Hi Martin, Regarding "contribute with others who only have 1.3 available": If this is about exchanging session files, it should be fine to use a recent version of PyMOL and set the "pse_export_version" setting before saving files:
set pse_export_version, 1.3 save compatible-with-1-3.pse https://pymolwiki.org/index.php/Pse_export_version Cheers, Thomas > On Mar 8, 2018, at 11:45 PM, Martin Plochberger > <martin.plochber...@univie.ac.at> wrote: > > Dear all, > > I recently was asked to install Pymol 1.3 from source on MacOSX 10.13. > > It had worked on 10.12 and after the update to 10.13 had stopped > working. > > The person needs that specific version to contribute with others who > only have 1.3 available. > > After my failed installation attempts we will probably try other > options (installing it on a Linux machine etc.), but I am still > wondering if it would be possible on MacOSX 10.13. > > What I did: > > 1. I downloaded the source code from sourceforge (https://sourceforge.n > et/projects/pymol/files/pymol/1.3r2/) > 2. I installed the dependencies described in the README to the best of > my knowledge :) > 3. I ran 'python setup.py build install > > At 3. I then got the "build errors" below. > > I am happy to provide more details on my installation steps if someone > wants to get into it :). > > My questions: > > * Did you have success installing the 1.3 sourceforge version I linked > above? If yes, please be so kind and share your findings. > * Are the below "build errors" only due to buggy code or does it look > like I am possibly missing a dependency? > > Thanks in advance for any help you can give me and ... Cheers ;) > > ======================= BUILD ERRORS START ======================= > python setup.py build install > running build > running build_py > package init file 'modules/web/javascript/__init__.py' not found (or > not > a regular file) > package init file 'modules/web/javascript/__init__.py' not found (or > not > a regular file) > running build_ext > building 'pymol._cmd' extension > clang -fno-strict-aliasing -fno-common -dynamic -g -O2 -DNDEBUG -g > -fwrapv -O3 -Wall -Wstrict-prototypes -D_PYMOL_MODULE -D_PYMOL_LIBPNG > -D_PYMOL_FREETYPE -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 > -Ilayer4 > -Ilayer5 -I/usr/X11R6/include > -I/Users/4dm1n1str4t0r/Desktop/1_3_source/pymol-1.3r2/ext/include > -I/Users/4dm1n1str4t0r/Desktop/1_3_source/pymol-1.3r2/ext/include/GL > -I/Users/4dm1n1str4t0r/Desktop/1_3_source/pymol- > 1.3r2/ext/include/freetype2 > -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/local/include > -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include > -I/usr/local/opt/tcl-tk/include > -I/usr/local/Cellar/python@2/2.7.14_2/Frameworks/Python.framework/Versi > ons/2.7/include/python2.7 > -c modules/cealign/src/ccealignmodule.cpp -o > build/temp.macosx-10.13-x86_64-2.7/modules/cealign/src/ccealignmodule.o > In file included from modules/cealign/src/ccealignmodule.cpp:32: > In file included from modules/cealign/src/ccealignmodule.H:36: > In file included from modules/cealign/src/tnt/tnt.h:41: > modules/cealign/src/tnt/tnt_array1d.h:238:15: warning: '&&' within '||' > [-Wlogical-op-parentheses] > if ((i0 > 0) && (i1 < n_) || (i0 <= i1)) > ~~~~~~~~~^~~~~~~~~~~~ ~~ > modules/cealign/src/tnt/tnt_array1d.h:238:15: note: place parentheses > around the > '&&' expression to silence this warning > if ((i0 > 0) && (i1 < n_) || (i0 <= i1)) > ^ > ( ) > In file included from modules/cealign/src/ccealignmodule.cpp:32: > In file included from modules/cealign/src/ccealignmodule.H:36: > In file included from modules/cealign/src/tnt/tnt.h:48: > modules/cealign/src/tnt/tnt_fortran_array1d.h:224:15: warning: '&&' > within '||' > [-Wlogical-op-parentheses] > if ((i0 > 0) && (i1 < n_) || (i0 <= i1)) > ~~~~~~~~~^~~~~~~~~~~~ ~~ > modules/cealign/src/tnt/tnt_fortran_array1d.h:224:15: note: place > parentheses > around the '&&' expression to silence this warning > if ((i0 > 0) && (i1 < n_) || (i0 <= i1)) > ^ > ( ) > In file included from modules/cealign/src/ccealignmodule.cpp:32: > In file included from modules/cealign/src/ccealignmodule.H:36: > In file included from modules/cealign/src/tnt/tnt.h:55: > modules/cealign/src/tnt/tnt_sparse_matrix_csr.h:97:3: error: no > matching > constructor for initialization of 'Array1D<int>' > rowptr_(M, r), colind_(nz, c), dim1_(M), dim2_(N) {} > ^ ~~~~ > modules/cealign/src/tnt/tnt_array1d.h:63:11: note: candidate > constructor > not > viable: no known conversion from 'const int *' to 'const int' > for > 2nd > argument; dereference the argument with * > Array1D(int n, const T &a); > ^ > modules/cealign/src/tnt/tnt_array1d.h:64:11: note: candidate > constructor > not > viable: 2nd argument ('const int *') would lose const qualifier > Array1D(int n, T *a); > ^ > modules/cealign/src/tnt/tnt_array1d.h:62:11: note: candidate > constructor > not > viable: requires single argument 'n', but 2 arguments were > provided > explicit Array1D(int n); > ^ > modules/cealign/src/tnt/tnt_array1d.h:65:14: note: candidate > constructor > not > viable: requires single argument 'A', but 2 arguments were > provided > inline Array1D(const Array1D &A); > ^ > modules/cealign/src/tnt/tnt_array1d.h:61:11: note: candidate > constructor > not > viable: requires 0 arguments, but 2 were provided > Array1D(); > ^ > In file included from modules/cealign/src/ccealignmodule.cpp:32: > In file included from modules/cealign/src/ccealignmodule.H:36: > In file included from modules/cealign/src/tnt/tnt.h:55: > modules/cealign/src/tnt/tnt_sparse_matrix_csr.h:97:18: error: no > matching > constructor for initialization of 'Array1D<int>' > rowptr_(M, r), colind_(nz, c), dim1_(M), dim2_(N) {} > ^ ~~~~~ > modules/cealign/src/tnt/tnt_array1d.h:63:11: note: candidate > constructor > not > viable: no known conversion from 'const int *' to 'const int' > for > 2nd > argument; dereference the argument with * > Array1D(int n, const T &a); > ^ > modules/cealign/src/tnt/tnt_array1d.h:64:11: note: candidate > constructor > not > viable: 2nd argument ('const int *') would lose const qualifier > Array1D(int n, T *a); > ^ > modules/cealign/src/tnt/tnt_array1d.h:62:11: note: candidate > constructor > not > viable: requires single argument 'n', but 2 arguments were > provided > explicit Array1D(int n); > ^ > modules/cealign/src/tnt/tnt_array1d.h:65:14: note: candidate > constructor > not > viable: requires single argument 'A', but 2 arguments were > provided > inline Array1D(const Array1D &A); > ^ > modules/cealign/src/tnt/tnt_array1d.h:61:11: note: candidate > constructor > not > viable: requires 0 arguments, but 2 were provided > Array1D(); > ^ > modules/cealign/src/ccealignmodule.cpp:588:5: warning: variable 'o' is > incremented both in the loop header and in the loop body > [-Wfor-loop-analysis] > o++; > ^ > modules/cealign/src/ccealignmodule.cpp:431:36: note: incremented here > for ( int o = 0; o < bufferSize; o++ ) { > ^ > 3 warnings and 2 errors generated. > error: command 'clang' failed with exit status 1 > ======================= BUILD ERRORS END ======================= > > -- > Martin Plochberger > ****************************** > Max F. Perutz Support GmbH > Dr. Bohr-Gasse 9, Room: 4.220 > A-1030 Vienna > ****************************** > Tel.: +43-1-4277-24041 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
