Re: [PyMOL] Has anybody had success installing Pymol 1.3 from source on MacOSX 10.13?

2018-03-09 Thread Thomas Holder 
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 
>  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'
> 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 );
>  ^
>

[PyMOL] Has anybody had success installing Pymol 1.3 from source on MacOSX 10.13?

2018-03-08 Thread Martin Plochberger 
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'
 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 );
  ^
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 );
  ^
modules/cealign/src/tnt/tnt_array1d.h:61:11: note: candidate