pymol-users

[PyMOL] Cannot compile svn source

[Arnaud B. <arn...@ne...>]

Dear all,

I am trying to compile pymol from source following the instructions 
here: http://www.pymolwiki.org/index.php/Linux_Install

It used to work for me a while ago but now the compilation hangs without 
error. Pressing return give me back the terminal prompt. The compiling 
process does not stop always at the same point.

I am using Linux Mint 17 64 bits (based on Ubuntu).

Anyone has seen such behaviour?

Cheers,
Arnaud
PS: see below example of output

layer3/Selector.cpp:11037:36: warning: comparison between signed and 
unsigned integer expressions [-Wsign-compare]
        for(a = cNDummyAtoms; a < I->NAtom; a++)
                                     ^
layer3/Selector.cpp: In function ‘int* SelectorEvaluate(PyMOLGlobals*, 
char (*)[1024], int, int)’:
layer3/Selector.cpp:11107:15: warning: variable ‘opFlag2’ set but not 
used [-Wunused-but-set-variable]
    int opFlag, opFlag2, maxLevel;
                ^
layer3/Selector.cpp:11108:19: warning: variable ‘cc2’ set but not used 
[-Wunused-but-set-variable]
    char *q, *cc1, *cc2;
                    ^
layer3/Selector.cpp: In function ‘char (* SelectorParse(PyMOLGlobals*, 
char*))[1024]’:
layer3/Selector.cpp:11562:51: warning: comparison between signed and 
unsigned integer expressions [-Wsign-compare]
          if((q - q_base) >= sizeof(SelectorWordType)) {
                                                    ^
layer3/Selector.cpp: In function ‘DistSet* 
SelectorGetDistSet(PyMOLGlobals*, DistSet*, int, int, int, int, int, 
float, float*)’:
layer3/Selector.cpp:11845:32: warning: comparison between signed and 
unsigned integer expressions [-Wsign-compare]
    for(a = cNDummyAtoms; a < I->NAtom; a++) {
                                 ^
layer3/Selector.cpp:11859:34: warning: comparison between signed and 
unsigned integer expressions [-Wsign-compare]
      for(a = cNDummyAtoms; a < I->NAtom; a++) {
                                   ^
layer3/Selector.cpp: In function ‘DistSet* 
SelectorGetAngleSet(PyMOLGlobals*, DistSet*, int, int, int, int, int, 
int, int, float*, int*)’:
layer3/Selector.cpp:12102:34: warning: comparison between signed and 
unsigned integer expressions [-Wsign-compare]
      for(a = cNDummyAtoms; a < I->NAtom; a++) {
                                   ^
layer3/Selector.cpp:12118:34: warning: comparison between signed and 
unsigned integer expressions [-Wsign-compare]
      for(a = cNDummyAtoms; a < I->NAtom; a++) {
                                   ^
layer3/Selector.cpp:12146:36: warning: comparison between signed and 
unsigned integer expressions [-Wsign-compare]
        for(a = cNDummyAtoms; a < I->NAtom; a++) {
                                     ^
layer3/Selector.cpp: In function ‘DistSet* 
SelectorGetDihedralSet(PyMOLGlobals*, DistSet*, int, int, int, int, int, 
int, int, int, int, float*, int*)’:
layer3/Selector.cpp:12378:34: warning: comparison between signed and 
unsigned integer expressions [-Wsign-compare]
      for(a = cNDummyAtoms; a < I->NAtom; a++) {
                                   ^
layer3/Selector.cpp:12428:34: warning: comparison between signed and 
unsigned integer expressions [-Wsign-compare]
      for(a = cNDummyAtoms; a < I->NAtom; a++) {
                                   ^
layer3/Selector.cpp:12474:38: warning: comparison between signed and 
unsigned integer expressions [-Wsign-compare]
          for(a = cNDummyAtoms; a < I->NAtom; a++) {
                                       ^
layer3/Selector.cpp: In function ‘int SelectorLoadCoords(PyMOLGlobals*, 
PyObject*, int, int)’:
layer3/Selector.cpp:6705:9: warning: ‘itemsize’ may be used 
uninitialized in this function [-Wmaybe-uninitialized]
          switch(itemsize) {
          ^


... and then nothing

-- 
Dr Arnaud Basle                     X-ray facilities manager
Newcastle Structural Biology Laboratory
University of Newcastle
Medical School
ICAMB
Framlington place
NE2 4HH Newcastle upon tyne
Phone 0191 208 8931
                        

Re: [PyMOL] Cannot compile svn source

[Thomas H. <tho...@sc...>]

Dear Arnaud,

we do parallel builds, that's why it doesn't always stop at the same file. You didn't even include the error in your example output, only (irrelevant) warnings. To find the error, do this:

export JOBS=1
python setup.py build install ...

Cheers,
  Thomas

On 30 Jan 2015, at 04:13, Arnaud Basle <arn...@ne...> wrote:

> Dear all,
> 
> I am trying to compile pymol from source following the instructions 
> here: http://www.pymolwiki.org/index.php/Linux_Install
> 
> It used to work for me a while ago but now the compilation hangs without 
> error. Pressing return give me back the terminal prompt. The compiling 
> process does not stop always at the same point.
> 
> I am using Linux Mint 17 64 bits (based on Ubuntu).
> 
> Anyone has seen such behaviour?
> 
> Cheers,
> Arnaud
> PS: see below example of output
> 
> layer3/Selector.cpp:11037:36: warning: comparison between signed and 
> unsigned integer expressions [-Wsign-compare]
>        for(a = cNDummyAtoms; a < I->NAtom; a++)
>                                     ^
> layer3/Selector.cpp: In function ‘int* SelectorEvaluate(PyMOLGlobals*, 
> char (*)[1024], int, int)’:
> layer3/Selector.cpp:11107:15: warning: variable ‘opFlag2’ set but not 
> used [-Wunused-but-set-variable]
>    int opFlag, opFlag2, maxLevel;
>                ^
> layer3/Selector.cpp:11108:19: warning: variable ‘cc2’ set but not used 
> [-Wunused-but-set-variable]
>    char *q, *cc1, *cc2;
>                    ^
> layer3/Selector.cpp: In function ‘char (* SelectorParse(PyMOLGlobals*, 
> char*))[1024]’:
> layer3/Selector.cpp:11562:51: warning: comparison between signed and 
> unsigned integer expressions [-Wsign-compare]
>          if((q - q_base) >= sizeof(SelectorWordType)) {
>                                                    ^
> layer3/Selector.cpp: In function ‘DistSet* 
> SelectorGetDistSet(PyMOLGlobals*, DistSet*, int, int, int, int, int, 
> float, float*)’:
> layer3/Selector.cpp:11845:32: warning: comparison between signed and 
> unsigned integer expressions [-Wsign-compare]
>    for(a = cNDummyAtoms; a < I->NAtom; a++) {
>                                 ^
> layer3/Selector.cpp:11859:34: warning: comparison between signed and 
> unsigned integer expressions [-Wsign-compare]
>      for(a = cNDummyAtoms; a < I->NAtom; a++) {
>                                   ^
> layer3/Selector.cpp: In function ‘DistSet* 
> SelectorGetAngleSet(PyMOLGlobals*, DistSet*, int, int, int, int, int, 
> int, int, float*, int*)’:
> layer3/Selector.cpp:12102:34: warning: comparison between signed and 
> unsigned integer expressions [-Wsign-compare]
>      for(a = cNDummyAtoms; a < I->NAtom; a++) {
>                                   ^
> layer3/Selector.cpp:12118:34: warning: comparison between signed and 
> unsigned integer expressions [-Wsign-compare]
>      for(a = cNDummyAtoms; a < I->NAtom; a++) {
>                                   ^
> layer3/Selector.cpp:12146:36: warning: comparison between signed and 
> unsigned integer expressions [-Wsign-compare]
>        for(a = cNDummyAtoms; a < I->NAtom; a++) {
>                                     ^
> layer3/Selector.cpp: In function ‘DistSet* 
> SelectorGetDihedralSet(PyMOLGlobals*, DistSet*, int, int, int, int, int, 
> int, int, int, int, float*, int*)’:
> layer3/Selector.cpp:12378:34: warning: comparison between signed and 
> unsigned integer expressions [-Wsign-compare]
>      for(a = cNDummyAtoms; a < I->NAtom; a++) {
>                                   ^
> layer3/Selector.cpp:12428:34: warning: comparison between signed and 
> unsigned integer expressions [-Wsign-compare]
>      for(a = cNDummyAtoms; a < I->NAtom; a++) {
>                                   ^
> layer3/Selector.cpp:12474:38: warning: comparison between signed and 
> unsigned integer expressions [-Wsign-compare]
>          for(a = cNDummyAtoms; a < I->NAtom; a++) {
>                                       ^
> layer3/Selector.cpp: In function ‘int SelectorLoadCoords(PyMOLGlobals*, 
> PyObject*, int, int)’:
> layer3/Selector.cpp:6705:9: warning: ‘itemsize’ may be used 
> uninitialized in this function [-Wmaybe-uninitialized]
>          switch(itemsize) {
>          ^
> 
> 
> ... and then nothing
> 
> -- 
> Dr Arnaud Basle                     X-ray facilities manager
> Newcastle Structural Biology Laboratory
> University of Newcastle
> Medical School
> ICAMB
> Framlington place
> NE2 4HH Newcastle upon tyne
> Phone 0191 208 8931

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Cannot compile svn source

[Arnaud B. <arn...@ne...>]

Hi Stephen,

I was missing libfreetype6 library and libxml2 needed to be updated.

Cheers,
Arnaud


On 31/01/15 19:09, Stephen P. Molnar wrote:
> Seeing as youa re using a Debian derivative try the following:
>
> sudo apt-get install subversion build-essential python-dev python-pmw 
> libglew-dev freeglut3-dev libpng-dev libfreetype6-dev libxml2-dev
>
> cd /tmp
> svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
> cd pymol
>
> prefix=/home/computation/Apps/pymol
> modules=$prefix/modules
>
> python setup.py build install \
>     --home=$prefix \
>     --install-lib=$modules \
>     --install-scripts=$prefix
>
> Of course, edit the file to suit your system.
>
>
> On 01/30/2015 04:13 AM, Arnaud Basle wrote:
>> Dear all,
>>
>> I am trying to compile pymol from source following the instructions
>> here: http://www.pymolwiki.org/index.php/Linux_Install
>>
>> It used to work for me a while ago but now the compilation hangs without
>> error. Pressing return give me back the terminal prompt. The compiling
>> process does not stop always at the same point.
>>
>> I am using Linux Mint 17 64 bits (based on Ubuntu).
>>
>> Anyone has seen such behaviour?
>>
>> Cheers,
>> Arnaud
>> PS: see below example of output
>>
>> layer3/Selector.cpp:11037:36: warning: comparison between signed and
>> unsigned integer expressions [-Wsign-compare]
>>          for(a = cNDummyAtoms; a < I->NAtom; a++)
>>                                       ^
>> layer3/Selector.cpp: In function ‘int* SelectorEvaluate(PyMOLGlobals*,
>> char (*)[1024], int, int)’:
>> layer3/Selector.cpp:11107:15: warning: variable ‘opFlag2’ set but not
>> used [-Wunused-but-set-variable]
>>      int opFlag, opFlag2, maxLevel;
>>                  ^
>> layer3/Selector.cpp:11108:19: warning: variable ‘cc2’ set but not used
>> [-Wunused-but-set-variable]
>>      char *q, *cc1, *cc2;
>>                      ^
>> layer3/Selector.cpp: In function ‘char (* SelectorParse(PyMOLGlobals*,
>> char*))[1024]’:
>> layer3/Selector.cpp:11562:51: warning: comparison between signed and
>> unsigned integer expressions [-Wsign-compare]
>>            if((q - q_base) >= sizeof(SelectorWordType)) {
>>                                                      ^
>> layer3/Selector.cpp: In function ‘DistSet*
>> SelectorGetDistSet(PyMOLGlobals*, DistSet*, int, int, int, int, int,
>> float, float*)’:
>> layer3/Selector.cpp:11845:32: warning: comparison between signed and
>> unsigned integer expressions [-Wsign-compare]
>>      for(a = cNDummyAtoms; a < I->NAtom; a++) {
>>                                   ^
>> layer3/Selector.cpp:11859:34: warning: comparison between signed and
>> unsigned integer expressions [-Wsign-compare]
>>        for(a = cNDummyAtoms; a < I->NAtom; a++) {
>>                                     ^
>> layer3/Selector.cpp: In function ‘DistSet*
>> SelectorGetAngleSet(PyMOLGlobals*, DistSet*, int, int, int, int, int,
>> int, int, float*, int*)’:
>> layer3/Selector.cpp:12102:34: warning: comparison between signed and
>> unsigned integer expressions [-Wsign-compare]
>>        for(a = cNDummyAtoms; a < I->NAtom; a++) {
>>                                     ^
>> layer3/Selector.cpp:12118:34: warning: comparison between signed and
>> unsigned integer expressions [-Wsign-compare]
>>        for(a = cNDummyAtoms; a < I->NAtom; a++) {
>>                                     ^
>> layer3/Selector.cpp:12146:36: warning: comparison between signed and
>> unsigned integer expressions [-Wsign-compare]
>>          for(a = cNDummyAtoms; a < I->NAtom; a++) {
>>                                       ^
>> layer3/Selector.cpp: In function ‘DistSet*
>> SelectorGetDihedralSet(PyMOLGlobals*, DistSet*, int, int, int, int, int,
>> int, int, int, int, float*, int*)’:
>> layer3/Selector.cpp:12378:34: warning: comparison between signed and
>> unsigned integer expressions [-Wsign-compare]
>>        for(a = cNDummyAtoms; a < I->NAtom; a++) {
>>                                     ^
>> layer3/Selector.cpp:12428:34: warning: comparison between signed and
>> unsigned integer expressions [-Wsign-compare]
>>        for(a = cNDummyAtoms; a < I->NAtom; a++) {
>>                                     ^
>> layer3/Selector.cpp:12474:38: warning: comparison between signed and
>> unsigned integer expressions [-Wsign-compare]
>>            for(a = cNDummyAtoms; a < I->NAtom; a++) {
>>                                         ^
>> layer3/Selector.cpp: In function ‘int SelectorLoadCoords(PyMOLGlobals*,
>> PyObject*, int, int)’:
>> layer3/Selector.cpp:6705:9: warning: ‘itemsize’ may be used
>> uninitialized in this function [-Wmaybe-uninitialized]
>>            switch(itemsize) {
>>            ^
>>
>>
>> ... and then nothing
>>
>


-- 
Dr Arnaud Basle                     X-ray facilities manager
Newcastle Structural Biology Laboratory
University of Newcastle
Medical School
ICAMB
Framlington place
NE2 4HH Newcastle upon tyne
Phone 0191 208 8931