From 0baf8e8cfcaacb4af128a1c0de3d3c9cfd3ab77f Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Sun, 8 Dec 2019 01:18:53 +0100 Subject: [PATCH] sci-libs/dcmtk: version bump to 3.6.5 and prefix fix Package-Manager: Portage-2.3.78, Repoman-2.3.17 Signed-off-by: Horea Christian --- sci-libs/dcmtk/ChangeLog | 9 + sci-libs/dcmtk/Manifest | 1 + sci-libs/dcmtk/dcmtk-3.6.5.ebuild | 87 +++++++++ .../dcmtk/files/dcmtk-3.6.3-dcmqrdb-cfg.patch | 87 +++++++++ .../dcmtk/files/dcmtk-3.6.3-fix-gcc9.patch | 29 +++ .../dcmtk/files/dcmtk-3.6.3-nostrip.patch | 171 ++++++++++++++++++ sci-libs/dcmtk/metadata.xml | 8 + 7 files changed, 392 insertions(+) create mode 100644 sci-libs/dcmtk/ChangeLog create mode 100644 sci-libs/dcmtk/Manifest create mode 100644 sci-libs/dcmtk/dcmtk-3.6.5.ebuild create mode 100644 sci-libs/dcmtk/files/dcmtk-3.6.3-dcmqrdb-cfg.patch create mode 100644 sci-libs/dcmtk/files/dcmtk-3.6.3-fix-gcc9.patch create mode 100644 sci-libs/dcmtk/files/dcmtk-3.6.3-nostrip.patch create mode 100644 sci-libs/dcmtk/metadata.xml diff --git a/sci-libs/dcmtk/ChangeLog b/sci-libs/dcmtk/ChangeLog new file mode 100644 index 0000000..c236f09 --- /dev/null +++ b/sci-libs/dcmtk/ChangeLog @@ -0,0 +1,9 @@ + 08 Dec 2019; dcmtk-3.6.5.ebuild: + sci-libs/dcmtk: f + +*dcmtk-3.6.5 (08 Dec 2019) + + 08 Dec 2019; +dcmtk-3.6.5.ebuild, + +files/dcmtk-3.6.3-dcmqrdb-cfg.patch, +files/dcmtk-3.6.3-fix-gcc9.patch, + +files/dcmtk-3.6.3-nostrip.patch, +metadata.xml: + sci-libs/dcmtk: version bump to 3.6.5 and prefix fix diff --git a/sci-libs/dcmtk/Manifest b/sci-libs/dcmtk/Manifest new file mode 100644 index 0000000..f51c939 --- /dev/null +++ b/sci-libs/dcmtk/Manifest @@ -0,0 +1 @@ +DIST dcmtk-3.6.5.tar.gz 6483626 SHA256 a05178665f21896dbb0974106dba1ad144975414abd760b4cf8f5cc979f9beb9 SHA512 c0cf61b0095c5708709406bfef5e8bb82dd01dbf77df7f2af2118004920bda68218eb1e4174bf92941cdae0acdb275c886570dafd29476eee2eb815e9a82830a WHIRLPOOL 14c0be8f35d0e513bb9cb03e5f30adf9b6bb1a5464a5cfee16e8261f9f304a73bd06e79c8d441d9ab8085f414a46112d58a1ccc5286dda11df6169df70dc4691 diff --git a/sci-libs/dcmtk/dcmtk-3.6.5.ebuild b/sci-libs/dcmtk/dcmtk-3.6.5.ebuild new file mode 100644 index 0000000..c7441d1 --- /dev/null +++ b/sci-libs/dcmtk/dcmtk-3.6.5.ebuild @@ -0,0 +1,87 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit cmake-utils + +DESCRIPTION="The DICOM Toolkit" +HOMEPAGE="https://dicom.offis.de/dcmtk.php.en" +SRC_URI="http://dicom.offis.de/download/dcmtk/release/${P}.tar.gz" + +LICENSE="OFFIS" +KEYWORDS="~amd64 ~arm ~x86" +SLOT="0" +IUSE="doc png ssl tcpd tiff +threads xml zlib" + +RDEPEND=" + dev-libs/icu:= + virtual/jpeg:0 + png? ( media-libs/libpng:* ) + ssl? ( dev-libs/openssl:0= ) + tcpd? ( sys-apps/tcp-wrappers ) + tiff? ( media-libs/tiff:0 ) + xml? ( dev-libs/libxml2:2 ) + zlib? ( sys-libs/zlib )" +DEPEND="${RDEPEND} + media-gfx/graphviz + doc? ( app-doc/doxygen )" + +src_prepare() { + cmake-utils_src_prepare + + sed -e "s:share/doc/dcmtk:&-${PV}:" \ + -e "s:DIR \"/:DIR \"/usr/:" \ + -e "s:usr/etc:etc:" \ + -e "s:/lib\":/$(get_libdir)\":" \ + -e "s:COPYRIGHT::" \ + -i CMakeLists.txt || die + sed -e 's:${CMAKE_INSTALL_PREFIX}/::' \ + -i dcmwlm/data/CMakeLists.txt doxygen/CMakeLists.txt || die + # Temporary workaround: docs are not built with CMake + sed -i -e '/include/d' doxygen/Makefile.in || die + + # fix -D deprecation warnings + sed -i -e "s|_BSD_SOURCE|_DEFAULT_SOURCE|g" \ + "${S}"/config/configure.in \ + "${S}"/CMakeLists.txt || die +} + +src_configure() { + local mycmakeargs=( + -DBUILD_SHARED_LIBS=ON + -DCMAKE_INSTALL_SYSCONFDIR=${EROOT%/}/etc + -DDCMTK_WITH_ICU=ON + -DDCMTK_WITH_TIFF=$(usex tiff) + -DDCMTK_WITH_PNG=$(usex png) + -DDCMTK_WITH_XML=$(usex xml) + -DDCMTK_WITH_ZLIB=$(usex zlib) + -DDCMTK_WITH_OPENSSL=$(usex ssl) + -DDCMTK_WITH_DOXYGEN=$(usex doc) + -DDCMTK_WITH_THREADS=$(usex threads) + ) + + cmake-utils_src_configure + + if use doc; then + cd "${S}"/doxygen || die + econf + fi +} + +src_compile() { + cmake-utils_src_compile + + if use doc; then + emake -C "${S}"/doxygen + fi +} + +src_install() { + doman doxygen/manpages/man1/* + + if use doc; then + local HTML_DOCS=( "${S}"/doxygen/htmldocs/. ) + fi + cmake-utils_src_install +} diff --git a/sci-libs/dcmtk/files/dcmtk-3.6.3-dcmqrdb-cfg.patch b/sci-libs/dcmtk/files/dcmtk-3.6.3-dcmqrdb-cfg.patch new file mode 100644 index 0000000..4ccb58d --- /dev/null +++ b/sci-libs/dcmtk/files/dcmtk-3.6.3-dcmqrdb-cfg.patch @@ -0,0 +1,87 @@ +Author: Jürgen Salk +Description: The original maintainer Jürgen Salk applied + a set of patches to the original code. This file contains + changes to C++ code + +Index: dcmtk-3.6.0/dcmqrdb/etc/dcmqrscp.cfg +=================================================================== +--- a/dcmqrdb/etc/dcmqrscp.cfg 2010-09-09 19:20:25.000000000 +0200 ++++ b/dcmqrdb/etc/dcmqrscp.cfg 2011-01-28 09:49:02.000000000 +0100 +@@ -10,7 +10,9 @@ + NetworkTCPPort = 104 + MaxPDUSize = 16384 + MaxAssociations = 16 ++UserName = "dcmtk" ++GroupName = "dcmtk" + + # + # Default settings for specific character set behavior: + # SpecificCharacterSet = fallback +@@ -28,12 +30,13 @@ + # NOTE: in the current implementation you cannot substitute an IP address + # for a hostname. + # +-acme1 = (ACME1, acmehost1, 5678) +-acme2 = (ACME2, acmehost2, 5678) +-acmeCTcompany = acme1, acme2 +-united1 = (UNITED1, unitedhost1, 104) +-united2 = (UNITED2, unitedhost2, 104) +-unitedMRcompany = united1, united2 ++# Example: ++#acme1 = (ACME1, acmehost1, 5678) ++#acme2 = (ACME2, acmehost2, 5678) ++#acmeCTcompany = acme1, acme2 ++#united1 = (UNITED1, unitedhost1, 104) ++#united2 = (UNITED2, unitedhost2, 104) ++#unitedMRcompany = united1, united2 + # + HostTable END + +@@ -51,8 +54,9 @@ + # VendorName = SymbolicName + # The symbolic name should be defined in the HostTable. + # +-"Acme CT Company" = acmeCTcompany +-"United MR Company" = unitedMRcompany ++# Example: ++#"Acme CT Company" = acmeCTcompany ++#"United MR Company" = unitedMRcompany + # + VendorTable END + +@@ -70,8 +74,13 @@ + # Entry in HostTable | + # ANY + # +-COMMON /home/dicom/db/COMMON R (200, 1024mb) ANY +-ACME_STORE /home/dicom/db/ACME_STORE RW (9, 1024mb) acmeCTcompany +-UNITED_STORE /home/dicom/db/UNITED_STORE RW (9, 1024mb) unitedMRcompany ++# Example: ++# ++#ACME_STORE /var/lib/dcmtk/db/ACME_STORE RW (9, 1024mb) acmeCTcompany ++#UNITED_STORE /var/lib/dcmtk/db/UNITED_STORE RW (9, 1024mb) unitedMRcompany ++# ++# Uncomment and adjust the following lines for a common r/rw storage area: ++#READWRITE /var/lib/dcmtk/db/READWRITE RW (10, 1024mb) ANY ++#READ /var/lib/dcmtk/db/READ R (200, 1024mb) ANY + # + AETable END +Index: dcmtk-3.6.0/dcmqrdb/docs/dcmqrcnf.txt +--- a/dcmqrdb/docs/dcmqrcnf.txt 2010-09-09 19:20:12.000000000 +0200 ++++ b/dcmqrdb/docs/dcmqrcnf.txt 2011-01-28 09:46:02.000000000 +0100 +@@ -44,8 +44,8 @@ + MaxPDUSize = 8192 + MaxAssociations = 20 + SpecificCharacterSet = fallback +-UserName = (do not change user) +-GroupName = (do not change group) ++UserName = "dcmtk" ++GroupName = "dcmtk" + + Available options for specific character sets are: + +Index: dcmtk-3.6.0/dcmwlm/wlistdb/OFFIS/lockfile +--- /dev/null 1970-01-01 00:00:00.000000000 +0000 ++++ dcmtk-3.6.0/dcmwlm/wlistdb/OFFIS/lockfile 2011-01-28 09:46:02.000000000 +0100 +@@ -0,0 +1 @@ ++ diff --git a/sci-libs/dcmtk/files/dcmtk-3.6.3-fix-gcc9.patch b/sci-libs/dcmtk/files/dcmtk-3.6.3-fix-gcc9.patch new file mode 100644 index 0000000..596a1ae --- /dev/null +++ b/sci-libs/dcmtk/files/dcmtk-3.6.3-fix-gcc9.patch @@ -0,0 +1,29 @@ +https://bugs.gentoo.org/686592 + +In file included from /var/tmp/portage/sci-libs/dcmtk-3.6.3/work/dcmtk-3.6.3/ofstd/include/dcmtk/ofstd/variadic/variant.h:19, + from /var/tmp/portage/sci-libs/dcmtk-3.6.3/work/dcmtk-3.6.3/ofstd/include/dcmtk/ofstd/ofvriant.h:379, + from /var/tmp/portage/sci-libs/dcmtk-3.6.3/work/dcmtk-3.6.3/ofstd/tests/tvariant.cc:26: +/var/tmp/portage/sci-libs/dcmtk-3.6.3/work/dcmtk-3.6.3/ofstd/include/dcmtk/ofstd/variadic/helpers.h:57:32: error: narrowing conversion of ‘-1’ from ‘int’ to ‘long unsigned int’ [-Wnarrowing] + 57 | : OFintegral_constant {}; + | + +--- a/ofstd/include/dcmtk/ofstd/variadic/helpers.h ++++ b/ofstd/include/dcmtk/ofstd/variadic/helpers.h +@@ -14,6 +14,8 @@ + #ifndef VARIADIC_HELPERS_H + #define VARIADIC_HELPERS_H + ++#include ++ + #include "dcmtk/config/osconfig.h" /* make sure OS specific configuration is included first */ + + #include "dcmtk/ofstd/oftraits.h" +@@ -54,7 +56,7 @@ + + template + struct OFvariadic_find_type_t +-: OFintegral_constant {}; ++: OFintegral_constant::max()> {}; + + template + struct OFvariadic_find_type diff --git a/sci-libs/dcmtk/files/dcmtk-3.6.3-nostrip.patch b/sci-libs/dcmtk/files/dcmtk-3.6.3-nostrip.patch new file mode 100644 index 0000000..83bd3a6 --- /dev/null +++ b/sci-libs/dcmtk/files/dcmtk-3.6.3-nostrip.patch @@ -0,0 +1,171 @@ +Remove all hardcoded calls to `strip` command + +Index: dcmtk-3.6.0/config/templates/Makefile.src +=================================================================== +--- a/config/templates/Makefile.src 2009-01-30 10:27:58.000000000 +0100 ++++ b/config/templates/Makefile.src 2011-01-28 09:53:28.000000000 +0100 +@@ -31,7 +31,7 @@ + install-bin: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmdata/apps/Makefile.in +=================================================================== +--- a/dcmdata/apps/Makefile.in 2009-11-04 10:58:05.000000000 +0100 ++++ b/dcmdata/apps/Makefile.in 2011-01-28 09:53:45.000000000 +0100 +@@ -76,7 +76,7 @@ + install-bin: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmimage/apps/Makefile.in +=================================================================== +--- a/dcmimage/apps/Makefile.in 2009-10-13 16:08:33.000000000 +0200 ++++ b/dcmimage/apps/Makefile.in 2011-01-28 09:53:59.000000000 +0100 +@@ -42,7 +42,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmimgle/apps/Makefile.in +=================================================================== +--- a/dcmimgle/apps/Makefile.in 2009-10-28 10:53:39.000000000 +0100 ++++ b/dcmimgle/apps/Makefile.in 2011-01-28 09:54:11.000000000 +0100 +@@ -39,7 +39,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmjpeg/apps/Makefile.in +=================================================================== +--- a/dcmjpeg/apps/Makefile.in 2009-10-07 14:44:33.000000000 +0200 ++++ b/dcmjpeg/apps/Makefile.in 2011-01-28 09:54:28.000000000 +0100 +@@ -72,7 +72,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + clean: +Index: dcmtk-3.6.0/dcmnet/apps/Makefile.in +=================================================================== +--- a/dcmnet/apps/Makefile.in 2009-11-04 11:24:29.000000000 +0100 ++++ b/dcmnet/apps/Makefile.in 2011-01-28 09:54:50.000000000 +0100 +@@ -52,7 +52,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmpstat/apps/Makefile.in +=================================================================== +--- a/dcmpstat/apps/Makefile.in 2009-10-13 16:57:49.000000000 +0200 ++++ b/dcmpstat/apps/Makefile.in 2011-01-28 09:55:10.000000000 +0100 +@@ -113,7 +113,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmqrdb/apps/Makefile.in +=================================================================== +--- a/dcmqrdb/apps/Makefile.in 2009-11-04 11:24:30.000000000 +0100 ++++ b/dcmqrdb/apps/Makefile.in 2011-01-28 09:55:24.000000000 +0100 +@@ -57,7 +57,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmsign/apps/Makefile.in +=================================================================== +--- a/dcmsign/apps/Makefile.in 2009-09-04 17:42:31.000000000 +0200 ++++ b/dcmsign/apps/Makefile.in 2011-01-28 09:55:35.000000000 +0100 +@@ -33,7 +33,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmsr/apps/Makefile.in +=================================================================== +--- a/dcmsr/apps/Makefile.in 2009-10-13 16:57:49.000000000 +0200 ++++ b/dcmsr/apps/Makefile.in 2011-01-28 09:55:48.000000000 +0100 +@@ -44,7 +44,7 @@ + install-bin: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmwlm/apps/Makefile.in +=================================================================== +--- a/dcmwlm/apps/Makefile.in 2009-11-04 11:24:30.000000000 +0100 ++++ b/dcmwlm/apps/Makefile.in 2011-01-28 09:55:58.000000000 +0100 +@@ -49,7 +49,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmwlm/wwwapps/Makefile.in +=================================================================== +--- a/dcmrt/apps/Makefile.in 2009-11-04 11:24:30.000000000 +0100 ++++ b/dcmrt/apps/Makefile.in 2011-01-28 09:56:33.000000000 +0100 +@@ -55,7 +55,7 @@ + install-bin: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmjpls/apps/Makefile.in +=================================================================== +--- a/dcmjpls/apps/Makefile.in 2011-01-28 09:56:54.000000000 +0100 ++++ b/dcmjpls/apps/Makefile.in 2011-01-28 09:57:00.000000000 +0100 +@@ -71,7 +71,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + diff --git a/sci-libs/dcmtk/metadata.xml b/sci-libs/dcmtk/metadata.xml new file mode 100644 index 0000000..ed91732 --- /dev/null +++ b/sci-libs/dcmtk/metadata.xml @@ -0,0 +1,8 @@ + + + + + sci-biology@gentoo.org + + DICOM ToolKit core medical imaging library and tools +