sci-chemistry

Bug Reports

• sci-chemistry/xcrysden-1.6 (new package)

  339440 - Assigned to Default Assignee for New Packages
• 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/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/namd-2.13 version bump request

  686856 - Assigned to Nicolas Bock
• sci-chemistry/namd-2.10 fetch issue, browsers download a tar.gz file that is only a tar

  686858 - Assigned to Nicolas Bock
• sci-chemistry/namd-2.10 fails to build

  686860 - Assigned to Nicolas Bock
• sci-chemistry/psi-3.4.0-r2 : configure: error: Did not find a BLAS library.

  689004 - 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 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/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/molden-5.5 fails to compile: xwin.c:13950:18: error: non-void function appchg_ should return a value [-Wreturn-type]

  831519 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/mpqc-2.3.1-r4 calls commands that do not exist

  832298 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/modeller-9.25 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-chemistry/modeller-9.25 - except ImportError:

  835004 - Assigned to Alexey Shvetsov
• sci-chemistry/vmd-1.9.4_alpha55 - catdcd segfaults immediately

  835604 - 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-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-chemistry/pymol-2.5.0-r4 fails to compile (lto): ReadPARM7.h:62:16: error: type struct parm violates the C++ One Definition Rule [-Werror=odr]

  862441 - 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/easychem-0.6-r1 - easychem.c: error: call to undeclared function gettext; ISO C99 and

  875272 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/mopac7-1.15-r1 - fdate.c: error: call to undeclared function s_copy; ISO C99 and later do

  877105 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/tinker-8.2.1 fails tests (lto)

  878059 - 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/molmol-2k_p2-r6 - make[4]: No rule to make target ../../tools/lib/libtools.a, needed by molmol. Stop.

  880621 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/molmol-2k_p2-r8 - MotOGLDump.c: error: incompatible function pointer types passing void

  884043 - 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/psi-3.4.0-r2 fails to compile (CLANG-STRICTER-SYSTEM): parse.y:68:2: error: call to undeclared function ip_error; ISO C99 and later do not support implicit function declarations [-Werror,-Wimplicit-function-declaration]

  886127 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/ParmEd: needs upgrade to Python 3.11 (PythonCompatUpdate)

  897196 - Assigned to Alexey Shvetsov
• sci-chemistry/modeller: needs upgrade to Python 3.11 (PythonCompatUpdate)

  897200 - 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-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/pymol-2.5.0-r3 segfaults when loading a PDB

  910511 - 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/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/molmol-2k_p2-r8 - MotOGLDump.c: error: passing argument 3 of png_create_write_struct from incompatible pointer type [-Wincompatible-poin

  923325 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/dssp-4.4.4.1 fails tests: 1 - unit-test-dssp (Failed)

  924695 - Assigned to Pacho Ramos
• 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/mopac7-1.15-r1 fails to compile: parsav.f:25:21: error: type of nllco2 does not match original declaration [-Werror=lto-type-mismatch]

  927389 - 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-9.25 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-chemistry/gromacs-2024.1 - -- Configuring incomplete, errors occurred!

  927990 - Assigned to Alexey Shvetsov
• sci-chemistry/procheck: treeclean request

  928067 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/aqua: treeclean request

  928068 - Assigned to Gentoo Chemistry-Related Packages
• 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/chemex: needs upgrade to Python 3.12 (PythonCompatUpdate)

  929756 - Assigned to Pacho Ramos
• sci-chemistry/modeller: needs upgrade to Python 3.12 (PythonCompatUpdate)

  929757 - Assigned to Alexey Shvetsov
• sci-chemistry/molequeue: needs upgrade to Python 3.12 (PythonCompatUpdate)

  929758 - Assigned to Gentoo Science Related Packages
• sci-chemistry/openbabel: needs upgrade to Python 3.12 (PythonCompatUpdate)

  929759 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/ParmEd: needs upgrade to Python 3.12 (PythonCompatUpdate)

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

  929761 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/pymol: needs upgrade to Python 3.12 (PythonCompatUpdate)

  929762 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/vmd: needs upgrade to Python 3.12 (PythonCompatUpdate)

  929763 - Assigned to Alexey Shvetsov
• sci-chemistry/votca: needs upgrade to Python 3.12 (PythonCompatUpdate)

  929764 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/gromacs-2024.1 - /.../pme_gpu_internal.cpp: error: MPI_INT was not declared in this scope

  930796 - Assigned to Alexey Shvetsov

Stabilization Bug Reports

• sci-chemistry/gromacs-2023.2 and friends: stablereq

  920130 - Assigned to Alexey Shvetsov