Gentoo Project

Chemistry Project

Bug Reports

• sci-chemistry/psi-4.0 version bump

  465124 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/molden-4.8-r2 - make -C surf depend: Makefile:47: recipe for target 'depend' failed

  534712 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/molden-4.8-r2 with app-vim/cvsmenu: sandbox issue

  575566 - 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/molden-5.5 : make[1]: *** [Makefile:61: depend] Error 1

  610968 - 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/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/molden-5.5 - sandbox issue

  775626 - 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-chemistry/ParmEd-3.4.3 fails tests: ModuleNotFoundError: No module named numpy - ModuleNotFoundError: No module named simtk

  833482 - Assigned to Alexey Shvetsov
• sci-chemistry/molden-6.9-r1 calls cc directly

  833771 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/molden-6.9-r1 - /.../rots.h:13329: undefined reference to memmove@GLIBC_2.2.5

  834602 - Assigned to Gentoo musl team
• 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-chemistry/gromacs-2022.4 does not enable tests

  836855 - 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/molden-6.9 - sandbox issue

  844205 - Assigned to Gentoo Chemistry-Related Packages
• 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-libs/avogadrolibs: drop dependency to sci-chemistry/molequeue

  869206 - Assigned to Gentoo Chemistry-Related Packages
• 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/molden-6.9-r1 calls commands that do not exist: uncompress

  878067 - 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/gromacs-2023.1 fails tests (MUSL-SYSTEM)

  907989 - Assigned to Alexey Shvetsov
• 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/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/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-libs/avogadrolibs-1.99.0 version bump and switch to Qt6

  926352 - Assigned to Gentoo Chemistry-Related Packages
• 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/gromacs-2024.1 fails to compile: identifyavx512fmaunits.cpp:205:5: error: the register zmm11 cannot be clobbered in asm for the current target

  927900 - Assigned to Alexey Shvetsov
• sci-chemistry/modeller-10.5 installs files that contain a TEXTREL

  927901 - Assigned to Alexey Shvetsov
• sci-chemistry/molden-6.9-r1 fails to compile: xwin.c:4620:17: error: implicit declaration of function tolower [-Wimplicit-function-declaration]

  927905 - Assigned to Gentoo Chemistry-Related Packages
• sci-libs/numkit-1.2.3 fails tests: ImportError: cannot import name Tester from numpy.testing __init__.py)

  928054 - Assigned to Alexey Shvetsov
• sci-chemistry/gromacs-2021.7-r1 fails to compile: modularsimulator.h:131:15: error: there are no arguments to getenv that depend on a template parameter, so a declaration of getenv must be available [-fpermissive]

  928852 - Assigned to Alexey Shvetsov
• sci-chemistry/molden-6.9-r1 - /.../rots.h:13329:(.text+<snip>): undefined reference to memmove@GLIBC_2.2.5

  929069 - Assigned to Gentoo musl team
• sci-chemistry/ParmEd: needs upgrade to Python 3.12 (PythonCompatUpdate)

  929760 - Assigned to Alexey Shvetsov
• sci-libs/numkit: needs upgrade to Python 3.12 (PythonCompatUpdate)

  929784 - 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-libs/spglib: 2.5.0 version bump

  937609 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/gromacs-2024.2 - [icu-75.1] [gcc-15] /.../energyhistory.cpp: error: nsum was not declared in this scope

  937696 - Assigned to Alexey Shvetsov
• sci-chemistry/gromacs-2024.3 fails to compile: energyhistory.h:89:5: error: int64_t does not name a type

  939006 - Assigned to Alexey Shvetsov
• 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