Gentoo Project

Chemistry Project

Bug Reports

• sci-chemistry/psi-4.0 version bump

  465124 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/tinker-7.1.2 : file collision with sci-libs/ssm-1.4:0::gentoo

  575908 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/mpqc-2.3.1-r4 : ../.../lapack.h:2:41: fatal error: chemistry/.../f77sym.h: No such file or directory

  595724 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/mpqc-2.3.1-r4 : make[4]: O2: Command not found

  662724 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/moldy: HOMEPAGE unavailable

  691170 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/modeller-9.22 : * (no error message)

  692308 - Assigned to Alexey Shvetsov
• sci-libs/avogadrolibs-1.93.0 fails to build with USE="vtk"

  712962 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/theseus-3.3.0-r1 : NWfill.c: fatal error: error.h: No such file or directory

  716280 - Assigned to Gentoo musl team
• sci-chemistry/modeller-10.5 installs files with broken symlink

  727980 - Assigned to Alexey Shvetsov
• sci-chemistry/mpqc-2.3.1-r4 fails tests

  741316 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/raster3d-3.0.6-r1 fails to compile

  743067 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/modeller-9.25 : /.../environment:line <snip>: 2to3: command not found

  765871 - Assigned to Alexey Shvetsov
• sci-chemistry/gperiodic-3.0.3 requires x11-libs/gtk+:2

  769485 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/tinker-8.2.1 fails to compile

  770496 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/modeller-9.25 - Package glib-2.0 was not found in the pkg-config search path.

  777351 - Assigned to Alexey Shvetsov
• sci-chemistry/tinker-8.2.1-r1 calls ar directly

  782619 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/cara-bin-1.8.4-r2 fails to fetch

  792597 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/modeller-10.2 version bump request

  829187 - Assigned to Alexey Shvetsov
• sci-chemistry/mpqc-2.3.1-r4 calls commands that do not exist

  832298 - Assigned to Gentoo Chemistry-Related Packages
• sci-libs/avogadrolibs-1.93.0 USE=vtk - fatal error: QVTKOpenGLWidget.h: No such file or directory

  832528 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/modeller-10.5 installs files with unresolved SONAME dependencies

  832745 - Assigned to Alexey Shvetsov
• sci-chemistry/xds-bin-20170930 installs files with unresolved SONAME dependencies

  832746 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/mpqc-2.3.1-r4 - /.../ld: .../libint.a(init_libint.o): relocation R_X86_64_PC32 against symbol build_eri can not be u

  832770 - Assigned to Gentoo Chemistry-Related Packages
• sci-libs/avogadrolibs-1.95.1 - /.../gl32.h: error: void _glewActiveTexture(GLenum) redeclared as different kind of entity

  834732 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/modeller-9.25 - except ImportError:

  835004 - Assigned to Alexey Shvetsov
• sci-chemistry/theseus: uses variables banned in scope (VariableScope)

  836095 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/vmd: uses variables banned in scope (VariableScope)

  836096 - Assigned to Alexey Shvetsov
• sci-libs/inchi-1.06-r1 fails to compile: ld: util.c:(.text+0x1b75): undefined reference to __isascii

  836860 - Assigned to Gentoo musl team
• sci-chemistry/modeller: fix distutils-r1 usage

  851585 - Assigned to Alexey Shvetsov
• sci-chemistry/gromacs: uses distuitls-r1.eclass incorrectly

  856415 - Assigned to Alexey Shvetsov
• sci-libs/avogadrolibs-1.97.0:0 - /.../spheregeometry.cpp: error: invalid cast from type std::nullptr_t to type const GLvoid {aka c

  866103 - Assigned to Gentoo musl team
• sci-chemistry/surf-1.0 - io.c: error: type specifier missing, defaults to int; ISO C99 and later

  874507 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/moldy-2.16e-r2 - configure: error: installation or configuration problem: C compiler cannot create executables.

  874741 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/mpqc: possible configure breakage with Clang 16

  879755 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/mpqc-2.3.1-r4 fails to compile (CLANG-STRICTER-SYSTEM): x86_64-pc-linux-gnu-ld.bfd: libSCdft.so: undefined reference to sc::SCF::init_threads()

  886107 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/mpqc-2.3.1-r4 fails to compile (MUSL-CLANG-SYSTEM): configure: error: could not determine F77 symbol names

  898134 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/moldy-2.16e-r2 has implicit function declarations in configure logs (GCC-13-SYSTEM)

  900671 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/bodr-10 fails tests (MUSL-SYSTEM)

  907973 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/votca-2022.1 fails tests (MUSL-SYSTEM)

  908020 - Assigned to Gentoo Chemistry-Related Packages
• sci-libs/avogadrolibs-1.97.0 failed to emerge with USE=vtk - Targets not yet defined

  909437 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/raster3d-3.0.6-r1 - Error: More actual than formal arguments in procedure call at (1)

  910753 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/gromacs: don't drop GMXRC files

  914360 - Assigned to Alexey Shvetsov
• sci-chemistry/pdbmat-3.89-r1 - -- Configuring incomplete, errors occurred!

  917252 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/modeller-9.25 installs deprecated .egg/.egg-info

  923272 - Assigned to Alexey Shvetsov
• sci-chemistry/gperiodic-3.0.3 fails to compile: install: cannot create regular file gperiodic.mo: No such file or directory

  924696 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/gelemental-2.0.2 calls commands that do not exist: dot

  924698 - Assigned to Matthias Maier
• sci-chemistry/chemtool-1.6.14-r1 calls commands that do not exist: LDFLAGS+=

  927167 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/autodock_vina-1.2.5 does not respect LDFLAGS

  927894 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/modeller-10.5 installs files that contain a TEXTREL

  927901 - Assigned to Alexey Shvetsov
• sci-chemistry/modeller-10.5 installs python packages with invalid/suspicious names or versions in the site-packages directory

  932087 - Assigned to Alexey Shvetsov
• sci-chemistry/pymol-3.0.0 does not enable tests

  932127 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/modeller-10.5 - [icu-75.1] Wheel build failed

  933877 - Assigned to Alexey Shvetsov
• sci-chemistry/votca-2022.1-r1 fails to compile: dlpolytrajectoryreader.cc:24:10: fatal error: convenience.hpp: No such file or directory

  936978 - Assigned to Gentoo Chemistry-Related Packages
• sci-libs/avogadrolibs-1.97.0 - [gcc-15] /.../cp2kinputdialog.cpp: error: type Avogadro::QtPlugins::BasisOption violates the C++ One Definition Rule [-Werror=odr]

  942463 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/psi-3.4.0-r3 - ../.../get_filename.cc: error: gprgid violates the C++ One Definition Rule [-Werror=odr]

  942838 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/easychem-0.6-r2 - [meson] [libtool] [gcc-15] easychem.c: error: initialization of void ( )(void) from incompatible pointer type void ( )(void , guint, GtkWi

  943932 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/surf-1.0 fails to compile: tessel_cases.c:110:16: error: too many arguments to function find_circle

  944873 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/moldy-2.16e-r2 fails to compile: algorith.c:225:7: error: too many arguments to function q_to_rot

  945790 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/surf-1.0 fails to compile: lp.c:29:1: error: number of arguments doesnt match prototype

  945791 - Assigned to Gentoo Chemistry-Related Packages
• sci-libs/fetk and subcomponents: tree clean request

  949099 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/gromacs-2025.0 - [go-1.24] [gcc-15] [ffmpeg] convert: MagickCore/string.c:1200: GetStringInfoDatum: Assertion string_info->signature == MagickCoreSignature

  950246 - Assigned to Alexey Shvetsov
• sci-chemistry/pymol-3.1.0 version bump request

  950338 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/modeller-10.5: swig 4.3.0 compat

  950475 - Assigned to Alexey Shvetsov
• sci-chemistry/gromacs-2025.0 - [meson] [go-1.24] [gcc-15] -- Configuring incomplete, errors occurred!

  951420 - Assigned to Alexey Shvetsov
• sci-chemistry/gromacs-2025.1 - [gcc-15] sandbox issue

  951722 - Assigned to Alexey Shvetsov
• sci-mathematics/diagrtb-2.64 - [gcc-15] [cmake-4] -- Configuring incomplete, errors occurred!

  952062 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/modeller: needs porting to Python 3.13, EAPI 8

  952653 - Assigned to Alexey Shvetsov
• sci-chemistry/votca: needs porting to Python 3.13

  952658 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/tm-align-20150914-r1 - [meson] [gcc-15] [cmake-4] -- Configuring incomplete, errors occurred!

  952793 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/pdbcat-1.3-r1 - [gcc-15] [cmake-4] -- Configuring incomplete, errors occurred!

  953912 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/tm-align-20150914-r1 - [cmake-4] QA Notice: S=WORKDIR is deprecated for cmake.eclass.

  954309 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/pymol-3.0.0-r1 - [gcc-15] x86_64-pc-linux-gnu-g++: fatal error: cannot read spec file libgomp.spec: No such file or directory

  955075 - Assigned to Gentoo Chemistry-Related Packages