gentoo · APN-Pucky · Nov 19, 2025 · Nov 19, 2025 · Nov 19, 2025 · Nov 19, 2025
diff --git 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="

diff --git 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}"

diff --git 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}"

diff --git a/profiles/package.mask b/profiles/package.mask
@@ -30,6 +30,33 @@
 
 #--- END OF EXAMPLES ---
 
+# Alexander Puck Neuwirth <apn-pucky@gentoo.org> (2025-11-19)
+# CMake Error at CMakeLists.txt:77 (add_library):
+#   No SOURCES given to target: vcflib
+sci-biology/vcflib
+
+# Alexander Puck Neuwirth <apn-pucky@gentoo.org> (2025-11-19)
+# CMake Error get_target_property() called with
+# non-existent target "doc". 
+sci-libs/ciftilib
+sci-biology/fsl
+
+# Alexander Puck Neuwirth <apn-pucky@gentoo.org> (2025-11-19)
+# SRC_URI dead and compiles in src_install.
+sci-biology/SPAdes
+
+# Alexander Puck Neuwirth <apn-pucky@gentoo.org> (2025-11-19)
+# megahit-1.2.9.ebuild: line 24: tc-has-openmp: command not found
+sci-biology/megahit
+
+# Alexander Puck Neuwirth <apn-pucky@gentoo.org> (2025-11-19)
+# There are no ebuilds to satisfy "sci-biology/ngs".
+sci-biology/sra-tools
+
+# Alexander Puck Neuwirth <apn-pucky@gentoo.org> (2025-11-17)
+# Installation fails. EAPI outdated.
+sci-chemistry/dl_poly
+
 # Alexander Puck Neuwirth <apn-pucky@gentoo.org> (2025-01-10)
 # Download server is gone since about 2014.
 sci-biology/vague-bin

diff --git 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}

diff --git 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"

diff --git 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}"

diff --git 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
@@ -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

diff --git 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
@@ -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/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
 

diff --git 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}
 	)"

diff --git 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}"

diff --git 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(){

diff --git 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(){

diff --git a/sci-biology/sga/metadata.xml b/sci-biology/sga/metadata.xml
diff --git a/sci-biology/sga/sga-9999.ebuild b/sci-biology/sga/sga-9999.ebuild
diff --git 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
@@ -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/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

diff --git 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(){

diff --git 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
 "

diff --git 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
@@ -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-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}"
 

diff --git 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
@@ -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]