sci-chemistry

Bug Reports

• sci-chemistry/bist ebuild request

  239172 - Assigned to Default Assignee for New Packages
• sci-chemistry/xcrysden-1.6 (new package)

  339440 - Assigned to Default Assignee for New Packages
• sci-chemistry/cclib-1.0.1 - Library for parsing and interpreting the results of computational chemistry packages

  415829 - Assigned to Default Assignee for New Packages
• 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/cyana: move to science overlay instead of complete removal?

  653474 - 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-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/GromacsWrapper-0.8.4 fails tests

  741214 - 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/molequeue-0.9.0-r1 - FileNotFoundError: [Errno 2] No such file or directory: b/var/tmp/portage/sci-chemistry/moleque

  801685 - Assigned to Gentoo Science 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-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-chemistry/ParmEd-3.4.3 fails tests: ModuleNotFoundError: No module named numpy - ModuleNotFoundError: No module named simtk

  833482 - Assigned to Alexey Shvetsov
• sci-chemistry/gypsumdl: Python framework for 3D small-molecule models (New Package)

  833845 - Assigned to Default Assignee for New 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-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-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/ParmEd: needs upgrade to Python 3.11 (PythonCompatUpdate)

  897196 - Assigned to Alexey Shvetsov
• 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-chemistry/ParmEd: needs to use PEP517 build (DistutilsNonPEP517Build)

  910018 - Assigned to Alexey Shvetsov
• sci-chemistry/modeller: needs to use PEP517 build (DistutilsNonPEP517Build)

  910020 - Assigned to Alexey Shvetsov
• 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/gnome-chemistry-utils-0.14.17_p6-r2 - [slibtool] cdx.cc:(.text+<snip>): undefined reference to pango_font_description_from_stri

  913669 - Assigned to Pacho Ramos
• sci-chemistry/molsketch-0.8.0 version bump

  913683 - 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/gperiodic-3.0.3 - gperiodic.c: error: passing argument 1 of gtk_label_set_selectable from incompatible pointer type [-Wincompatible-poin

  919213 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/modeller-9.25 installs deprecated .egg/.egg-info

  923272 - Assigned to Alexey Shvetsov
• sci-chemistry/ParmEd-3.4.3 installs deprecated .egg/.egg-info

  923273 - 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/ParmEd: needs upgrade to Python 3.12 (PythonCompatUpdate)

  929760 - Assigned to Alexey Shvetsov
• sci-chemistry/gromacs-2024.1 - /.../pme_gpu_internal.cpp: error: MPI_INT was not declared in this scope

  930796 - 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-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/molmol-2k_p2-r9 - [libtool] [gcc-15] PuCB.c: error: passing argument 2 of insertCallback from incompatible pointer type [-Wincompatible-pointer-types]

  944200 - 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: xdr.c:364:1: error: number of arguments doesnt match prototype

  944874 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/dssp-3.0.11 fails to compile: hssp-nt.cpp:17:10: fatal error: convenience.hpp: No such file or directory

  944939 - Assigned to Pacho Ramos
• sci-chemistry/gromacs-2025.0_beta - -- Configuring incomplete, errors occurred!

  945066 - Assigned to Alexey Shvetsov
• sci-chemistry/gromacs-2025.0_beta fails to compile: gmxapicompat.h:103:23: error: int64_t was not declared in this scope

  945789 - Assigned to Alexey Shvetsov
• 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-chemistry/gromacs-2025.0_beta - [texlive] convert: MagickCore/string.c:1200: GetStringInfoDatum: Assertion string_info->signature == MagickCoreSignature failed.

  946372 - Assigned to Alexey Shvetsov