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-libs/cifparse-obj-7.105 : make[1]: c: Command not found

  646346 - 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-libs/cifparse-obj-7.025-r1 : make: *** [Makefile:<snip>: compile] Error 1

  685552 - 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-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-libs/cifparse-obj calls cc directly

  725426 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/modeller installs files with broken symlink

  727980 - Assigned to Alexey Shvetsov
• sci-libs/cifparse-obj-7.105 fails to compile: llvm-ar: error: unknown option .

  731896 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/GromacsWrapper-0.8.0 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/wxmacmolplt-7.5-r1 fails to compile: aboutwxmacmolplt.cpp:167:43: error: invalid suffix on literal; C++11 requires a

  741366 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/raster3d-3.0.6-r1 fails to compile

  743067 - Assigned to Gentoo Chemistry-Related Packages
• sci-libs/cifparse-obj-7.105 : src/CifParser.c: fatal error: CifParser.tab.h: No such file or directory

  751550 - 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/openbabel-2.4.1-r2 fails tests

  778851 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/tinker-8.2.1 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-libs/cifparse-obj-7.105 - ar: invalid option -- .

  799620 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/modeller-10.2 version bump request

  829187 - Assigned to Alexey Shvetsov
• sci-chemistry/gelemental-2.0.0-r1 - value.cc: error: pango_parse_markup was not declared in this scope

  829653 - Assigned to Matthias Maier
• 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-libs/libghemical-3.0.0 fails to compile: typerule.cpp:172:22: error: non-constant-expression cannot be narrowed from type size_t (aka unsigned long) to i32s (aka int) in initializer list [-Wc++11-narrowing]

  831798 - 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-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-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-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/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-libs/inchi-1.06 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-libs/libghemical-3.0.0 installs libtool files (.la) without corresponding static libraries

  850739 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/modeller: fix distutils-r1 usage

  851585 - Assigned to Alexey Shvetsov
• sci-chemistry/pymol: fix distutils-r1 usage

  851588 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/gromacs: uses distuitls-r1.eclass incorrectly

  856415 - Assigned to Alexey Shvetsov
• sci-chemistry/pymol-2.5.0-r1 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/wxmacmolplt-7.5-r1 fails to compile (lto): coordinateswindow.cpp:50:6: error: type [-Werror=odr]

  862447 - Assigned to Gentoo Chemistry-Related Packages
• sci-libs/avogadrolibs-1.95.1:0 - /.../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/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/nmrglue: still depends on dev-python/nose

  878725 - 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-r6 - MotOGLDump.c: error: incompatible function pointer types passing void

  884043 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/easychem-0.6-r1 fails to compile (CLANG-STRICTER-SYSTEM): easychem.c:2857:10: error: incompatible integer to pointer conversion returning int from a function with result type gchar (aka char ) [-Wint-conversion]

  886085 - 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-libs/libghemical-3.0.0 fails to compile (USR-MERGE-SYSTEM): Failed running intltoolize!

  891895 - 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/autodock-4.2.6 fails to compile (MUSL-CLANG-SYSTEM): cluster_analysis.cc:61:5: error: ISO C++17 does not allow register storage class specifier [-Wregister]

  898130 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/cluster-1.3.081231-r1 fails to compile (MUSL-CLANG-SYSTEM): utility.cpp:110:2: error: ISO C++17 does not allow register storage class specifier [-Wregister]

  898132 - 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/tinker-8.2.1: uses deprecated EAPI 6

  905682 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/gromacs-2023.1 - -- Configuring incomplete, errors occurred!

  905865 - Assigned to Alexey Shvetsov

Stabilization Bug Reports

• sci-chemistry/molden-6.9-r1 stabilisation and cleanup old

  867223 - Assigned to Gentoo Chemistry-Related Packages
• sci-chemistry/gromacs-2021.7 stable request

  906679 - Assigned to Alexey Shvetsov