From 35312ec7967b852b7481a0250eaa77bc509d0f89 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 07:26:40 +0100 Subject: [PATCH 01/31] sci-biology/fsl: sys-libs/zlib -> virtual/zlib Signed-off-by: Alexander Puck Neuwirth --- sci-biology/fsl/fsl-6.0.4.ebuild | 2 +- sci-biology/fsl/fsl-6.0.5.ebuild | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/sci-biology/fsl/fsl-6.0.4.ebuild b/sci-biology/fsl/fsl-6.0.4.ebuild index d839a7b5e4e..a7a4b798fef 100644 --- a/sci-biology/fsl/fsl-6.0.4.ebuild +++ b/sci-biology/fsl/fsl-6.0.4.ebuild @@ -23,7 +23,7 @@ DEPEND=" media-libs/libpng:0= sci-libs/ciftilib sci-libs/nlopt - sys-libs/zlib + virtual/zlib:= dev-lang/tcl:0= dev-lang/tk:0= >=virtual/lapack-3.8 diff --git a/sci-biology/fsl/fsl-6.0.5.ebuild b/sci-biology/fsl/fsl-6.0.5.ebuild index 6da2ab5b86e..828309f89d1 100644 --- a/sci-biology/fsl/fsl-6.0.5.ebuild +++ b/sci-biology/fsl/fsl-6.0.5.ebuild @@ -33,7 +33,7 @@ DEPEND=" sci-libs/fftw sci-libs/nlopt sci-libs/vtk - sys-libs/zlib + virtual/zlib:= dev-lang/tcl:0= dev-lang/tk:0= >=virtual/lapack-3.8 From e6bac56a7622475f1f053fadfb666dbdc29a41b3 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 07:27:38 +0100 Subject: [PATCH 02/31] sci-biology/flexbar: sys-libs/zlib -> virtual/zlib Signed-off-by: Alexander Puck Neuwirth --- sci-biology/flexbar/flexbar-3.5.0.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sci-biology/flexbar/flexbar-3.5.0.ebuild b/sci-biology/flexbar/flexbar-3.5.0.ebuild index 22d334ddc9f..7010cd01844 100644 --- a/sci-biology/flexbar/flexbar-3.5.0.ebuild +++ b/sci-biology/flexbar/flexbar-3.5.0.ebuild @@ -16,7 +16,7 @@ KEYWORDS="~amd64 ~x86" CDEPEND=" dev-cpp/tbb >=sci-biology/seqan-2.1.1:0 - sys-libs/zlib + virtual/zlib:= app-arch/bzip2" DEPEND="${CDEPEND}" RDEPEND="${CDEPEND}" From 3fea2cedb956938755c213d17e2c60814693c96e Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 07:28:37 +0100 Subject: [PATCH 03/31] sci-biology/megahit: sys-libs/zlib -> virtual/zlib Signed-off-by: Alexander Puck Neuwirth --- sci-biology/megahit/megahit-1.2.9.ebuild | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/sci-biology/megahit/megahit-1.2.9.ebuild b/sci-biology/megahit/megahit-1.2.9.ebuild index 9d607551303..054de49d36a 100644 --- a/sci-biology/megahit/megahit-1.2.9.ebuild +++ b/sci-biology/megahit/megahit-1.2.9.ebuild @@ -15,9 +15,8 @@ SLOT="0" KEYWORDS="~amd64" IUSE="+openmp cuda" -DEPEND="" -RDEPEND="${DEPEND} - sys-libs/zlib +RDEPEND=" + virtual/zlib:= cuda? ( >=dev-util/nvidia-cuda-toolkit-5 dev-libs/cudnn )" # contains bundled copy og idba from https://github.com/loneknightpy/idba From 2f82c13bf19fcb3aaf301883fe782690f8a93652 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 07:29:45 +0100 Subject: [PATCH 04/31] sci-libs/ciftilib: sys-libs/zlib -> virtual/zlib Signed-off-by: Alexander Puck Neuwirth --- sci-libs/ciftilib/ciftilib-1.6.0.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sci-libs/ciftilib/ciftilib-1.6.0.ebuild b/sci-libs/ciftilib/ciftilib-1.6.0.ebuild index 05ebc04250a..3d515aacae3 100644 --- a/sci-libs/ciftilib/ciftilib-1.6.0.ebuild +++ b/sci-libs/ciftilib/ciftilib-1.6.0.ebuild @@ -18,7 +18,7 @@ DEPEND=" dev-libs/boost qt5? ( dev-qt/qtcore:5 ) !qt5? ( dev-cpp/libxmlpp:2.6 ) - sys-libs/zlib + virtual/zlib:= " RDEPEND="${DEPEND}" From 8d3cc9e642d61f07da06a7499c37daa67ab18f5e Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Mon, 17 Nov 2025 12:57:42 +0100 Subject: [PATCH 05/31] profiles: mask failing sci-chemistry/dl_poly Signed-off-by: Alexander Puck Neuwirth --- profiles/package.mask | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index d9e0f4c865b..3ac0b4add80 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -30,6 +30,11 @@ #--- END OF EXAMPLES --- + +# Alexander Puck Neuwirth (2025-11-17) +# Installation fails. EAPI outdated. +sci-chemistry/dl_poly + # Alexander Puck Neuwirth (2025-01-10) # Download server is gone since about 2014. sci-biology/vague-bin From 268fbed496d146b3e335fb25046d3eea9882a780 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 07:32:58 +0100 Subject: [PATCH 06/31] dev-python/astropy: sys-libs/zlib -> virtual/zlib Signed-off-by: Alexander Puck Neuwirth --- dev-python/astropy/astropy-5.2.1.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dev-python/astropy/astropy-5.2.1.ebuild b/dev-python/astropy/astropy-5.2.1.ebuild index b52d1e6f50f..f310627d3f3 100644 --- a/dev-python/astropy/astropy-5.2.1.ebuild +++ b/dev-python/astropy/astropy-5.2.1.ebuild @@ -31,7 +31,7 @@ RDEPEND=" >=dev-python/packaging-19.0[${PYTHON_USEDEP}] sci-astronomy/wcslib:0= >=sci-libs/cfitsio-3.350:0= - sys-libs/zlib:0= + virtual/zlib:0= " DEPEND="${RDEPEND}" BDEPEND=" From 3f7ac544fb8b73ca9424ee0265ab505c07dce763 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 07:33:12 +0100 Subject: [PATCH 07/31] dev-python/llvmlite: sys-libs/zlib -> virtual/zlib Signed-off-by: Alexander Puck Neuwirth --- dev-python/llvmlite/llvmlite-0.45.1.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dev-python/llvmlite/llvmlite-0.45.1.ebuild b/dev-python/llvmlite/llvmlite-0.45.1.ebuild index ffbb5cb4169..2431c59d54e 100644 --- a/dev-python/llvmlite/llvmlite-0.45.1.ebuild +++ b/dev-python/llvmlite/llvmlite-0.45.1.ebuild @@ -19,7 +19,7 @@ SLOT="0" KEYWORDS="~amd64" RDEPEND=" - sys-libs/zlib:0= + virtual/zlib:0= $(llvm_gen_dep 'llvm-core/llvm:${LLVM_SLOT}=') " DEPEND="${RDEPEND}" From 71303806f711547ef3be0bbb1d1f7309555b04c8 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 07:33:30 +0100 Subject: [PATCH 08/31] dev-python/pyBigWig: sys-libs/zlib -> virtual/zlib Signed-off-by: Alexander Puck Neuwirth --- dev-python/pyBigWig/pyBigWig-0.3.24.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dev-python/pyBigWig/pyBigWig-0.3.24.ebuild b/dev-python/pyBigWig/pyBigWig-0.3.24.ebuild index 2b5bd449d11..ae3b7ce9bee 100644 --- a/dev-python/pyBigWig/pyBigWig-0.3.24.ebuild +++ b/dev-python/pyBigWig/pyBigWig-0.3.24.ebuild @@ -18,7 +18,7 @@ SLOT="0" KEYWORDS="~amd64 ~x86" REPEND=" - sys-libs/zlib:0= + virtual/zlib:0= sci-biology/libBigWig " DEPEND="${RDEPEND}" From 1891a4d48cfe89e8e845d75707947a1a703ec47f Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 07:45:29 +0100 Subject: [PATCH 09/31] sci-biology/SPAdes: sys-libs/zlib -> virtual/zlib Signed-off-by: Alexander Puck Neuwirth --- sci-biology/SPAdes/SPAdes-3.15.5.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sci-biology/SPAdes/SPAdes-3.15.5.ebuild b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild index 026dd0476f4..1f6495007cd 100644 --- a/sci-biology/SPAdes/SPAdes-3.15.5.ebuild +++ b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild @@ -21,7 +21,7 @@ KEYWORDS="~amd64" REQUIRED_USE="${PYTHON_REQUIRED_USE}" DEPEND=" - sys-libs/zlib + virtual/zlib:= app-arch/bzip2 dev-python/regex ${PYTHON_DEPS} From 4c1d76bed49d3a8501bc60a614dac6cfff0f810e Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 07:45:47 +0100 Subject: [PATCH 10/31] sci-biology/SolexaQA: sys-libs/zlib -> virtual/zlib Signed-off-by: Alexander Puck Neuwirth --- sci-biology/SolexaQA/SolexaQA-3.1.7.1.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sci-biology/SolexaQA/SolexaQA-3.1.7.1.ebuild b/sci-biology/SolexaQA/SolexaQA-3.1.7.1.ebuild index 81258a0ef29..a674d230583 100644 --- a/sci-biology/SolexaQA/SolexaQA-3.1.7.1.ebuild +++ b/sci-biology/SolexaQA/SolexaQA-3.1.7.1.ebuild @@ -12,7 +12,7 @@ SLOT="0" KEYWORDS="~amd64" DEPEND=" - sys-libs/zlib + virtual/zlib:= dev-libs/boost " BDEPEND="app-arch/unzip" From 68754c205a75ff95969889564367f241531219d5 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 07:46:04 +0100 Subject: [PATCH 11/31] sci-biology/lighter: sys-libs/zlib -> virtual/zlib Signed-off-by: Alexander Puck Neuwirth --- sci-biology/lighter/lighter-1.1.2.ebuild | 2 +- sci-biology/lighter/lighter-9999.ebuild | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/sci-biology/lighter/lighter-1.1.2.ebuild b/sci-biology/lighter/lighter-1.1.2.ebuild index 2d08c45c427..aee8d038515 100644 --- a/sci-biology/lighter/lighter-1.1.2.ebuild +++ b/sci-biology/lighter/lighter-1.1.2.ebuild @@ -17,7 +17,7 @@ fi LICENSE="GPL-2+" SLOT="0" -DEPEND="sys-libs/zlib" +DEPEND="virtual/zlib:=" RDEPEND="${DEPEND}" src_install(){ diff --git a/sci-biology/lighter/lighter-9999.ebuild b/sci-biology/lighter/lighter-9999.ebuild index 2d08c45c427..aee8d038515 100644 --- a/sci-biology/lighter/lighter-9999.ebuild +++ b/sci-biology/lighter/lighter-9999.ebuild @@ -17,7 +17,7 @@ fi LICENSE="GPL-2+" SLOT="0" -DEPEND="sys-libs/zlib" +DEPEND="virtual/zlib:=" RDEPEND="${DEPEND}" src_install(){ From 088a6f45fe775885f10ef131da4f1535931ecfce Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 07:46:20 +0100 Subject: [PATCH 12/31] sci-biology/minimap2: sys-libs/zlib -> virtual/zlib Signed-off-by: Alexander Puck Neuwirth --- sci-biology/minimap2/minimap2-2.24-r1.ebuild | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/sci-biology/minimap2/minimap2-2.24-r1.ebuild b/sci-biology/minimap2/minimap2-2.24-r1.ebuild index 96b427ef09d..4f4cf123f48 100644 --- a/sci-biology/minimap2/minimap2-2.24-r1.ebuild +++ b/sci-biology/minimap2/minimap2-2.24-r1.ebuild @@ -19,7 +19,8 @@ KEYWORDS="~amd64 ~x86" IUSE="python cpu_flags_x86_sse4_1" REQUIRED_USE="${PYTHON_REQUIRED_USE}" -DEPEND="sys-libs/zlib +DEPEND=" + virtual/zlib:= python? ( ${PYTHON_DEPS} )" From 8e4cfca75782f65272912679ec30e7e00bfc0155 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 07:46:35 +0100 Subject: [PATCH 13/31] sci-biology/mmseqs2: sys-libs/zlib -> virtual/zlib Signed-off-by: Alexander Puck Neuwirth --- sci-biology/mmseqs2/mmseqs2-13.0-r1.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sci-biology/mmseqs2/mmseqs2-13.0-r1.ebuild b/sci-biology/mmseqs2/mmseqs2-13.0-r1.ebuild index 6cbd139d8e8..3755626f824 100644 --- a/sci-biology/mmseqs2/mmseqs2-13.0-r1.ebuild +++ b/sci-biology/mmseqs2/mmseqs2-13.0-r1.ebuild @@ -22,7 +22,7 @@ IUSE="cpu_flags_x86_sse4_1 cpu_flags_x86_sse2 cpu_flags_x86_avx2" RDEPEND=" app-arch/zstd[static-libs] - sys-libs/zlib + virtual/zlib:= app-arch/bzip2 " DEPEND="${RDEPEND}" From 6344c3a72adb27920facd1698cd5f970f15da93e Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 07:46:49 +0100 Subject: [PATCH 14/31] sci-biology/sabre: sys-libs/zlib -> virtual/zlib Signed-off-by: Alexander Puck Neuwirth --- sci-biology/sabre/sabre-9999.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sci-biology/sabre/sabre-9999.ebuild b/sci-biology/sabre/sabre-9999.ebuild index 222fcac9a8b..8e7f369b07a 100644 --- a/sci-biology/sabre/sabre-9999.ebuild +++ b/sci-biology/sabre/sabre-9999.ebuild @@ -18,7 +18,7 @@ fi LICENSE="MIT" # almost verbatim SLOT="0" -DEPEND="sys-libs/zlib" +DEPEND="virtual/zlib:=" RDEPEND="${DEPEND}" src_prepare(){ From cef338f684d80d3df73dbb6bc3f37a29f8900661 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 07:47:22 +0100 Subject: [PATCH 15/31] sci-biology/scythe: sys-libs/zlib -> virtual/zlib Signed-off-by: Alexander Puck Neuwirth --- sci-biology/scythe/scythe-9999.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sci-biology/scythe/scythe-9999.ebuild b/sci-biology/scythe/scythe-9999.ebuild index d2f051ef1ed..e38cb84feb1 100644 --- a/sci-biology/scythe/scythe-9999.ebuild +++ b/sci-biology/scythe/scythe-9999.ebuild @@ -15,7 +15,7 @@ KEYWORDS="" RESTRICT="test" -DEPEND="sys-libs/zlib" +DEPEND="virtual/zlib:=" RDEPEND="${DEPEND}" src_install(){ From 661a7aef4069ec4279af889a6f3fd3ffa3233c61 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 07:47:44 +0100 Subject: [PATCH 16/31] sci-biology/sga: sys-libs/zlib -> virtual/zlib Signed-off-by: Alexander Puck Neuwirth --- sci-biology/sga/sga-9999.ebuild | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/sci-biology/sga/sga-9999.ebuild b/sci-biology/sga/sga-9999.ebuild index 7519b3e2ad4..ac1e208ac9b 100644 --- a/sci-biology/sga/sga-9999.ebuild +++ b/sci-biology/sga/sga-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -17,7 +17,7 @@ IUSE="jemalloc python" DEPEND=" dev-cpp/sparsehash sci-biology/bamtools - sys-libs/zlib + virtual/zlib:= jemalloc? ( dev-libs/jemalloc ) " RDEPEND="${DEPEND} From a74043179060e846c106d4e0e444619f51016fa5 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 07:48:06 +0100 Subject: [PATCH 17/31] sci-biology/sickle: sys-libs/zlib -> virtual/zlib Signed-off-by: Alexander Puck Neuwirth --- sci-biology/sickle/sickle-1.33.ebuild | 4 ++-- sci-biology/sickle/sickle-9999.ebuild | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/sci-biology/sickle/sickle-1.33.ebuild b/sci-biology/sickle/sickle-1.33.ebuild index e2ebdb3a3dc..ddd4debcbd3 100644 --- a/sci-biology/sickle/sickle-1.33.ebuild +++ b/sci-biology/sickle/sickle-1.33.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -16,7 +16,7 @@ fi LICENSE="MIT" SLOT="0" -DEPEND="sys-libs/zlib" +DEPEND="virtual/zlib:=" RDEPEND="${DEPEND}" src_install(){ diff --git a/sci-biology/sickle/sickle-9999.ebuild b/sci-biology/sickle/sickle-9999.ebuild index e2ebdb3a3dc..ddd4debcbd3 100644 --- a/sci-biology/sickle/sickle-9999.ebuild +++ b/sci-biology/sickle/sickle-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -16,7 +16,7 @@ fi LICENSE="MIT" SLOT="0" -DEPEND="sys-libs/zlib" +DEPEND="virtual/zlib:=" RDEPEND="${DEPEND}" src_install(){ From 1c58356228e455c1bbbdedf6f701c745d3570678 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 07:48:25 +0100 Subject: [PATCH 18/31] sci-biology/sra-tools: sys-libs/zlib -> virtual/zlib Signed-off-by: Alexander Puck Neuwirth --- sci-biology/sra-tools/sra-tools-2.11.3.ebuild | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/sci-biology/sra-tools/sra-tools-2.11.3.ebuild b/sci-biology/sra-tools/sra-tools-2.11.3.ebuild index 57c5b881ebc..e6e6096f9fd 100644 --- a/sci-biology/sra-tools/sra-tools-2.11.3.ebuild +++ b/sci-biology/sra-tools/sra-tools-2.11.3.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -13,7 +13,7 @@ SLOT="0" KEYWORDS="" DEPEND=" - sys-libs/zlib + virtual/zlib:= app-arch/bzip2 dev-libs/libxml2:2= sci-libs/hdf5 From 469518d47c09cc2230c5162b9a2162c79efd32af Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 07:48:46 +0100 Subject: [PATCH 19/31] sci-biology/subread: sys-libs/zlib -> virtual/zlib Signed-off-by: Alexander Puck Neuwirth --- sci-biology/subread/subread-2.0.3.ebuild | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/sci-biology/subread/subread-2.0.3.ebuild b/sci-biology/subread/subread-2.0.3.ebuild index 624509aa544..c8bd2ad44cd 100644 --- a/sci-biology/subread/subread-2.0.3.ebuild +++ b/sci-biology/subread/subread-2.0.3.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -12,7 +12,7 @@ LICENSE="GPL-3" SLOT="0" KEYWORDS="~amd64" -DEPEND="sys-libs/zlib" +DEPEND="virtual/zlib:=" RDEPEND="${DEPEND}" src_prepare(){ From 24ed8fb722dcb19df539b7a2c1ab77a0c18a5105 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 07:49:15 +0100 Subject: [PATCH 20/31] sci-biology/vcflib: sys-libs/zlib -> virtual/zlib Signed-off-by: Alexander Puck Neuwirth --- sci-biology/vcflib/vcflib-1.0.3.ebuild | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/sci-biology/vcflib/vcflib-1.0.3.ebuild b/sci-biology/vcflib/vcflib-1.0.3.ebuild index d4cf1e02f61..932439199d9 100644 --- a/sci-biology/vcflib/vcflib-1.0.3.ebuild +++ b/sci-biology/vcflib/vcflib-1.0.3.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -16,7 +16,7 @@ KEYWORDS="" IUSE="openmp" DEPEND=" - sys-libs/zlib + virtual/zlib:= sci-libs/htslib sci-biology/tabixpp " From fb9ce46cd22d6f0b93124a9f60f288e436e132ca Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 07:49:38 +0100 Subject: [PATCH 21/31] sci-chemistry/chimera: sys-libs/zlib -> virtual/zlib Signed-off-by: Alexander Puck Neuwirth --- sci-chemistry/chimera/chimera-1.18.ebuild | 4 ++-- sci-chemistry/chimera/chimera-1.19.ebuild | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/sci-chemistry/chimera/chimera-1.18.ebuild b/sci-chemistry/chimera/chimera-1.18.ebuild index b4b3b164e0d..b7d105ea985 100644 --- a/sci-chemistry/chimera/chimera-1.18.ebuild +++ b/sci-chemistry/chimera/chimera-1.18.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -24,7 +24,7 @@ RDEPEND=" dev-libs/libotf dev-libs/openssl:0 dev-libs/libpcre - sys-libs/zlib + virtual/zlib:= media-libs/fontconfig media-libs/freetype media-libs/ftgl diff --git a/sci-chemistry/chimera/chimera-1.19.ebuild b/sci-chemistry/chimera/chimera-1.19.ebuild index b4b3b164e0d..b7d105ea985 100644 --- a/sci-chemistry/chimera/chimera-1.19.ebuild +++ b/sci-chemistry/chimera/chimera-1.19.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -24,7 +24,7 @@ RDEPEND=" dev-libs/libotf dev-libs/openssl:0 dev-libs/libpcre - sys-libs/zlib + virtual/zlib:= media-libs/fontconfig media-libs/freetype media-libs/ftgl From f5024120d9199040e4925672e57e361b2aa8cf5e Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 07:50:00 +0100 Subject: [PATCH 22/31] sci-libs/gdcm: sys-libs/zlib -> virtual/zlib Signed-off-by: Alexander Puck Neuwirth --- sci-libs/gdcm/gdcm-3.0.14-r1.ebuild | 4 ++-- sci-libs/gdcm/gdcm-3.0.24.ebuild | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/sci-libs/gdcm/gdcm-3.0.14-r1.ebuild b/sci-libs/gdcm/gdcm-3.0.14-r1.ebuild index 8b2fc2cba57..68c3b58562b 100644 --- a/sci-libs/gdcm/gdcm-3.0.14-r1.ebuild +++ b/sci-libs/gdcm/gdcm-3.0.14-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 2022 Gentoo Authors +# Copyright 2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -29,7 +29,7 @@ DEPEND=" >=media-libs/charls-2.0.0:0= >=media-libs/openjpeg-2.0.0:2= sys-apps/util-linux:0= - sys-libs/zlib:0= + virtual/zlib:0= python? ( ${PYTHON_DEPS} ) vtk? ( sci-libs/vtk[rendering] diff --git a/sci-libs/gdcm/gdcm-3.0.24.ebuild b/sci-libs/gdcm/gdcm-3.0.24.ebuild index 2813a8e16bc..a4678658ed8 100644 --- a/sci-libs/gdcm/gdcm-3.0.24.ebuild +++ b/sci-libs/gdcm/gdcm-3.0.24.ebuild @@ -1,4 +1,4 @@ -# Copyright 2022 Gentoo Authors +# Copyright 2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -29,7 +29,7 @@ DEPEND=" >=media-libs/charls-2.0.0:0= >=media-libs/openjpeg-2.0.0:2= sys-apps/util-linux:0= - sys-libs/zlib:0= + virtual/zlib:0= python? ( ${PYTHON_DEPS} ) vtk? ( sci-libs/vtk[rendering] From 2a8033f9ecd81cbc3e4c162af884a670ba39bd4c Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 07:50:17 +0100 Subject: [PATCH 23/31] sci-libs/itk: sys-libs/zlib -> virtual/zlib Signed-off-by: Alexander Puck Neuwirth --- sci-libs/itk/itk-5.2.1-r2.ebuild | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/sci-libs/itk/itk-5.2.1-r2.ebuild b/sci-libs/itk/itk-5.2.1-r2.ebuild index 0b1f25860d2..993f3215e44 100644 --- a/sci-libs/itk/itk-5.2.1-r2.ebuild +++ b/sci-libs/itk/itk-5.2.1-r2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -54,7 +54,7 @@ RDEPEND=" sci-libs/dcmtk:0= sci-libs/hdf5:0=[cxx] sci-libs/gdcm:0= - sys-libs/zlib:0= + virtual/zlib:0= media-libs/libjpeg-turbo:0= fftw? ( sci-libs/fftw:3.0= ) vtkglue? ( From 5b596d82a3c08d44a6688cd6c581de37b1a5ca8c Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 07:50:36 +0100 Subject: [PATCH 24/31] sci-physics/madgraph5: sys-libs/zlib -> virtual/zlib Signed-off-by: Alexander Puck Neuwirth --- sci-physics/madgraph5/madgraph5-3.5.3.ebuild | 4 ++-- sci-physics/madgraph5/madgraph5-3.5.8.ebuild | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/sci-physics/madgraph5/madgraph5-3.5.3.ebuild b/sci-physics/madgraph5/madgraph5-3.5.3.ebuild index 3ced7918c31..050396c02a9 100644 --- a/sci-physics/madgraph5/madgraph5-3.5.3.ebuild +++ b/sci-physics/madgraph5/madgraph5-3.5.3.ebuild @@ -26,7 +26,7 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}" RDEPEND=" ${PYTHON_DEPS} - sys-libs/zlib + virtual/zlib:= sys-devel/gcc:*[fortran] $(python_gen_cond_dep ' dev-python/numpy[${PYTHON_USEDEP}] @@ -37,7 +37,7 @@ RDEPEND=" hepmc2? ( sci-physics/hepmc:2 ) collier? ( sci-physics/collier[static-libs] ) thepeg? ( - sci-physics/thepeg[hepmc3(-),fastjet?,lhapdf?] + sci-physics/thepeg[hepmc3(-),fastjet?,lhapdf?] ) " # madanalysis5? ( sci-physics/madanalysis5 ) diff --git a/sci-physics/madgraph5/madgraph5-3.5.8.ebuild b/sci-physics/madgraph5/madgraph5-3.5.8.ebuild index acfbff70aa9..9d74cc9c170 100644 --- a/sci-physics/madgraph5/madgraph5-3.5.8.ebuild +++ b/sci-physics/madgraph5/madgraph5-3.5.8.ebuild @@ -1,4 +1,4 @@ -# Copyright 2024 Gentoo Authors +# Copyright 2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -29,7 +29,7 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}" RDEPEND=" ${PYTHON_DEPS} - sys-libs/zlib + virtual/zlib:= sys-devel/gcc:*[fortran] $(python_gen_cond_dep ' dev-python/numpy[${PYTHON_USEDEP}] From 2c51a43a90dcfc272d74afca09aa9ecbc283280c Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 08:57:53 +0100 Subject: [PATCH 25/31] profiles: mask failing sci-biology/sra-tools Signed-off-by: Alexander Puck Neuwirth --- profiles/package.mask | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index 3ac0b4add80..ab9e1de10bf 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -31,6 +31,10 @@ #--- END OF EXAMPLES --- +# Alexander Puck Neuwirth (2025-11-19) +# There are no ebuilds to satisfy "sci-biology/ngs". +sci-biology/sra-tools + # Alexander Puck Neuwirth (2025-11-17) # Installation fails. EAPI outdated. sci-chemistry/dl_poly From 35bfe55ebfbc5372176a5da0d4023f6a7d93a885 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 09:04:25 +0100 Subject: [PATCH 26/31] profiles: mask failing sci-biology/megahit Signed-off-by: Alexander Puck Neuwirth --- profiles/package.mask | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index ab9e1de10bf..c8faf414b90 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -31,6 +31,10 @@ #--- END OF EXAMPLES --- +# Alexander Puck Neuwirth (2025-11-19) +# megahit-1.2.9.ebuild: line 24: tc-has-openmp: command not found +sci-biology/megahit + # Alexander Puck Neuwirth (2025-11-19) # There are no ebuilds to satisfy "sci-biology/ngs". sci-biology/sra-tools From dd8278f0a3e901a3cfb3b4dd4b75ea21d4d92b71 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 09:28:16 +0100 Subject: [PATCH 27/31] sci-biology/sga: treeclean Signed-off-by: Alexander Puck Neuwirth --- sci-biology/sga/metadata.xml | 18 ---------- sci-biology/sga/sga-9999.ebuild | 58 --------------------------------- 2 files changed, 76 deletions(-) delete mode 100644 sci-biology/sga/metadata.xml delete mode 100644 sci-biology/sga/sga-9999.ebuild diff --git a/sci-biology/sga/metadata.xml b/sci-biology/sga/metadata.xml deleted file mode 100644 index 51beb3925c5..00000000000 --- a/sci-biology/sga/metadata.xml +++ /dev/null @@ -1,18 +0,0 @@ - - - - - mmokrejs@fold.natur.cuni.cz - Martin Mokrejs - - - sci-biology@gentoo.org - Gentoo Biology Project - - - Use dev-libs/jemalloc - - - jts/sga - - diff --git a/sci-biology/sga/sga-9999.ebuild b/sci-biology/sga/sga-9999.ebuild deleted file mode 100644 index ac1e208ac9b..00000000000 --- a/sci-biology/sga/sga-9999.ebuild +++ /dev/null @@ -1,58 +0,0 @@ -# Copyright 1999-2025 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit git-r3 autotools - -DESCRIPTION="String Graph OLC Assembler for short reads (overlap-layout-consensus)" -HOMEPAGE="https://github.com/jts/sga" -EGIT_REPO_URI="https://github.com/jts/sga" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="" -IUSE="jemalloc python" - -DEPEND=" - dev-cpp/sparsehash - sci-biology/bamtools - virtual/zlib:= - jemalloc? ( dev-libs/jemalloc ) -" -RDEPEND="${DEPEND} - sci-biology/abyss - python? ( sci-biology/pysam - sci-biology/ruffus )" - -S="${WORKDIR}/${P}/src" - -src_prepare() { - default - eautoreconf -} - -# http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/install/sga.htm -src_configure(){ - econf --with-bamtools="${EPREFIX}"/usr --with-sparsehash="${EPREFIX}"/usr -} - -src_compile(){ - # https://github.com/AlgoLab/FastStringGraph/issues/1#issuecomment-345999596 - # https://github.com/jts/sga/issues/106 - # https://github.com/jts/sga/pull/110 - # https://github.com/jts/sga/issues/108 - # - # other unreviewed patches: - # https://github.com/jts/sga/issues/96 - default -} - -src_install(){ - dodoc README - emake install DESTDIR="${D}" - insinto /usr/share/sga/examples - doins -r examples/* - cd .. || - dodoc README.md -} From a2d6e76ded698c13eb5970d41adb1ea467cedf35 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 09:45:42 +0100 Subject: [PATCH 28/31] profiles: mask failing sci-biology/SPAdes Signed-off-by: Alexander Puck Neuwirth --- profiles/package.mask | 3 +++ 1 file changed, 3 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index c8faf414b90..d1b93843d34 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -30,6 +30,9 @@ #--- END OF EXAMPLES --- +# Alexander Puck Neuwirth (2025-11-19) +# SRC_URI dead and compiles in src_install. +sci-biology/SPAdes # Alexander Puck Neuwirth (2025-11-19) # megahit-1.2.9.ebuild: line 24: tc-has-openmp: command not found From 6d7f78fba7a3a413f8988b16f913f7c212c6115d Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 09:51:07 +0100 Subject: [PATCH 29/31] profiles: mask failing sci-libs/ciftilib Signed-off-by: Alexander Puck Neuwirth --- profiles/package.mask | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index d1b93843d34..c22c0bd111d 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -30,6 +30,11 @@ #--- END OF EXAMPLES --- +# Alexander Puck Neuwirth (2025-11-19) +# CMake Error get_target_property() called with +# non-existent target "doc". +sci-libs/ciftilib + # Alexander Puck Neuwirth (2025-11-19) # SRC_URI dead and compiles in src_install. sci-biology/SPAdes From 8e2eb3953121361512611ad86cfe7405e95af477 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 09:57:31 +0100 Subject: [PATCH 30/31] profiles: mask failing sci-biology/vcflib Signed-off-by: Alexander Puck Neuwirth --- profiles/package.mask | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index c22c0bd111d..e753653add7 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -30,6 +30,11 @@ #--- END OF EXAMPLES --- +# Alexander Puck Neuwirth (2025-11-19) +# CMake Error at CMakeLists.txt:77 (add_library): +# No SOURCES given to target: vcflib +sci-biology/vcflib + # Alexander Puck Neuwirth (2025-11-19) # CMake Error get_target_property() called with # non-existent target "doc". From 477388bb433b935b8d6f04cd9c1e30067b05b6e3 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 19 Nov 2025 10:04:07 +0100 Subject: [PATCH 31/31] profiles: mask sci-biology/fsl Signed-off-by: Alexander Puck Neuwirth --- profiles/package.mask | 1 + 1 file changed, 1 insertion(+) diff --git a/profiles/package.mask b/profiles/package.mask index e753653add7..9617e38faad 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -39,6 +39,7 @@ sci-biology/vcflib # CMake Error get_target_property() called with # non-existent target "doc". sci-libs/ciftilib +sci-biology/fsl # Alexander Puck Neuwirth (2025-11-19) # SRC_URI dead and compiles in src_install.