subject:"\[PyMOL\] Installation PyMOL failure in Linux $CentOS$"

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

2011-12-07 Thread grantaka36

Dear Thomas and all advisers,

Thanks for all, I've got installed pymol in CentOS5 from EPEL
repository. Turning back to the package list by Yum Extender (yumex),
I found 'pymol' appeared as
http://lockerz.com/s/162790999
after
http://lockerz.com/s/162790733

cf.)
- Might need installed 'epel*'
# rpm -i 
http://download.fedora.redhat.com/pub/epel/6/x86_64/epel-release-6-5.noarch.rpm
- 'yumex' can be installed:
# yum install yumex

Can I add this information to pymolwiki (Need an account) ?
http://www.pymolwiki.org/index.php/Linux_Install

After PyMOL running, console says:
freeglut (pymol): Unable to create direct context rendering for
window 'PyMOL Viewer'
but I will try to check and contact here as another issue if not succeeded.

Regards,
Masataka


2011/12/6 grantaka36 grantak...@gmail.com:
 Dear Thomas,

 Thanks for good pointing for the weird problem, which I couldn't notice at 
 all.

 You do compile with -D_FORTIFY_SOURCE=2, could you remove that?
 I'm afraid, I know not related PyMOL itself, but I wish to know how to
 do that. Searching 'setup.py', 'setup2.py' or some 'Makefile*' with
 the string 'D_FORTIFY_SOURCE' or 'gcc' returned no matches.

 And Zhijian and Andreas,

 Thank you for advices through your experiences, I will pursue at first
 as Thomas advised.

 Regards,
 Masataka


 2011/12/5 Andreas Förster docandr...@gmail.com:
 Dear Masataka,

 a few months ago, I upgraded most of our computers from RHEL 5.x to 6.1.  If
 version 6 of CentOS (free RHEL clone) is out, I would highly recommend, no I
 would urge you, to upgrade as well.  RHEL and CentOS are rock-solid
 operating systems, but their libraries and dependencies show their age.


 Andreas



 On 05/12/2011 1:50, grantaka36 wrote:

 Hi, Marius, Troels and David,

 I appreciate very much for guiding, tried in three ways but no success
 currently.

 - I also think some difference on distributions (CentOS 5 here,) trapped
 at

 function 'IsosurfGetRange'

 Does anyone have information to workaround?
 - Do you think if any dependency on Python version (2.4.3 here)?

 Attached '20111205_script_and_error.zip' is for information sharing:
 - 'install_pymol.sh' : followed by below, some package name modified for
 CentOS

 http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_with_MPEG_support
 - 'install_pymol_sh_error.txt'

 layer0/Isosurf.c:2197:1: error: unterminated argument list invoking macro
 fprintf
 layer0/Isosurf.c: In function 'IsosurfGetRange':


 - 'install_pymol_gcc45.sh' - aiming to use default installed gcc4.5
 instead of 4.4
 - 'install_pymol_gcc45_sh_error.txt'

 layer0/Isosurf.c: In function 'IsosurfGetRange':
 layer0/Isosurf.c:2197:0: error: unterminated argument list invoking macro
 fprintf


 - 'compile_pymol.sh' : again by initial trying
 http://www.pymolwiki.org/index.php/Linux_Install#Install_from_source
 - 'compile_pymol_sh_error.txt'

 layer0/Isosurf.c: In function 'IsosurfGetRange':
 layer0/Isosurf.c:2197:0: error: unterminated argument list invoking macro
 fprintf



 Regards,
 Masataka


 --
        Andreas Förster, Research Associate
        Paul Freemont  Xiaodong Zhang Labs
 Department of Biochemistry, Imperial College London
            http://www.msf.bio.ic.ac.uk

--
Cloud Services Checklist: Pricing and Packaging Optimization
This white paper is intended to serve as a reference, checklist and point of 
discussion for anyone considering optimizing the pricing and packaging model 
of a cloud services business. Read Now!
http://www.accelacomm.com/jaw/sfnl/114/51491232/
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Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

2011-12-07 Thread Thomas Holder

Hi Masataka,

 Thanks for all, I've got installed pymol in CentOS5 from EPEL
 repository. Turning back to the package list by Yum Extender (yumex),
 I found 'pymol' appeared as
 http://lockerz.com/s/162790999
 after
 http://lockerz.com/s/162790733

 cf.)
 - Might need installed 'epel*'
 # rpm -i 
 http://download.fedora.redhat.com/pub/epel/6/x86_64/epel-release-6-5.noarch.rpm
 - 'yumex' can be installed:
 # yum install yumex

 Can I add this information to pymolwiki (Need an account) ?
 http://www.pymolwiki.org/index.php/Linux_Install

sure, that would be great. But first try to solve the freeglut issue.

Jason can give you an account for the PyMOLWiki. Or I can update the 
Linux_Install page.

 After PyMOL running, console says:
 freeglut (pymol): Unable to create direct context rendering for
 window 'PyMOL Viewer'
 but I will try to check and contact here as another issue if not succeeded.

do you have a graphics driver with direct rendering support installed?

glxinfo | grep direct

Cheers,
   Thomas

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

--
Cloud Services Checklist: Pricing and Packaging Optimization
This white paper is intended to serve as a reference, checklist and point of 
discussion for anyone considering optimizing the pricing and packaging model 
of a cloud services business. Read Now!
http://www.accelacomm.com/jaw/sfnl/114/51491232/
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Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

2011-12-07 Thread Thomas Holder

Hi Masataka,

 Thanks for all, I've got installed pymol in CentOS5 from EPEL
 repository. Turning back to the package list by Yum Extender (yumex),
 I found 'pymol' appeared as
 http://lockerz.com/s/162790999
 after
 http://lockerz.com/s/162790733
 
 cf.)
 - Might need installed 'epel*'
 # rpm -i 
 http://download.fedora.redhat.com/pub/epel/6/x86_64/epel-release-6-5.noarch.rpm
 - 'yumex' can be installed:
 # yum install yumex
 
 Can I add this information to pymolwiki (Need an account) ?
 http://www.pymolwiki.org/index.php/Linux_Install

I'd like to figure out the minimal efford to get PyMOL installed this 
way before adding it to the wiki. I guess yumex is not necessary, does 
this command work as well?

yum --enablerepo=epel install pymol

Cheers,
   Thomas

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

--
Cloud Services Checklist: Pricing and Packaging Optimization
This white paper is intended to serve as a reference, checklist and point of 
discussion for anyone considering optimizing the pricing and packaging model 
of a cloud services business. Read Now!
http://www.accelacomm.com/jaw/sfnl/114/51491232/
___
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Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

2011-12-06 Thread grantaka36

Dear Thomas,

Thanks for good pointing for the weird problem, which I couldn't notice at all.

 You do compile with -D_FORTIFY_SOURCE=2, could you remove that?
I'm afraid, I know not related PyMOL itself, but I wish to know how to
do that. Searching 'setup.py', 'setup2.py' or some 'Makefile*' with
the string 'D_FORTIFY_SOURCE' or 'gcc' returned no matches.

And Zhijian and Andreas,

Thank you for advices through your experiences, I will pursue at first
as Thomas advised.

Regards,
Masataka


2011/12/5 Andreas Förster docandr...@gmail.com:
 Dear Masataka,

 a few months ago, I upgraded most of our computers from RHEL 5.x to 6.1.  If
 version 6 of CentOS (free RHEL clone) is out, I would highly recommend, no I
 would urge you, to upgrade as well.  RHEL and CentOS are rock-solid
 operating systems, but their libraries and dependencies show their age.


 Andreas



 On 05/12/2011 1:50, grantaka36 wrote:

 Hi, Marius, Troels and David,

 I appreciate very much for guiding, tried in three ways but no success
 currently.

 - I also think some difference on distributions (CentOS 5 here,) trapped
 at

 function 'IsosurfGetRange'

 Does anyone have information to workaround?
 - Do you think if any dependency on Python version (2.4.3 here)?

 Attached '20111205_script_and_error.zip' is for information sharing:
 - 'install_pymol.sh' : followed by below, some package name modified for
 CentOS

 http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_with_MPEG_support
 - 'install_pymol_sh_error.txt'

 layer0/Isosurf.c:2197:1: error: unterminated argument list invoking macro
 fprintf
 layer0/Isosurf.c: In function 'IsosurfGetRange':


 - 'install_pymol_gcc45.sh' - aiming to use default installed gcc4.5
 instead of 4.4
 - 'install_pymol_gcc45_sh_error.txt'

 layer0/Isosurf.c: In function 'IsosurfGetRange':
 layer0/Isosurf.c:2197:0: error: unterminated argument list invoking macro
 fprintf


 - 'compile_pymol.sh' : again by initial trying
 http://www.pymolwiki.org/index.php/Linux_Install#Install_from_source
 - 'compile_pymol_sh_error.txt'

 layer0/Isosurf.c: In function 'IsosurfGetRange':
 layer0/Isosurf.c:2197:0: error: unterminated argument list invoking macro
 fprintf



 Regards,
 Masataka


 --
        Andreas Förster, Research Associate
        Paul Freemont  Xiaodong Zhang Labs
 Department of Biochemistry, Imperial College London
            http://www.msf.bio.ic.ac.uk

--
Cloud Services Checklist: Pricing and Packaging Optimization
This white paper is intended to serve as a reference, checklist and point of 
discussion for anyone considering optimizing the pricing and packaging model 
of a cloud services business. Read Now!
http://www.accelacomm.com/jaw/sfnl/114/51491232/
___
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Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

2011-12-05 Thread Thomas Holder

Hi Masataka,

this is really a weird problem. I have none of CentOS, gcc45 or 
python2.4 so can't really simulate any of your setup. But from the 
message I would say it's related to the C preprocessor rather than the 
compiler or python itself. Also, a google search pointed me to this 
messages:

http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg05501.html

http://archives.neohapsis.com/archives/linux/immunix/2004-q1/0011.html

The fact that it says

 macro fprintf

suggests that fprintf has been replaced by a preprocessor macro, which 
may interfere with the macro that PyMOL defines in this case I guess.

You do compile with -D_FORTIFY_SOURCE=2, could you remove that? If it 
does not help, check if you have FormatGuard installed.

Cheers,
   Thomas

grantaka36 wrote, On 12/05/11 02:50:
 Hi, Marius, Troels and David,
 
 I appreciate very much for guiding, tried in three ways but no success
 currently.
 
 - I also think some difference on distributions (CentOS 5 here,) trapped at
 function 'IsosurfGetRange'
 Does anyone have information to workaround?
 - Do you think if any dependency on Python version (2.4.3 here)?
 
 Attached '20111205_script_and_error.zip' is for information sharing:
 - 'install_pymol.sh' : followed by below, some package name modified for 
 CentOS
 http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_with_MPEG_support
 - 'install_pymol_sh_error.txt'
 layer0/Isosurf.c:2197:1: error: unterminated argument list invoking macro 
 fprintf
 layer0/Isosurf.c: In function 'IsosurfGetRange':
 
 - 'install_pymol_gcc45.sh' - aiming to use default installed gcc4.5
 instead of 4.4
 - 'install_pymol_gcc45_sh_error.txt'
 layer0/Isosurf.c: In function 'IsosurfGetRange':
 layer0/Isosurf.c:2197:0: error: unterminated argument list invoking macro 
 fprintf
 
 - 'compile_pymol.sh' : again by initial trying
 http://www.pymolwiki.org/index.php/Linux_Install#Install_from_source
 - 'compile_pymol_sh_error.txt'
 layer0/Isosurf.c: In function 'IsosurfGetRange':
 layer0/Isosurf.c:2197:0: error: unterminated argument list invoking macro 
 fprintf
 
 
 Regards,
 Masataka
 
 
 2011/12/3 David Hall li...@cowsandmilk.net:
 the builds on 
 https://build.opensuse.org/package/show?package=pymolproject=devel%3Alanguages%3Apython
 for opensuse 11.3 and 11.4 use gcc4.5 successfully.  I blame ubuntu or
 linux mint.

 -David

 On Dec 2, 2011, at 10:21 AM, Marius Retegan marius.s.rete...@gmail.com 
 wrote:

 Could you please specified what exactly did the gcc 4.5 broke in Pymol?
 Maybe this is not the case for every linux distribution.

 Cheers,
 Marius

 2011/12/2 Troels Emtekær Linnet tlin...@gmail.com:
 Try Following this script.

 http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_with_MPEG_support

 Please report if you are successful.
 It would be interesting to see how it works on CentOS

 /T



 2011/12/2 grantaka36 grantak...@gmail.com
 Referring the following, I'm trying to install PyMOL 1.4.1 with
 attached 'compile_pymol.sh', but no success. Would you please help to
 finish installation, or give me some advices? If information
 inadequate, please contact me.

 http://www.pymolwiki.org/index.php/Linux_Install
 - Requirements
 - Get latest Source from SVN
 - Compile and install
 - Problems - gcc-4.5 is broken for pymol install, use gcc-4.4
 -- My distribution has gcc4.5, so installed /usr/bin/gcc44,
 /usr/bin/g++44.

 Attached 'install_error.txt' gathers some information:
 - Original module files are in $HOME/install_module/pymol-archive
 - Intends to install in $HOME/pymol-svn
 - Original log has some Japanese messages so I added /* means ... */

 Regards,
 Masataka

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

--
All the data continuously generated in your IT infrastructure 
contains a definitive record of customers, application performance, 
security threats, fraudulent activity, and more. Splunk takes this 
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
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Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

2011-12-05 Thread Andreas Förster

Dear Masataka,

a few months ago, I upgraded most of our computers from RHEL 5.x to 6.1. 
  If version 6 of CentOS (free RHEL clone) is out, I would highly 
recommend, no I would urge you, to upgrade as well.  RHEL and CentOS are 
rock-solid operating systems, but their libraries and dependencies show 
their age.


Andreas


On 05/12/2011 1:50, grantaka36 wrote:
 Hi, Marius, Troels and David,

 I appreciate very much for guiding, tried in three ways but no success
 currently.

 - I also think some difference on distributions (CentOS 5 here,) trapped at
 function 'IsosurfGetRange'
 Does anyone have information to workaround?
 - Do you think if any dependency on Python version (2.4.3 here)?

 Attached '20111205_script_and_error.zip' is for information sharing:
 - 'install_pymol.sh' : followed by below, some package name modified for 
 CentOS
 http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_with_MPEG_support
 - 'install_pymol_sh_error.txt'
 layer0/Isosurf.c:2197:1: error: unterminated argument list invoking macro 
 fprintf
 layer0/Isosurf.c: In function 'IsosurfGetRange':

 - 'install_pymol_gcc45.sh' - aiming to use default installed gcc4.5
 instead of 4.4
 - 'install_pymol_gcc45_sh_error.txt'
 layer0/Isosurf.c: In function 'IsosurfGetRange':
 layer0/Isosurf.c:2197:0: error: unterminated argument list invoking macro 
 fprintf

 - 'compile_pymol.sh' : again by initial trying
 http://www.pymolwiki.org/index.php/Linux_Install#Install_from_source
 - 'compile_pymol_sh_error.txt'
 layer0/Isosurf.c: In function 'IsosurfGetRange':
 layer0/Isosurf.c:2197:0: error: unterminated argument list invoking macro 
 fprintf


 Regards,
 Masataka


-- 
 Andreas Förster, Research Associate
 Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
 http://www.msf.bio.ic.ac.uk

--
All the data continuously generated in your IT infrastructure 
contains a definitive record of customers, application performance, 
security threats, fraudulent activity, and more. Splunk takes this 
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
___
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

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

2011-12-04 Thread zjxu

Dear Masataka,

Will you try update python 2.4.3 to python 2.6 or later?
Pymol 1.4.1 works well on my centos5.4.
In my case, I both have python 2.7.1 and pytnon 2.4 in the system, and 
use python 2.7.1 to compile pymol.
In addition, the gcc version is 4.1.2.

Hope it helps,

Zhijian Xu


grantaka36 wrote:
 Hi, Marius, Troels and David,

 I appreciate very much for guiding, tried in three ways but no success
 currently.

 - I also think some difference on distributions (CentOS 5 here,) trapped at
   
 function 'IsosurfGetRange'
 
 Does anyone have information to workaround?
 - Do you think if any dependency on Python version (2.4.3 here)?

 Attached '20111205_script_and_error.zip' is for information sharing:
 - 'install_pymol.sh' : followed by below, some package name modified for 
 CentOS
 http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_with_MPEG_support
 - 'install_pymol_sh_error.txt'
   
 layer0/Isosurf.c:2197:1: error: unterminated argument list invoking macro 
 fprintf
 layer0/Isosurf.c: In function 'IsosurfGetRange':
 

 - 'install_pymol_gcc45.sh' - aiming to use default installed gcc4.5
 instead of 4.4
 - 'install_pymol_gcc45_sh_error.txt'
   
 layer0/Isosurf.c: In function 'IsosurfGetRange':
 layer0/Isosurf.c:2197:0: error: unterminated argument list invoking macro 
 fprintf
 

 - 'compile_pymol.sh' : again by initial trying
 http://www.pymolwiki.org/index.php/Linux_Install#Install_from_source
 - 'compile_pymol_sh_error.txt'
   
 layer0/Isosurf.c: In function 'IsosurfGetRange':
 layer0/Isosurf.c:2197:0: error: unterminated argument list invoking macro 
 fprintf
 


 Regards,
 Masataka


 2011/12/3 David Hall li...@cowsandmilk.net:
   
 the builds on 
 https://build.opensuse.org/package/show?package=pymolproject=devel%3Alanguages%3Apython
 for opensuse 11.3 and 11.4 use gcc4.5 successfully.  I blame ubuntu or
 linux mint.

 -David

 On Dec 2, 2011, at 10:21 AM, Marius Retegan marius.s.rete...@gmail.com 
 wrote:

 
 Could you please specified what exactly did the gcc 4.5 broke in Pymol?
 Maybe this is not the case for every linux distribution.

 Cheers,
 Marius

 2011/12/2 Troels Emtekær Linnet tlin...@gmail.com:
   
 Try Following this script.

 http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_with_MPEG_support

 Please report if you are successful.
 It would be interesting to see how it works on CentOS

 /T



 2011/12/2 grantaka36 grantak...@gmail.com
 
 Referring the following, I'm trying to install PyMOL 1.4.1 with
 attached 'compile_pymol.sh', but no success. Would you please help to
 finish installation, or give me some advices? If information
 inadequate, please contact me.

 http://www.pymolwiki.org/index.php/Linux_Install
 - Requirements
 - Get latest Source from SVN
 - Compile and install
 - Problems - gcc-4.5 is broken for pymol install, use gcc-4.4
 -- My distribution has gcc4.5, so installed /usr/bin/gcc44,
 /usr/bin/g++44.

 Attached 'install_error.txt' gathers some information:
 - Original module files are in $HOME/install_module/pymol-archive
 - Intends to install in $HOME/pymol-svn
 - Original log has some Japanese messages so I added /* means ... */

 Regards,
 Masataka


 --
 All the data continuously generated in your IT infrastructure
 contains a definitive record of customers, application performance,
 security threats, fraudulent activity, and more. Splunk takes this
 data and makes sense of it. IT sense. And common sense.
 http://p.sf.net/sfu/splunk-novd2d
 ___
 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
   

 --
 All the data continuously generated in your IT infrastructure
 contains a definitive record of customers, application performance,
 security threats, fraudulent activity, and more. Splunk takes this
 data and makes sense of it. IT sense. And common sense.
 http://p.sf.net/sfu/splunk-novd2d
 ___
 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
 
 --
 All the data continuously generated in your IT infrastructure
 contains a definitive record of customers, application performance,
 security threats, fraudulent activity, and more. Splunk takes this
 data and makes sense of it. IT sense. And common sense.
 http://p.sf.net/sfu/splunk-novd2d
 ___
 PyMOL-users mailing list

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

2011-12-02 Thread Marius Retegan

Hello,

The latest revision 3971 compiles without problems with gcc 4.5.1 on Fedora 14.
I usually install all the dependencies with yum.
My suggestion would be to try compiling with gcc4.5.

Marius

On Fri, Dec 2, 2011 at 8:19 AM, grantaka36 grantak...@gmail.com wrote:
 Referring the following, I'm trying to install PyMOL 1.4.1 with
 attached 'compile_pymol.sh', but no success. Would you please help to
 finish installation, or give me some advices? If information
 inadequate, please contact me.

 http://www.pymolwiki.org/index.php/Linux_Install
 - Requirements
 - Get latest Source from SVN
 - Compile and install
 - Problems - gcc-4.5 is broken for pymol install, use gcc-4.4
 -- My distribution has gcc4.5, so installed /usr/bin/gcc44, /usr/bin/g++44.

 Attached 'install_error.txt' gathers some information:
 - Original module files are in $HOME/install_module/pymol-archive
 - Intends to install in $HOME/pymol-svn
 - Original log has some Japanese messages so I added /* means ... */

 Regards,
 Masataka

 --
 All the data continuously generated in your IT infrastructure
 contains a definitive record of customers, application performance,
 security threats, fraudulent activity, and more. Splunk takes this
 data and makes sense of it. IT sense. And common sense.
 http://p.sf.net/sfu/splunk-novd2d
 ___
 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

--
All the data continuously generated in your IT infrastructure 
contains a definitive record of customers, application performance, 
security threats, fraudulent activity, and more. Splunk takes this 
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
___
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

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

2011-12-02 Thread Troels Emtekær Linnet

Try Following this script.

http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_with_MPEG_support

Please report if you are successful.
It would be interesting to see how it works on CentOS

2011/12/2 grantaka36 grantak...@gmail.com

Referring the following, I'm trying to install PyMOL 1.4.1 with
attached 'compile_pymol.sh', but no success. Would you please help to
finish installation, or give me some advices? If information
inadequate, please contact me.

http://www.pymolwiki.org/index.php/Linux_Install
- Requirements
- Get latest Source from SVN
- Compile and install
- Problems - gcc-4.5 is broken for pymol install, use gcc-4.4
-- My distribution has gcc4.5, so installed /usr/bin/gcc44, /usr/bin/g++44.

Attached 'install_error.txt' gathers some information:
- Original module files are in $HOME/install_module/pymol-archive
- Intends to install in $HOME/pymol-svn
- Original log has some Japanese messages so I added /* means ... */

Regards,
Masataka

--
All the data continuously generated in your IT infrastructure
contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
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All the data continuously generated in your IT infrastructure
contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d___
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Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

2011-12-02 Thread Marius Retegan

Could you please specified what exactly did the gcc 4.5 broke in Pymol?
Maybe this is not the case for every linux distribution.

Cheers,
Marius

2011/12/2 Troels Emtekær Linnet tlin...@gmail.com:
Try Following this script.

http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_with_MPEG_support

Please report if you are successful.
It would be interesting to see how it works on CentOS

2011/12/2 grantaka36 grantak...@gmail.com

Regards,
Masataka

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

2011-12-02 Thread Troels Emtekær Linnet

Hi Marius.

The last test I had on a Ubuntu/Mint box (1 month ago), it would not
compile with gcc 4.5.
So, it is necessary to change to gcc 4.4
I have made a script that auto compile on Ubuntu/Mint.
I have not checked the last release with hcc 4.5

I have not tried CentOS.
It would be interesting to have a compile script, for RPM package system.
I do not know if gcc 4.5 works on CentOS.

Best
Troels

2011/12/2 Marius Retegan marius.s.rete...@gmail.com

Could you please specified what exactly did the gcc 4.5 broke in Pymol?
Maybe this is not the case for every linux distribution.

Cheers,
Marius

2011/12/2 Troels Emtekær Linnet tlin...@gmail.com:
Try Following this script.

http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_with_MPEG_support

Please report if you are successful.
It would be interesting to see how it works on CentOS

2011/12/2 grantaka36 grantak...@gmail.com

Regards,
Masataka

--
All the data continuously generated in your IT infrastructure
contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

2011-12-02 Thread David Hall

the builds on
https://build.opensuse.org/package/show?package=pymolproject=devel%3Alanguages%3Apython
for opensuse 11.3 and 11.4 use gcc4.5 successfully. I blame ubuntu or
linux mint.

-David

On Dec 2, 2011, at 10:21 AM, Marius Retegan marius.s.rete...@gmail.com wrote:

Could you please specified what exactly did the gcc 4.5 broke in Pymol?
Maybe this is not the case for every linux distribution.

Cheers,
Marius

2011/12/2 Troels Emtekær Linnet tlin...@gmail.com:
Try Following this script.

http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_with_MPEG_support

Please report if you are successful.
It would be interesting to see how it works on CentOS

2011/12/2 grantaka36 grantak...@gmail.com

Regards,
Masataka

[PyMOL] Installation PyMOL failure in Linux (CentOS)

2011-12-01 Thread grantaka36

Referring the following, I'm trying to install PyMOL 1.4.1 with
attached 'compile_pymol.sh', but no success. Would you please help to
finish installation, or give me some advices? If information
inadequate, please contact me.

http://www.pymolwiki.org/index.php/Linux_Install
- Requirements
- Get latest Source from SVN
- Compile and install
- Problems - gcc-4.5 is broken for pymol install, use gcc-4.4
-- My distribution has gcc4.5, so installed /usr/bin/gcc44, /usr/bin/g++44.

Attached 'install_error.txt' gathers some information:
- Original module files are in $HOME/install_module/pymol-archive
- Intends to install in $HOME/pymol-svn
- Original log has some Japanese messages so I added /* means ... */

Regards,
Masataka
# 
--
[user01@rain02 etc]$ cat /etc/issue
CentOS release 5.5 (Final)
Kernel \r on an \m

# 
--
[user01@rain02 etc]$ python -V
Python 2.4.3
[user01@rain02 etc]$

# 
--
[user01@rain02 pymol-archive]$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc/x86_64-unknown-linux-gnu/4.5.1/lto-wrapper
Target: x86_64-unknown-linux-gnu
/* means config option */: ./configure -disable-multilib 
--with-gmp=/usr/local --with-mpfr=/usr/local --with-mpc=/usr/local
/* means thread model */: posix
gcc version 4.5.1 (GCC)

# 
--
[user01@rain02 pymol-archive]$ which gcc44
/usr/bin/gcc44
[user01@rain02 pymol-archive]$ which g++44
/usr/bin/g++44
[user01@rain02 pymol-archive]$ export CC=/usr/bin/gcc44
[user01@rain02 pymol-archive]$ echo $CC
/usr/bin/gcc44
[user01@rain02 pymol-archive]$ ./compile_pymol.sh
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
/usr/bin/gcc44 -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall 
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
--param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fPIC 
-D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG 
-D_PYMOL_OPENGL_SHADERS -DNO_MMLIBS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 
-Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Imodules/cealign/src 
-Imodules/cealign/src/tnt -I/usr/include/python2.4 -c layer0/Isosurf.c -o 
build/temp.linux-x86_64-2.4/layer0/Isosurf.o -ffast-math -funroll-loops -O3
layer0/Isosurf.c:2197:1: error: I[³êÄ¢È¢øXgª}N fprintf 
ðN®µæ¤ÆµÜµ½ /* means unterminated argument list invoking macro 
\fprintf\ */
layer0/Isosurf.c: In function eIsosurfGetRangef:
layer0/Isosurf.c:765: x: /* means warning */ statement with no effect
layer0/Isosurf.c:765: error: expected e;f at end of input
layer0/Isosurf.c:765: error: expected declaration or statement at end of input
layer0/Isosurf.c:765: error: expected declaration or statement at end of input
layer0/Isosurf.c:765: error: expected declaration or statement at end of input
layer0/Isosurf.c:764: x: unused variable eclampedf
layer0/Isosurf.c:763: x: unused variable ebf
layer0/Isosurf.c:763: x: unused variable eaf
layer0/Isosurf.c:762: x: unused variable eimixf
layer0/Isosurf.c:762: x: unused variable emixf
layer0/Isosurf.c:761: x: unused variable eimxf
layer0/Isosurf.c:761: x: unused variable eimnf
layer0/Isosurf.c:760: x: unused variable ermxf
layer0/Isosurf.c:760: x: unused variable ermnf
error: command '/usr/bin/gcc44' failed with exit status 1
[user01@rain02 pymol-archive]$



compile_pymol.sh
Description: Bourne shell script
--
All the data continuously generated in your IT infrastructure 
contains a definitive record of customers, application performance, 
security threats, fraudulent activity, and more. Splunk takes this 
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d___
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

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

[PyMOL] Installation PyMOL failure in Linux (CentOS)

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