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 ------------------------------------------------------------------------------ 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
