index 000000000000..d492173da8eb
--- /dev/null
+++ b/sci-astronomy/esorex/files/esorex-3.10-remove-empty-configdir.patch
@@ -0,0 +1,13 @@
+Author: Ole Streicher <debian@liska.ath.cx>
+Description: Avoid creation of an empty directory "/usr/share/esorex/config"
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -51,8 +51,6 @@
+ 
+ bin_PROGRAMS = esorex
+ 
+-config_DATA =
+-
+ esorex_LDFLAGS = $(CPL_LDFLAGS) $(LIBLTDL)
+ esorex_LDADD = @GETOPT@ $(LIBCPLDFS) $(LIBCPLUI) $(LIBCPLCORE) $(LIBCEXT) $(LIBLTDL)
+ esorex_DEPENDENCIES = @GETOPT@ $(LIBLTDL)
diff --git a/sci-astronomy/esorex/files/esorex-3.10-remove-private-ltdl.patch b/sci-astronomy/esorex/files/esorex-3.10-remove-private-ltdl.patch
new file mode 100644
index 000000000000..e675cdbb8f73
--- /dev/null
+++ b/sci-astronomy/esorex/files/esorex-3.10-remove-private-ltdl.patch
@@ -0,0 +1,39 @@
+Author: Ole Streicher <debian@liska.ath.cx>
+Subject: Remove private library libltdl and use the installed one.
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -37,10 +37,7 @@
+ if MAINTAINER_MODE
+ 
+ MAINTAINERCLEANFILES = $(top_srcdir)/Makefile.in $(top_srcdir)/aclocal.m4 \
+-	$(top_srcdir)/config.h.in $(top_srcdir)/configure config.status config.log \
+-	$(top_srcdir)/libltdl/Makefile.in $(top_srcdir)/libltdl/aclocal.m4 \
+-	$(top_srcdir)/libltdl/config-h.in $(top_srcdir)/libltdl/configure \
+-	libltdl/config.status libltdl/config.log
++	$(top_srcdir)/config.h.in $(top_srcdir)/configure config.status config.log
+ 
+ clean-local: clean-doxygen
+ 
+--- a/configure.ac
++++ b/configure.ac
+@@ -30,7 +30,9 @@
+ 
+ ESO_CHECK_DOCTOOLS
+ 
+-AC_LIBLTDL_CONVENIENCE
++LT_INIT
++LT_CONFIG_LTDL_DIR([libltdl])
++AC_LIB_LTDL
+ AC_SUBST(INCLTDL)
+ AC_SUBST(LIBLTDL)
+ 
+@@ -76,9 +78,6 @@
+ # Determine the shared library suffix on this platform
+ AC_LTDL_SHLIBEXT
+ 
+-
+-AC_CONFIG_SUBDIRS(libltdl)
+-
+ AC_CONFIG_FILES(Makefile
+                 Makefile.purify
+                 doxygen/Doxyfile
diff --git a/sci-astronomy/esorex/files/esorex-3.10-set-default-plugin-path.patch b/sci-astronomy/esorex/files/esorex-3.10-set-default-plugin-path.patch
new file mode 100644
index 000000000000..1289bed5ab0d
--- /dev/null
+++ b/sci-astronomy/esorex/files/esorex-3.10-set-default-plugin-path.patch
@@ -0,0 +1,28 @@
+Author: Ole Streicher <debian@liska.ath.cx>
+Description: Set the default plugin path to the one where recipes are
+ installed in Debian.
+--- a/etc/esorex.rc.in
++++ b/etc/esorex.rc.in
+@@ -130,7 +130,7 @@
+ # as well. Multiple directory heads may be specified, by separating the
+ # starting paths with colons (:). This option may also be set using the
+ # environment variable ESOREX_PLUGIN_DIR.
+-esorex.caller.recipe-dir=@recipedir@/esopipes-plugins
++esorex.caller.recipe-dir=@recipedir@
+ 
+ # --suppress-link
+ # When TRUE, no symbolic link is created to the output product. However, if
+--- a/acinclude.m4
++++ b/acinclude.m4
+@@ -35,7 +35,10 @@
+     AC_SUBST(configdir)
+ 
+     if test -z "$recipedir"; then
+-	    recipedir="`eval echo $libdir`"
++       	    recipedir="`eval echo $libdir`/cpl/plugins"
++       	    if test $libdir != "/usr/lib"; then
++                recipedir="$recipedir:/usr/lib/cpl/plugins"
++            fi
+ 	fi
+ 	AC_SUBST(recipedir)
+