sci-libs/cbflib & sci-chemistry/rasmol: remove last-rited packages

Closes: https://bugs.gentoo.org/788508
Closes: https://bugs.gentoo.org/668568
Closes: https://bugs.gentoo.org/721998
Signed-off-by: Joonas Niilola <juippis@gentoo.org>

4 files changed, 0 insertions, 262 deletions

diff --git a/sci-libs/cbflib/Manifest b/sci-libs/cbflib/Manifest
deleted file mode 100644
index 83e5d601f292..000000000000
--- a/sci-libs/cbflib/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST CBFlib-0.9.3.3.tar.gz 5787633 BLAKE2B c07b73f037f84c84613dd33a7b403d9f934d58abe12016167a6d9ef7633827ad46bef0813b5040790d4da03980285527b43ec0a899e46d8e4823f68fdcbe0765 SHA512 e041c26770e12e09110d7c4f39737406c6ade6cae6fa941cd31dd3b90432a034426272b8daa851a8a23baceb7189479d2d8bde882b7cfdb8ae666fadc5be57ff
diff --git a/sci-libs/cbflib/cbflib-0.9.3.3.ebuild b/sci-libs/cbflib/cbflib-0.9.3.3.ebuild
deleted file mode 100644
index 4d53d2881cf6..000000000000
--- a/sci-libs/cbflib/cbflib-0.9.3.3.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-CMAKE_MAKEFILE_GENERATOR=emake
-
-inherit cmake-utils flag-o-matic fortran-2 toolchain-funcs
-
-MY_P1="CBFlib-${PV}"
-#MY_P2="CBFlib_${PV}"
-MY_P2="CBFlib_0.9.3"
-
-DESCRIPTION="Library providing a simple mechanism for accessing CBF files and imgCIF files"
-HOMEPAGE="http://www.bernstein-plus-sons.com/software/CBF/"
-BASE_TEST_URI="http://arcib.dowling.edu/software/CBFlib/downloads/version_${PV}/"
-SRC_URI="mirror://sourceforge/${PN}/${MY_P1}.tar.gz"
-#	test? (
-#		mirror://sourceforge/${PN}/${MY_P2}_Data_Files_Input.tar.gz
-#		mirror://sourceforge/${PN}/${MY_P2}_Data_Files_Output.tar.gz
-#	)"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
-IUSE="doc test"
-
-S=${WORKDIR}/${MY_P1}
-
-RDEPEND="sci-libs/hdf5:="
-DEPEND="${RDEPEND}"
-
-RESTRICT="test"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-unbundle.patch
-)
-
-src_prepare() {
-	rm -rf Py* drel* dRel* ply* || die
-
-	append-fflags -fno-range-check
-
-	tc-export CC CXX AR RANLIB FC F77
-	cmake-utils_src_prepare
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DUNPACKED_DIRECTORY="${S}"
-	)
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-	dosym ${PN} /usr/include/cbf
-}
diff --git a/sci-libs/cbflib/files/cbflib-0.9.3.3-unbundle.patch b/sci-libs/cbflib/files/cbflib-0.9.3.3-unbundle.patch
deleted file mode 100644
index ef24c4b94b22..000000000000
--- a/sci-libs/cbflib/files/cbflib-0.9.3.3-unbundle.patch
+++ /dev/null
@@ -1,181 +0,0 @@
- CMakeLists.txt | 118 +++------------------------------------------------------
- 1 file changed, 6 insertions(+), 112 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 75054d6..15bab99 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -279,7 +279,7 @@ project (CBFlib C CXX Fortran)
- enable_testing()
- set (CBF_CMAKE_DEBUG "ON")
- 
--set(CMAKE_C_FLAGS "-Wall -fno-strict-aliasing")
-+set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wall -fno-strict-aliasing")
- 
- #
- #  User setable parameters
-@@ -530,42 +530,6 @@ find_package(ZLIB)
- 
- 
- 
--#Load external packages in build directory at cmake time
--add_subdirectory(${CBF__EXTERNAL_PACKAGES}  "${CBF__EXT_PKG}")
--
--find_file(CBF_EXT_PKG_BLD_RUNNING cbf_ext_pkg_build_running "${CBF__EXT_PKG}")
--if (${CBF_EXT_PKG_BLD_RUNNING} STREQUAL "CBF_EXT_PKG_BLD_RUNNING-NOTFOUND")
--  file(WRITE "${CBF__EXT_PKG}/cbf_ext_pkg_build_running" "cbf_ext_pkg_build_running")
--  CBF_DEBUG_MESSAGE("CMAKE_COMMAND:        ${CMAKE_COMMAND}")
--  CBF_DEBUG_MESSAGE("CBFlib_SOURCE_DIR:    ${CBFlib_SOURCE_DIR} ")
--  execute_process(
--    COMMAND ${CMAKE_COMMAND} ${CBFlib_SOURCE_DIR}
--    RESULT_VARIABLE CBF_BUILD_RESULT)
--  CBF_DEBUG_MESSAGE("CBF_BUILD_RESULT: ${CBF_BUILD_RESULT}")
--  execute_process(
--    COMMAND ${CMAKE_COMMAND} --build ${CBFlib_BINARY_DIR} --target HDF5
--    RESULT_VARIABLE CBF_BUILD_RESULT)
--  CBF_DEBUG_MESSAGE("CBF_BUILD_RESULT: ${CBF_BUILD_RESULT}")
--  execute_process(
--    COMMAND ${CMAKE_COMMAND} --build ${CBFlib_BINARY_DIR} --target TIFF
--    RESULT_VARIABLE CBF_BUILD_RESULT)
--  CBF_DEBUG_MESSAGE("CBF_BUILD_RESULT: ${CBF_BUILD_RESULT}")
--  file(REMOVE "${CBF__EXT_PKG}/cbf_ext_pkg_build_running")
--endif (${CBF_EXT_PKG_BLD_RUNNING} STREQUAL "CBF_EXT_PKG_BLD_RUNNING-NOTFOUND")
--
--
--file(GLOB CBF_HDF5_LIBRARY_PATH "${CMAKE_CURRENT_BINARY_DIR}/lib/*hdf5*")
--CBF_DEBUG_MESSAGE( "CBF_HDF5_LIBRARY_PATH:  ${CBF_HDF5_LIBRARY_PATH}")
--file(GLOB CBF_TIFF_LIBRARY_PATH "${CMAKE_CURRENT_BINARY_DIR}/lib/*tif*")
--CBF_DEBUG_MESSAGE( "CBF_TIFF_LIBRARY_PATH: ${CBF_TIFF_LIBRARY_PATH}")
--
--if ("|${CBF_HDF5_LIBRARY_PATH}|" STREQUAL "||" OR "|${CBF_TIFF_LIBRARY_PATH}|" STREQUAL "||")
--  MESSAGE(STATUS "Must build external packages in ${CBF__EXT_PKG}")
--  MESSAGE(STATUS "Then rerun cmake")
--  MESSAGE(WARNING "Finishing run to make Makefiles")
--endif ("|${CBF_HDF5_LIBRARY_PATH}|" STREQUAL "||" OR "|${CBF_TIFF_LIBRARY_PATH}|" STREQUAL "||")
--
--
- #
- # Data Directories
- #
-@@ -579,35 +543,6 @@ set(CBF_DATAURLBASE	"http://downloads.sf.net/cbflib")
- set(CBF_DATAURLI  "${CBF_DATAURLBASE}/CBFlib_${CBF_VERSION}_Data_Files_Input.tar.gz")
- set(CBF_DATAURLO  "${CBF_DATAURLBASE}/CBFlib_${CBF_VERSION}_Data_Files_Output.tar.gz")
- set(CBF_DATAURLS  "${CBF_DATAURLBASE}/CBFlib_${CBF_VERSION}_Data_Files_Output_Sigs_Only.tar.gz")
--#
--# Load and unpack the Data Files
--#
--CBF_LOAD_TARBALL(${CBF__DATA} ${CBF_DATADIRI} ${CBF_DATAURLI})
--CBF_LOAD_TARBALL(${CBF__DATA} ${CBF_DATADIRO} ${CBF_DATAURLO})
--CBF_LOAD_TARBALL(${CBF__DATA} ${CBF_DATADIRS} ${CBF_DATAURLS})
--#
--# Verify the checksums
--#
--file(GLOB CBF_DATADIRI_FILES "${CBF_DATADIRI}/*")
--file(GLOB CBF_DATADIRO_FILES "${CBF_DATADIRO}/*")
--foreach(loop_file ${CBF_DATADIRI_FILES} )
--  if (NOT "${loop_file}" MATCHES "[*.]md5")
--    file(MD5 "${loop_file}" loop_file_md5)
--    file(STRINGS "${loop_file}.md5" loop_file_md5_orig LIMIT_COUNT 1)
--    if (NOT ("${loop_file_md5}" STREQUAL "${loop_file_md5_orig}"))
--      message(WARNINH "loop_file: ${loop_file}:|${loop_file_md5}|${loop_file_md5_orig}|")
--    endif (NOT ("${loop_file_md5}" STREQUAL "${loop_file_md5_orig}"))
--  endif (NOT "${loop_file}" MATCHES "[*.]md5")
--endforeach(loop_file)
--foreach(loop_file ${CBF_DATADIRO_FILES} )
--  if (NOT "${loop_file}" MATCHES "[*.]md5")
--    file(MD5 "${loop_file}" loop_file_md5)
--    file(STRINGS "${loop_file}.md5" loop_file_md5_orig LIMIT_COUNT 1)
--    if (NOT ("${loop_file_md5}" STREQUAL "${loop_file_md5_orig}"))
--      message(WARNING "loop_file: ${loop_file}:|${loop_file_md5}|${loop_file_md5_orig}|")
--    endif (NOT ("${loop_file_md5}" STREQUAL "${loop_file_md5_orig}"))
--  endif (NOT "${loop_file}" MATCHES "[*.]md5")
--endforeach(loop_file)
- 
- 
- #
-@@ -775,7 +710,7 @@ add_library(cbf_shared SHARED  ${CBF_C_SOURCES})
- set_target_properties(cbf_shared PROPERTIES OUTPUT_NAME "cbf")
- set_target_properties(cbf_shared PROPERTIES LINKER_LANGUAGE C)
- set_target_properties(cbf_shared PROPERTIES SOVERSION "${CBF_APIVERSION}")
--target_link_libraries(cbf_shared ${CBF_HDF5_LIBRARY_PATH})
-+target_link_libraries(cbf_shared hdf5)
- 
- #
- # Build the static and shared IMG libraries
-@@ -791,7 +726,7 @@ set(CMAKE_LIBRARY_OUTPUT_DIRECTORY "${CBFlib_BINARY_DIR}/solib")
- add_library(img_shared SHARED  ${CBF__EXAMPLES}/img.c)
- set_target_properties(img_shared PROPERTIES OUTPUT_NAME "img")
- set_target_properties(img_shared PROPERTIES LINKER_LANGUAGE C)
--target_link_libraries(img_shared ${CBF_HDF5_LIBRARY_PATH})
-+target_link_libraries(img_shared hdf5 m )
- 
- 
- #
-@@ -829,26 +764,6 @@ target_link_libraries(fcb_shared ${CBF_HDF5_LIBRARY_PATH})
- #
- #  C and C++ examples
- #
--CBF_ADD_C_EXAMPLE(convert_image "${CBF__EXAMPLES}" "" "img_static")
--CBF_ADD_C_EXAMPLE(convert_minicbf "${CBF__EXAMPLES}" "" "")
--CBF_ADD_C_EXAMPLE(makecbf "${CBF__EXAMPLES}" "" "img_static")
--CBF_ADD_C_EXAMPLE(adscimg2cbf "${CBF__EXAMPLES}" "${CBF__EXAMPLES}/adscimg2cbf_sub.c" "")
--CBF_ADD_C_EXAMPLE(cbf2adscimg "${CBF__EXAMPLES}" "${CBF__EXAMPLES}/cbf2adscimg_sub.c" "")
--CBF_ADD_C_EXAMPLE(cbf_tail "${CBF__EXAMPLES}" "" "")
--CBF_ADD_C_EXAMPLE(changtestcompression "${CBF__EXAMPLES}" "" "")
--CBF_ADD_C_EXAMPLE(img2cif "${CBF__EXAMPLES}" "" "img_static")
--CBF_ADD_C_EXAMPLE(cif2cbf "${CBF__EXAMPLES}" "" "")
--CBF_ADD_C_EXAMPLE(cbf2nexus "${CBF__EXAMPLES}" "" "")
--CBF_ADD_C_EXAMPLE(minicbf2nexus "${CBF__EXAMPLES}" "" "")
--CBF_ADD_C_EXAMPLE(cbf_template_t "${CBF__DECTRIS_EXAMPLES}" "" "")
--CBF_ADD_CXX_EXAMPLE(testcell "${CBF__EXAMPLES}" "" "")
--CBF_ADD_CXX_EXAMPLE(sauter_test "${CBF__EXAMPLES}" "" "")
--CBF_ADD_C_EXAMPLE(sequence_match "${CBF__EXAMPLES}" "" "")
--CBF_ADD_C_EXAMPLE(tiff2cbf "${CBF__EXAMPLES}" "${CBF__EXT_PKG}/${CBF_TIFF}/libtiff/tif_sprint.c" "${CBF_TIFF_LIBRARY_PATH}")
--CBF_ADD_C_EXAMPLE(testulp "${CBF__EXAMPLES}" "" "")
--CBF_ADD_C_EXAMPLE(testhdf5 "${CBF__EXAMPLES}" "" "")
--CBF_ADD_C_EXAMPLE(testtree "${CBF__EXAMPLES}" "" "")
--CBF_ADD_C_EXAMPLE(testalloc "${CBF__EXAMPLES}" "" "")
- 
- 
- 
-@@ -876,26 +791,9 @@ target_link_libraries(test_xds_binary     fcb_static)
- #
- # install
- #
--install (TARGETS makecbf DESTINATION bin)
--install (TARGETS img2cif DESTINATION bin)
--install (TARGETS cif2cbf DESTINATION bin)
--install (TARGETS adscimg2cbf DESTINATION bin)
--install (TARGETS cbf2adscimg DESTINATION bin)
--install (TARGETS changtestcompression DESTINATION bin)
--install (TARGETS convert_image DESTINATION bin)
--install (TARGETS convert_minicbf DESTINATION bin)
--install (TARGETS minicbf2nexus DESTINATION bin)
--install (TARGETS cbf_template_t DESTINATION bin)
--install (TARGETS testcell DESTINATION bin)
--install (TARGETS sauter_test DESTINATION bin)
--install (TARGETS sequence_match DESTINATION bin)
--install (TARGETS tiff2cbf DESTINATION bin)
--install (TARGETS cbf_static DESTINATION lib)
--install (TARGETS cbf_shared DESTINATION lib)
--install (TARGETS fcb_static DESTINATION lib)
--install (TARGETS fcb_shared DESTINATION lib)
--install (TARGETS img_static DESTINATION lib)
--install (TARGETS img_shared DESTINATION lib)
-+install (TARGETS cbf_shared DESTINATION lib${LIB_SUFFIX})
-+install (TARGETS fcb_shared DESTINATION lib${LIB_SUFFIX})
-+install (TARGETS img_shared DESTINATION lib${LIB_SUFFIX})
- install (DIRECTORY ${CBF__INCLUDE}/ DESTINATION include/cbflib FILES_MATCHING PATTERN "*.h")
- install (DIRECTORY ${CBF__BIN_INCLUDE}/* DESTINATION include/cbflib FILES_MATCHING PATTERN "*.h")
- 
-@@ -914,10 +812,6 @@ endif ()
- #
- # tests  -- to be extended
- #
--add_test(NAME cbftest_makecbf
--  COMMAND ${CMAKE_COMMAND}
--    -DCMD1=$<TARGET_FILE:makecbf> -DARG11=${CBF_DATADIRI}/example.mar2300 -DARG12=makecbf.cbf
--    -P ${CMAKE_CURRENT_SOURCE_DIR}/runcommands.cmake)
- add_test(cbftest_testalloc ${VALGRIND_COMMAND} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/testalloc)
- add_test(cbftest_testhdf5 ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/testhdf5)
- add_test(cbftest_testtree ${VALGRIND_COMMAND} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/testtree)
diff --git a/sci-libs/cbflib/metadata.xml b/sci-libs/cbflib/metadata.xml
deleted file mode 100644
index e0080f59068f..000000000000
--- a/sci-libs/cbflib/metadata.xml
+++ /dev/null
@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-CBFLIB is a library of ANSI-C functions providing a simple mechanism
-for accessing Crystallographic Binary Files (CBF files) and Image-supporting
-CIF (imgCIF) files. The CBFLIB API is loosely based on the CIFPARSE API for
-mmCIF files. Starting with this release, CBFLIB performs validation checks
-on reading of a CBF. If a dictionary is provided, values will be validated
-against dictionary ranges and enumerations. Tags missing under parent-child
-relationships or category key requirements will be reported. CBFlib provides
-functions to create, read, modify and write CBF binary data files and imgCIF
-ASCII data files.
-</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">cbflib</remote-id>
-	</upstream>
-</pkgmetadata>