gentoo auto-resync : 18:05:2024 - 00:01:41

7 files changed, 50 insertions, 51 deletions

diff --git a/metadata/md5-cache/sci-chemistry/Manifest.gz b/metadata/md5-cache/sci-chemistry/Manifest.gz
index bb89ea3b37c3..57aac3338e2b 100644
--- a/metadata/md5-cache/sci-chemistry/Manifest.gz
+++ b/metadata/md5-cache/sci-chemistry/Manifest.gz
diff --git a/metadata/md5-cache/sci-chemistry/gromacs-2024.2 b/metadata/md5-cache/sci-chemistry/gromacs-2024.2
new file mode 100644
index 000000000000..f8bcdea0ae61
--- /dev/null
+++ b/metadata/md5-cache/sci-chemistry/gromacs-2024.2
@@ -0,0 +1,16 @@
+BDEPEND=blas? ( virtual/blas ) cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] ) opencl? ( virtual/opencl ) fftw? ( sci-libs/fftw:3.0= ) hwloc? ( sys-apps/hwloc:= ) lapack? ( virtual/lapack ) mkl? ( sci-libs/mkl ) mpi? ( virtual/mpi[cxx] ) sci-libs/lmfit:= >=dev-cpp/muParser-2.3:= python_single_target_python3_10? ( dev-lang/python:3.10 ) python_single_target_python3_11? ( dev-lang/python:3.11 ) python_single_target_python3_12? ( dev-lang/python:3.12 ) virtual/pkgconfig clang? ( >=sys-devel/clang-6:* ) build-manual? ( app-text/doxygen python_single_target_python3_10? ( dev-python/sphinx[python_targets_python3_10(-)] dev-python/sphinx-copybutton[python_targets_python3_10(-)] dev-python/sphinx-inline-tabs[python_targets_python3_10(-)] dev-python/sphinx-argparse[python_targets_python3_10(-)] dev-python/sphinxcontrib-autoprogram[python_targets_python3_10(-)] ) python_single_target_python3_11? ( dev-python/sphinx[python_targets_python3_11(-)] dev-python/sphinx-copybutton[python_targets_python3_11(-)] dev-python/sphinx-inline-tabs[python_targets_python3_11(-)] dev-python/sphinx-argparse[python_targets_python3_11(-)] dev-python/sphinxcontrib-autoprogram[python_targets_python3_11(-)] ) python_single_target_python3_12? ( dev-python/sphinx[python_targets_python3_12(-)] dev-python/sphinx-copybutton[python_targets_python3_12(-)] dev-python/sphinx-inline-tabs[python_targets_python3_12(-)] dev-python/sphinx-argparse[python_targets_python3_12(-)] dev-python/sphinxcontrib-autoprogram[python_targets_python3_12(-)] ) media-gfx/mscgen media-gfx/graphviz dev-texlive/texlive-latex dev-texlive/texlive-latexextra media-gfx/imagemagick ) app-alternatives/ninja >=dev-build/cmake-3.20.5
+DEFINED_PHASES=compile configure install postinst prepare pretend setup test unpack
+DESCRIPTION=The ultimate molecular dynamics simulation package
+EAPI=8
+HOMEPAGE=https://www.gromacs.org/
+INHERIT=bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils
+IUSE=blas clang clang-cuda cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon python_single_target_python3_10 python_single_target_python3_11 python_single_target_python3_12
+KEYWORDS=~amd64 -arm ~arm64 ~x86 ~amd64-linux ~x86-linux ~x64-macos
+LICENSE=LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )
+RDEPEND=blas? ( virtual/blas ) cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] ) opencl? ( virtual/opencl ) fftw? ( sci-libs/fftw:3.0= ) hwloc? ( sys-apps/hwloc:= ) lapack? ( virtual/lapack ) mkl? ( sci-libs/mkl ) mpi? ( virtual/mpi[cxx] ) sci-libs/lmfit:= >=dev-cpp/muParser-2.3:= python_single_target_python3_10? ( dev-lang/python:3.10 ) python_single_target_python3_11? ( dev-lang/python:3.11 ) python_single_target_python3_12? ( dev-lang/python:3.12 )
+REQUIRED_USE=|| ( single-precision double-precision ) doc? ( !build-manual ) cuda? ( single-precision ) opencl? ( single-precision ) cuda? ( !opencl ) clang-cuda? ( clang cuda ) mkl? ( !blas !fftw !lapack ) ^^ ( python_single_target_python3_10 python_single_target_python3_11 python_single_target_python3_12 )
+RESTRICT=!test? ( test )
+SLOT=0/2024.2
+SRC_URI=https://ftp.gromacs.org/gromacs/gromacs-2024.2.tar.gz doc? ( https://ftp.gromacs.org/manual/manual-2024.2.pdf ) test? ( https://ftp.gromacs.org/regressiontests/regressiontests-2024.2.tar.gz )
+_eclasses_=bash-completion-r1	f5e7a020fd9c741740756aac61bf75ff	cmake	c7c9a62d6232cac66d4ea32d575c3e7c	cuda	283d0f298f6c196c755a0f8d50daca85	distutils-r1	a9e13d91cb9541a054827cb1d957a660	flag-o-matic	d309b9713dfc18e754cba88d3ba69653	multibuild	d67e78a235f541871c7dfe4cf7931489	multilib	c19072c3cd7ac5cb21de013f7e9832e0	multiprocessing	30ead54fa2e2b5f9cd4e612ffc34d0fe	ninja-utils	2df4e452cea39a9ec8fb543ce059f8d6	out-of-source-utils	1a9007554652a6e627edbccb3c25a439	python-single-r1	75118e916668a74c660a13b0ecb22562	python-utils-r1	e527bb25fc6ab8bb127b889b8f62500a	readme.gentoo-r1	204091a2cde6179cd9d3db26d09412d3	toolchain-funcs	e56c7649b804f051623c8bc1a1c44084	xdg-utils	baea6080dd821f5562d715887954c9d3
+_md5_=2913fa98274b71a930f88d0aaee5c3fd
diff --git a/metadata/md5-cache/sci-chemistry/modeller-10.5 b/metadata/md5-cache/sci-chemistry/modeller-10.5
new file mode 100644
index 000000000000..6f9f217b5300
--- /dev/null
+++ b/metadata/md5-cache/sci-chemistry/modeller-10.5
@@ -0,0 +1,17 @@
+BDEPEND=python_targets_python3_10? ( dev-lang/python:3.10 ) python_targets_python3_11? ( dev-lang/python:3.11 ) python_targets_python3_12? ( dev-lang/python:3.12 ) >=dev-python/gpep517-15[python_targets_python3_10(-)?,python_targets_python3_11(-)?,python_targets_python3_12(-)?] >=dev-python/setuptools-69.0.3[python_targets_python3_10(-)?,python_targets_python3_11(-)?,python_targets_python3_12(-)?]
+DEFINED_PHASES=compile config configure install postinst postrm prepare setup test
+DEPEND=>=dev-lang/swig-1.3 python_targets_python3_10? ( dev-lang/python:3.10 ) python_targets_python3_11? ( dev-lang/python:3.11 ) python_targets_python3_12? ( dev-lang/python:3.12 )
+DESCRIPTION=Homology or comparative modeling of protein three-dimensional structures
+EAPI=7
+HOMEPAGE=https://salilab.org/modeller/
+INHERIT=distutils-r1
+IUSE=doc examples python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 debug
+KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux
+LICENSE=modeller
+RDEPEND=python_targets_python3_10? ( dev-lang/python:3.10 ) python_targets_python3_11? ( dev-lang/python:3.11 ) python_targets_python3_12? ( dev-lang/python:3.12 )
+REQUIRED_USE=|| ( python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 )
+RESTRICT=mirror
+SLOT=0
+SRC_URI=https://salilab.org/modeller/10.5/modeller-10.5.tar.gz
+_eclasses_=distutils-r1	a9e13d91cb9541a054827cb1d957a660	eapi8-dosym	5ac4857ad078256d939c44f7c64197a9	flag-o-matic	d309b9713dfc18e754cba88d3ba69653	multibuild	d67e78a235f541871c7dfe4cf7931489	multilib	c19072c3cd7ac5cb21de013f7e9832e0	multiprocessing	30ead54fa2e2b5f9cd4e612ffc34d0fe	ninja-utils	2df4e452cea39a9ec8fb543ce059f8d6	out-of-source-utils	1a9007554652a6e627edbccb3c25a439	python-r1	8a28fa6d3e3bc96ff8a7eff2badbe71f	python-utils-r1	e527bb25fc6ab8bb127b889b8f62500a	toolchain-funcs	e56c7649b804f051623c8bc1a1c44084
+_md5_=c389b9e9e74f5718f27ab8b4c1311583
diff --git a/metadata/md5-cache/sci-chemistry/modeller-9.25 b/metadata/md5-cache/sci-chemistry/modeller-9.25
deleted file mode 100644
index 2d04383eb7d0..000000000000
--- a/metadata/md5-cache/sci-chemistry/modeller-9.25
+++ /dev/null
@@ -1,17 +0,0 @@
-BDEPEND=python_targets_python3_10? ( dev-lang/python:3.10 )
-DEFINED_PHASES=compile config configure install postinst postrm prepare setup test
-DEPEND=>=dev-lang/swig-1.3
-DESCRIPTION=Homology or comparative modeling of protein three-dimensional structures
-EAPI=7
-HOMEPAGE=https://salilab.org/modeller/
-INHERIT=distutils-r1
-IUSE=doc examples python_targets_python3_10
-KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux
-LICENSE=modeller
-RDEPEND=python_targets_python3_10? ( dev-lang/python:3.10 )
-REQUIRED_USE=|| ( python_targets_python3_10 )
-RESTRICT=mirror
-SLOT=0
-SRC_URI=https://salilab.org/modeller/9.25/modeller-9.25.tar.gz
-_eclasses_=distutils-r1	a9e13d91cb9541a054827cb1d957a660	eapi8-dosym	5ac4857ad078256d939c44f7c64197a9	flag-o-matic	d309b9713dfc18e754cba88d3ba69653	multibuild	d67e78a235f541871c7dfe4cf7931489	multilib	c19072c3cd7ac5cb21de013f7e9832e0	multiprocessing	30ead54fa2e2b5f9cd4e612ffc34d0fe	ninja-utils	2df4e452cea39a9ec8fb543ce059f8d6	out-of-source-utils	1a9007554652a6e627edbccb3c25a439	python-r1	8a28fa6d3e3bc96ff8a7eff2badbe71f	python-utils-r1	e527bb25fc6ab8bb127b889b8f62500a	toolchain-funcs	e56c7649b804f051623c8bc1a1c44084
-_md5_=1c68117b2425090a258fc04144469ec6
diff --git a/metadata/md5-cache/sci-chemistry/pymol-2.5.0-r3 b/metadata/md5-cache/sci-chemistry/pymol-2.5.0-r3
deleted file mode 100644
index 7537ef36be41..000000000000
--- a/metadata/md5-cache/sci-chemistry/pymol-2.5.0-r3
+++ /dev/null
@@ -1,17 +0,0 @@
-BDEPEND=python_targets_python3_10? ( dev-lang/python:3.10 ) python_targets_python3_11? ( dev-lang/python:3.11 )
-DEFINED_PHASES=compile configure install postinst postrm preinst prepare test
-DEPEND=dev-cpp/msgpack-cxx dev-libs/mmtf-cpp dev-python/pyopengl[python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/PyQt5[opengl,python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/numpy[python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/pmw[python_targets_python3_10(-)?,python_targets_python3_11(-)?] media-libs/freetype:2 media-libs/glew:0= media-libs/glm media-libs/libpng:0= media-video/mpeg-tools sys-libs/zlib netcdf? ( sci-libs/netcdf:0= ) python_targets_python3_10? ( dev-lang/python:3.10 ) python_targets_python3_11? ( dev-lang/python:3.11 )
-DESCRIPTION=A Python-extensible molecular graphics system
-EAPI=8
-HOMEPAGE=https://www.pymol.org/
-IDEPEND=dev-util/desktop-file-utils x11-misc/shared-mime-info
-INHERIT=desktop flag-o-matic xdg distutils-r1
-IUSE=+netcdf web python_targets_python3_10 python_targets_python3_11 debug
-KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos
-LICENSE=BitstreamVera BSD freedist HPND OFL-1.0 public-domain UoI-NCSA
-RDEPEND=dev-cpp/msgpack-cxx dev-libs/mmtf-cpp dev-python/pyopengl[python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/PyQt5[opengl,python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/numpy[python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/pmw[python_targets_python3_10(-)?,python_targets_python3_11(-)?] media-libs/freetype:2 media-libs/glew:0= media-libs/glm media-libs/libpng:0= media-video/mpeg-tools sys-libs/zlib netcdf? ( sci-libs/netcdf:0= ) sci-chemistry/chemical-mime-data python_targets_python3_10? ( dev-lang/python:3.10 ) python_targets_python3_11? ( dev-lang/python:3.11 )
-REQUIRED_USE=|| ( python_targets_python3_10 python_targets_python3_11 )
-SLOT=0
-SRC_URI=https://dev.gentoo.org/~pacho/pymol/pymol-1.8.4.0.png.xz https://github.com/schrodinger/pymol-open-source/archive/v2.5.0.tar.gz -> pymol-2.5.0.tar.gz
-_eclasses_=desktop	021728fdc1b03b36357dbc89489e0f0d	distutils-r1	a9e13d91cb9541a054827cb1d957a660	flag-o-matic	d309b9713dfc18e754cba88d3ba69653	multibuild	d67e78a235f541871c7dfe4cf7931489	multilib	c19072c3cd7ac5cb21de013f7e9832e0	multiprocessing	30ead54fa2e2b5f9cd4e612ffc34d0fe	ninja-utils	2df4e452cea39a9ec8fb543ce059f8d6	out-of-source-utils	1a9007554652a6e627edbccb3c25a439	python-r1	8a28fa6d3e3bc96ff8a7eff2badbe71f	python-utils-r1	e527bb25fc6ab8bb127b889b8f62500a	toolchain-funcs	e56c7649b804f051623c8bc1a1c44084	xdg	4a14c5c24f121e7da66e5aab4a168c6e	xdg-utils	baea6080dd821f5562d715887954c9d3
-_md5_=6607ce1e302070ec05c002c00947e19a
diff --git a/metadata/md5-cache/sci-chemistry/pymol-2.5.0-r5 b/metadata/md5-cache/sci-chemistry/pymol-2.5.0-r5
deleted file mode 100644
index 119e6555650b..000000000000
--- a/metadata/md5-cache/sci-chemistry/pymol-2.5.0-r5
+++ /dev/null
@@ -1,17 +0,0 @@
-BDEPEND=python_targets_python3_10? ( dev-lang/python:3.10 ) python_targets_python3_11? ( dev-lang/python:3.11 ) >=dev-python/gpep517-15[python_targets_python3_10(-)?,python_targets_python3_11(-)?] >=dev-python/setuptools-69.0.3[python_targets_python3_10(-)?,python_targets_python3_11(-)?]
-DEFINED_PHASES=compile configure install postinst postrm preinst prepare test
-DEPEND=dev-cpp/msgpack-cxx dev-libs/mmtf-cpp dev-python/pyopengl[python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/PyQt5[opengl,python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/numpy[python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/pmw[python_targets_python3_10(-)?,python_targets_python3_11(-)?] media-libs/freetype:2 media-libs/glew:0= media-libs/glm media-libs/libpng:0= media-video/mpeg-tools sys-libs/zlib netcdf? ( sci-libs/netcdf:0= ) python_targets_python3_10? ( dev-lang/python:3.10 ) python_targets_python3_11? ( dev-lang/python:3.11 )
-DESCRIPTION=A Python-extensible molecular graphics system
-EAPI=8
-HOMEPAGE=https://www.pymol.org/
-IDEPEND=dev-util/desktop-file-utils x11-misc/shared-mime-info
-INHERIT=desktop flag-o-matic xdg distutils-r1
-IUSE=+netcdf web python_targets_python3_10 python_targets_python3_11 debug
-KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos
-LICENSE=BitstreamVera BSD freedist HPND OFL-1.0 public-domain UoI-NCSA
-RDEPEND=dev-cpp/msgpack-cxx dev-libs/mmtf-cpp dev-python/pyopengl[python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/PyQt5[opengl,python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/numpy[python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/pmw[python_targets_python3_10(-)?,python_targets_python3_11(-)?] media-libs/freetype:2 media-libs/glew:0= media-libs/glm media-libs/libpng:0= media-video/mpeg-tools sys-libs/zlib netcdf? ( sci-libs/netcdf:0= ) sci-chemistry/chemical-mime-data python_targets_python3_10? ( dev-lang/python:3.10 ) python_targets_python3_11? ( dev-lang/python:3.11 )
-REQUIRED_USE=|| ( python_targets_python3_10 python_targets_python3_11 )
-SLOT=0
-SRC_URI=https://dev.gentoo.org/~pacho/pymol/pymol-1.8.4.0.png.xz https://github.com/schrodinger/pymol-open-source/archive/v2.5.0.tar.gz -> pymol-2.5.0.tar.gz
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-_md5_=66904734ae77d89c05d8c24d7d6f4f50
diff --git a/metadata/md5-cache/sci-chemistry/pymol-3.0.0 b/metadata/md5-cache/sci-chemistry/pymol-3.0.0
new file mode 100644
index 000000000000..740dcb71d4fa
--- /dev/null
+++ b/metadata/md5-cache/sci-chemistry/pymol-3.0.0
@@ -0,0 +1,17 @@
+BDEPEND=python_targets_python3_10? ( dev-lang/python:3.10 ) python_targets_python3_11? ( dev-lang/python:3.11 ) python_targets_python3_12? ( dev-lang/python:3.12 ) >=dev-python/gpep517-15[python_targets_python3_10(-)?,python_targets_python3_11(-)?,python_targets_python3_12(-)?] >=dev-python/setuptools-69.0.3[python_targets_python3_10(-)?,python_targets_python3_11(-)?,python_targets_python3_12(-)?]
+DEFINED_PHASES=compile configure install postinst postrm preinst prepare test
+DEPEND=dev-cpp/msgpack-cxx dev-libs/mmtf-cpp dev-python/pyopengl[python_targets_python3_10(-)?,python_targets_python3_11(-)?,python_targets_python3_12(-)?] dev-python/PyQt5[opengl,python_targets_python3_10(-)?,python_targets_python3_11(-)?,python_targets_python3_12(-)?] dev-python/numpy[python_targets_python3_10(-)?,python_targets_python3_11(-)?,python_targets_python3_12(-)?] dev-python/pmw[python_targets_python3_10(-)?,python_targets_python3_11(-)?,python_targets_python3_12(-)?] media-libs/freetype:2 media-libs/glew:0= media-libs/glm media-libs/libpng:0= media-video/mpeg-tools sys-libs/zlib netcdf? ( sci-libs/netcdf:0= ) python_targets_python3_10? ( dev-lang/python:3.10 ) python_targets_python3_11? ( dev-lang/python:3.11 ) python_targets_python3_12? ( dev-lang/python:3.12 )
+DESCRIPTION=A Python-extensible molecular graphics system
+EAPI=8
+HOMEPAGE=https://www.pymol.org/
+IDEPEND=dev-util/desktop-file-utils x11-misc/shared-mime-info
+INHERIT=desktop flag-o-matic xdg distutils-r1
+IUSE=+netcdf web python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 debug
+KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos
+LICENSE=BitstreamVera BSD freedist HPND OFL-1.0 public-domain UoI-NCSA
+RDEPEND=dev-cpp/msgpack-cxx dev-libs/mmtf-cpp dev-python/pyopengl[python_targets_python3_10(-)?,python_targets_python3_11(-)?,python_targets_python3_12(-)?] dev-python/PyQt5[opengl,python_targets_python3_10(-)?,python_targets_python3_11(-)?,python_targets_python3_12(-)?] dev-python/numpy[python_targets_python3_10(-)?,python_targets_python3_11(-)?,python_targets_python3_12(-)?] dev-python/pmw[python_targets_python3_10(-)?,python_targets_python3_11(-)?,python_targets_python3_12(-)?] media-libs/freetype:2 media-libs/glew:0= media-libs/glm media-libs/libpng:0= media-video/mpeg-tools sys-libs/zlib netcdf? ( sci-libs/netcdf:0= ) sci-chemistry/chemical-mime-data python_targets_python3_10? ( dev-lang/python:3.10 ) python_targets_python3_11? ( dev-lang/python:3.11 ) python_targets_python3_12? ( dev-lang/python:3.12 )
+REQUIRED_USE=|| ( python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 )
+SLOT=0
+SRC_URI=https://dev.gentoo.org/~pacho/pymol/pymol-1.8.4.0.png.xz https://github.com/schrodinger/pymol-open-source/archive/v3.0.0.tar.gz -> pymol-3.0.0.tar.gz
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+_md5_=bfedc24544735cdbc2b161b08589c5b7