Re: [Fink-users] the problem with installing ccp4
Hi, Directory is not empty! /sw/bin/dpkg-lockwait --remove ccp4 ccp4-shlibs (Reading database ... 311403 files and directories currently installed.) Removing ccp4 ... dpkg - warning: while removing ccp4, directory `/sw/share/xtal/ccp4-6.2.0/ccp4i/etc/UNIX' not empty so not removed. dpkg - warning: while removing ccp4, directory `/sw/share/xtal/ccp4-6.2.0/ccp4i/etc' not empty so not removed. dpkg - warning: while removing ccp4, directory `/sw/share/xtal/ccp4-6.2.0/ccp4i' not empty so not removed. dpkg - warning: while removing ccp4, directory `/sw/share/xtal/ccp4-6.2.0' not empty so not removed. Removing ccp4-shlibs ... Is it right? fink remove -r ccp4 Thanks, Shih-Kai Chou On Wed, Jan 16, 2013 at 5:46 AM, Alexander Hansen alexanderk.han...@gmail.com wrote: That might be worth a try. The command is: fink remove ccp4 ccp4-dev ccp4-shlibs On 1/15/13 9:18 AM, Shih-Kai Chou wrote: Hi, Sorry, bad news : the same message as before. Do you think that removing ccp4, than reinstalling it would be better? ( I don not what is the command to do remove.) Thanks, Shih-Kai Chou On Tue, Jan 15, 2013 at 10:28 PM, Alexander Hansen alexanderk.han...@gmail.com mailto:alexanderk.han...@gmail.com wrote: Hmm... Perhaps try fink --no-build-as-nobody build cpp4? On 1/14/13 8:25 AM, Shih-Kai Chou wrote: Hi, drwxr-xr-x 16 fink-bld fink-bld 544 Jan 12 00:57 /sw/src/fink.build/ccp4-6.3.0-5/ccp4-6.3.0/lib/libccp4/data Thanks, Shih-Kai Chou On Mon, Jan 14, 2013 at 11:10 PM, Alexander Hansen alexanderk.han...@gmail.com mailto:alexanderk.han...@gmail.com mailto:alexanderk.han...@gmail.com mailto:alexanderk.han...@gmail.com wrote: Ok, so as I expected from the error message, font84.dat didn't get written, but everything looks normal otherwise. What do you get from ls -ld /sw/src/fink.build/ccp4-6.3.0-5/ccp4-6.3.0/lib/libccp4/data ? The only thing that I can think of that would cause this is a permissions problem. On 1/13/13 7:22 PM, Shih-Kai Chou wrote: Hi, I get : ( ls -l /sw/src/fink.build/ccp4-6.3.0-5/ccp4-6.3.0/lib/libccp4/data ) -rwxr-xr-x 1 fink-bld fink-bld1791 Mar 7 2012 README -rwxr-xr-x 1 fink-bld fink-bld 53152 Jan 8 2009 atomsf.lib -rwxr-xr-x 1 fink-bld fink-bld 51863 Jul 24 1996 atomsf_neutron.lib -rwxr-xr-x 1 fink-bld fink-bld 521160 May 19 1992 font84.ascii -rw-r--r-- 1 fink-bld fink-bld 0 Jan 4 18:29 font84.dat -rwxr-xr-x 1 fink-bld fink-bld 13624 Jan 4 18:29 fontpack -rwxr-xr-x 1 fink-bld fink-bld 518 May 12 2005 fontpack.f -rw-r--r-- 1 fink-bld fink-bld4272 Jan 4 17:42 fontpack.o -rw-r--r-- 1 fink-bld fink-bld 0 Jan 4 18:29 fort.10 -rwxr-xr-x 1 fink-bld fink-bld 323020 Mar 7 2012 syminfo.lib -rwxr-xr-x 1 fink-bld fink-bld 75406 Aug 5 2009 symop.lib Thanks, Shih-Kai Chou -- Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery and much more. Keep your Java skills current with LearnJavaNow - 200+ hours of step-by-step video tutorials by Java experts. SALE $49.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122612 ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] the problem with installing ccp4
Hmm... Perhaps try fink --no-build-as-nobody build cpp4? On 1/14/13 8:25 AM, Shih-Kai Chou wrote: Hi, drwxr-xr-x 16 fink-bld fink-bld 544 Jan 12 00:57 /sw/src/fink.build/ccp4-6.3.0-5/ccp4-6.3.0/lib/libccp4/data Thanks, Shih-Kai Chou On Mon, Jan 14, 2013 at 11:10 PM, Alexander Hansen alexanderk.han...@gmail.com mailto:alexanderk.han...@gmail.com wrote: Ok, so as I expected from the error message, font84.dat didn't get written, but everything looks normal otherwise. What do you get from ls -ld /sw/src/fink.build/ccp4-6.3.0-5/ccp4-6.3.0/lib/libccp4/data ? The only thing that I can think of that would cause this is a permissions problem. On 1/13/13 7:22 PM, Shih-Kai Chou wrote: Hi, I get : ( ls -l /sw/src/fink.build/ccp4-6.3.0-5/ccp4-6.3.0/lib/libccp4/data ) -rwxr-xr-x 1 fink-bld fink-bld1791 Mar 7 2012 README -rwxr-xr-x 1 fink-bld fink-bld 53152 Jan 8 2009 atomsf.lib -rwxr-xr-x 1 fink-bld fink-bld 51863 Jul 24 1996 atomsf_neutron.lib -rwxr-xr-x 1 fink-bld fink-bld 521160 May 19 1992 font84.ascii -rw-r--r-- 1 fink-bld fink-bld 0 Jan 4 18:29 font84.dat -rwxr-xr-x 1 fink-bld fink-bld 13624 Jan 4 18:29 fontpack -rwxr-xr-x 1 fink-bld fink-bld 518 May 12 2005 fontpack.f -rw-r--r-- 1 fink-bld fink-bld4272 Jan 4 17:42 fontpack.o -rw-r--r-- 1 fink-bld fink-bld 0 Jan 4 18:29 fort.10 -rwxr-xr-x 1 fink-bld fink-bld 323020 Mar 7 2012 syminfo.lib -rwxr-xr-x 1 fink-bld fink-bld 75406 Aug 5 2009 symop.lib Thanks, Shih-Kai Chou -- Master SQL Server Development, Administration, T-SQL, SSAS, SSIS, SSRS and more. Get SQL Server skills now (including 2012) with LearnDevNow - 200+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only - learn more at: http://p.sf.net/sfu/learnmore_122512 ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] the problem with installing ccp4
Hi, Sorry, bad news : the same message as before. Do you think that removing ccp4, than reinstalling it would be better? ( I don not what is the command to do remove.) Thanks, Shih-Kai Chou On Tue, Jan 15, 2013 at 10:28 PM, Alexander Hansen alexanderk.han...@gmail.com wrote: Hmm... Perhaps try fink --no-build-as-nobody build cpp4? On 1/14/13 8:25 AM, Shih-Kai Chou wrote: Hi, drwxr-xr-x 16 fink-bld fink-bld 544 Jan 12 00:57 /sw/src/fink.build/ccp4-6.3.0-5/ccp4-6.3.0/lib/libccp4/data Thanks, Shih-Kai Chou On Mon, Jan 14, 2013 at 11:10 PM, Alexander Hansen alexanderk.han...@gmail.com mailto:alexanderk.han...@gmail.com wrote: Ok, so as I expected from the error message, font84.dat didn't get written, but everything looks normal otherwise. What do you get from ls -ld /sw/src/fink.build/ccp4-6.3.0-5/ccp4-6.3.0/lib/libccp4/data ? The only thing that I can think of that would cause this is a permissions problem. On 1/13/13 7:22 PM, Shih-Kai Chou wrote: Hi, I get : ( ls -l /sw/src/fink.build/ccp4-6.3.0-5/ccp4-6.3.0/lib/libccp4/data ) -rwxr-xr-x 1 fink-bld fink-bld1791 Mar 7 2012 README -rwxr-xr-x 1 fink-bld fink-bld 53152 Jan 8 2009 atomsf.lib -rwxr-xr-x 1 fink-bld fink-bld 51863 Jul 24 1996 atomsf_neutron.lib -rwxr-xr-x 1 fink-bld fink-bld 521160 May 19 1992 font84.ascii -rw-r--r-- 1 fink-bld fink-bld 0 Jan 4 18:29 font84.dat -rwxr-xr-x 1 fink-bld fink-bld 13624 Jan 4 18:29 fontpack -rwxr-xr-x 1 fink-bld fink-bld 518 May 12 2005 fontpack.f -rw-r--r-- 1 fink-bld fink-bld4272 Jan 4 17:42 fontpack.o -rw-r--r-- 1 fink-bld fink-bld 0 Jan 4 18:29 fort.10 -rwxr-xr-x 1 fink-bld fink-bld 323020 Mar 7 2012 syminfo.lib -rwxr-xr-x 1 fink-bld fink-bld 75406 Aug 5 2009 symop.lib Thanks, Shih-Kai Chou -- Master SQL Server Development, Administration, T-SQL, SSAS, SSIS, SSRS and more. Get SQL Server skills now (including 2012) with LearnDevNow - 200+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only - learn more at: http://p.sf.net/sfu/learnmore_122512___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] the problem with installing ccp4
That might be worth a try. The command is: fink remove ccp4 ccp4-dev ccp4-shlibs On 1/15/13 9:18 AM, Shih-Kai Chou wrote: Hi, Sorry, bad news : the same message as before. Do you think that removing ccp4, than reinstalling it would be better? ( I don not what is the command to do remove.) Thanks, Shih-Kai Chou On Tue, Jan 15, 2013 at 10:28 PM, Alexander Hansen alexanderk.han...@gmail.com mailto:alexanderk.han...@gmail.com wrote: Hmm... Perhaps try fink --no-build-as-nobody build cpp4? On 1/14/13 8:25 AM, Shih-Kai Chou wrote: Hi, drwxr-xr-x 16 fink-bld fink-bld 544 Jan 12 00:57 /sw/src/fink.build/ccp4-6.3.0-5/ccp4-6.3.0/lib/libccp4/data Thanks, Shih-Kai Chou On Mon, Jan 14, 2013 at 11:10 PM, Alexander Hansen alexanderk.han...@gmail.com mailto:alexanderk.han...@gmail.com mailto:alexanderk.han...@gmail.com mailto:alexanderk.han...@gmail.com wrote: Ok, so as I expected from the error message, font84.dat didn't get written, but everything looks normal otherwise. What do you get from ls -ld /sw/src/fink.build/ccp4-6.3.0-5/ccp4-6.3.0/lib/libccp4/data ? The only thing that I can think of that would cause this is a permissions problem. On 1/13/13 7:22 PM, Shih-Kai Chou wrote: Hi, I get : ( ls -l /sw/src/fink.build/ccp4-6.3.0-5/ccp4-6.3.0/lib/libccp4/data ) -rwxr-xr-x 1 fink-bld fink-bld1791 Mar 7 2012 README -rwxr-xr-x 1 fink-bld fink-bld 53152 Jan 8 2009 atomsf.lib -rwxr-xr-x 1 fink-bld fink-bld 51863 Jul 24 1996 atomsf_neutron.lib -rwxr-xr-x 1 fink-bld fink-bld 521160 May 19 1992 font84.ascii -rw-r--r-- 1 fink-bld fink-bld 0 Jan 4 18:29 font84.dat -rwxr-xr-x 1 fink-bld fink-bld 13624 Jan 4 18:29 fontpack -rwxr-xr-x 1 fink-bld fink-bld 518 May 12 2005 fontpack.f -rw-r--r-- 1 fink-bld fink-bld4272 Jan 4 17:42 fontpack.o -rw-r--r-- 1 fink-bld fink-bld 0 Jan 4 18:29 fort.10 -rwxr-xr-x 1 fink-bld fink-bld 323020 Mar 7 2012 syminfo.lib -rwxr-xr-x 1 fink-bld fink-bld 75406 Aug 5 2009 symop.lib Thanks, Shih-Kai Chou -- Master SQL Server Development, Administration, T-SQL, SSAS, SSIS, SSRS and more. Get SQL Server skills now (including 2012) with LearnDevNow - 200+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only - learn more at: http://p.sf.net/sfu/learnmore_122512 ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] the problem with installing ccp4
Hi,
Thank you for your responding.
But (I'm sorry for that I'm not familiar with programing language)
I did not know how to do
and I am also not sure if I understand what you say.
If I
fink install libiconv,
It could fix my problem!?
I am confused which bit used by my machine, i386 or x86_64.
In the beginning, I install fink with 32-bit. But later, I change to 64-bit.
Thanks,
Shih-Kai Chou
On Mon, Jan 14, 2013 at 1:00 PM, Daniel Macks dma...@netspace.org wrote:
On Sun, 13 Jan 2013 20:28:59 -0500, Daniel Macks dma...@netspace.org
wrote:
On Sun, 13 Jan 2013 16:24:43 -0700, Alexander Hansen
alexanderk.han...@gmail.com wrote:
Putting this on the list, because this is not MY package.
On 1/13/13 11:31 AM, Shih-Kai Chou wrote:
So far, I think my problem is not fixed. (no one mail to me)
I didn't reproduce your problem, no.
I tried to realized it on my own way although I am not good at Linux
and
programming language.Because It says : cd data/ ( the path
is /sw/lib/ccp4-6.2.0//data ) (In your case, I think
it is ccp4-6.3.0 ?)
./fontpack
At line 12 ..I just cd there, and execute it (./fontpack)
to see what is information
it will give me!
//**//**
//**//**
//**//
At line 14 of file
/sw/src/fink.build/ccp4-6.2.0-**102/ccp4-6.2.0/lib/data/**fontpack.f
(unit =
11, file = 'font84.dat')
Fortran runtime error: Cannot write to file opened for READ
It _shouldn't_ say
/sw/src/fink.build/ccp4-6.2.**0-102/ccp4-6.2.0/lib/data/**
fontpack.f--apparently
this got set during the build and probably needs to be fixed.
However, this probably isn't relevant, since you're comparing files from
two different versions of the package. I don't know anything about this
package or its confusing build system, but I do see two places in
ccp4.info that do hard-code non-constant paths. line 298: perl -pi.bak
-e 's|/src/fink.build/ccp4-%v-%r|**/opt|g' bin/clipper-config
line 307: perl -pi.bak -e
's|/src/fink.build/ccp4-%v-%r/**ccp4-%v/lib|/lib/ccp4-%v|g'
lib/**/*.la
It is not valid to assume the path to the build-dir (the src/fink.build
part there). I assume those lines have the fink prefix first
(/sw/src/fink.build for example), so one should be using something
related to the %b token. If one is hacking .la files that are actually
generated by libtool (rather than a custom-written script that simulates
some features of it) and you're getting build-dir paths in it, the *actual*
problem is in the makefiles or use of libtool. Modern libtool knows the
difference between build dir and eventual runtime dir and especially
knows to use the latter for .la.
Couldn't even get that far. First, missing BuildDepends:libiconv-dev (no
big deal). Then 6K lines of linker errors (no, seriously!) because I'm on
10.6/i386 and the .info hardcodes /usr/bin/{gcc,g++} which use the x86_64
arch instead. Need to use just gcc and g++ because fink does some
behind-the-scenes magic to make the compiler use the right arch for how
the user has fink configured, whereas hardcoding uses whatever apple
decides is best this week.
dan
--
Daniel Macks
dma...@netspace.org
--
Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
MVPs and experts. SALE $99.99 this month only -- learn more at:
http://p.sf.net/sfu/learnmore_122412___
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Re: [Fink-users] the problem with installing ccp4
On 1/13/13 10:19 PM, Shih-Kai Chou wrote: Hi, Thank you for your responding. But (I'm sorry for that I'm not familiar with programing language) I did not know how to do and I am also not sure if I understand what you say. If I fink install libiconv, It could fix my problem!? No. I am confused which bit used by my machine, i386 or x86_64. In the beginning, I install fink with 32-bit. But later, I change to 64-bit. Quoting your initial output: Distribution version: selfupdate-rsync Wed Jan 9 23:24:23 2013, 10.6, x86_64 Thanks, Shih-Kai Chou Daniel was pointing out that there are other problems with the package, but nothing that you need to do yourself. -- Alexander Hansen, Ph.D. Fink User Liaison My package updates: http://finkakh.wordpress.com/ -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122412 ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] the problem with installing ccp4
Ok, so as I expected from the error message, font84.dat didn't get written, but everything looks normal otherwise. What do you get from ls -ld /sw/src/fink.build/ccp4-6.3.0-5/ccp4-6.3.0/lib/libccp4/data ? The only thing that I can think of that would cause this is a permissions problem. On 1/13/13 7:22 PM, Shih-Kai Chou wrote: Hi, I get : ( ls -l /sw/src/fink.build/ccp4-6.3.0-5/ccp4-6.3.0/lib/libccp4/data ) -rwxr-xr-x 1 fink-bld fink-bld1791 Mar 7 2012 README -rwxr-xr-x 1 fink-bld fink-bld 53152 Jan 8 2009 atomsf.lib -rwxr-xr-x 1 fink-bld fink-bld 51863 Jul 24 1996 atomsf_neutron.lib -rwxr-xr-x 1 fink-bld fink-bld 521160 May 19 1992 font84.ascii -rw-r--r-- 1 fink-bld fink-bld 0 Jan 4 18:29 font84.dat -rwxr-xr-x 1 fink-bld fink-bld 13624 Jan 4 18:29 fontpack -rwxr-xr-x 1 fink-bld fink-bld 518 May 12 2005 fontpack.f -rw-r--r-- 1 fink-bld fink-bld4272 Jan 4 17:42 fontpack.o -rw-r--r-- 1 fink-bld fink-bld 0 Jan 4 18:29 fort.10 -rwxr-xr-x 1 fink-bld fink-bld 323020 Mar 7 2012 syminfo.lib -rwxr-xr-x 1 fink-bld fink-bld 75406 Aug 5 2009 symop.lib Thanks, Shih-Kai Chou -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122412 ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] the problem with installing ccp4
Putting this on the list, because this is not MY package. On 1/13/13 11:31 AM, Shih-Kai Chou wrote: Hi, So far, I think my problem is not fixed. (no one mail to me) I didn't reproduce your problem, no. I tried to realized it on my own way although I am not good at Linux and programming language. Because It says : cd data/ ( the path is /sw/lib/ccp4-6.2.0//data ) (In your case, I think it is ccp4-6.3.0 ?) ./fontpack At line 12 .. I just cd there, and execute it (./fontpack) to see what is information it will give me! At line 14 of file /sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/lib/data/fontpack.f (unit = 11, file = 'font84.dat') Fortran runtime error: Cannot write to file opened for READ It _shouldn't_ say /sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/lib/data/fontpack.f--apparently this got set during the build and probably needs to be fixed. However, this probably isn't relevant, since you're comparing files from two different versions of the package. Very similar message but a little different! I gauss the difference comes from the different fontpack.f file, one is 6.2.0 and the other is 6.3.0. The error above looks like it's because you're trying to write files a directory where you don't have write permissions, as opposed to your reported error in ccp-6.3.0-5: ./fontpack At line 12 of file data/fontpack.f (unit = 10, file = 'fort.10') Fortran runtime error: End of file I find a strange thing : It says /sw/src/fink.build/ (I did not edit the file there!) Then, I cd /sw/src/fink.buid/ and ls ccp4-6.3.0-5root-ccp4-6.3.0-5 suitesparse-3.1.0-1 no ccp4-6.2.0-102 How about ls -al total 0 ... drwxr-xr-x4 fink-bld fink-bld136 Jan 12 00:26 ccp4-6.3.0-5 drwxr-xr-x4 fink-bld fink-bld136 Jan 12 00:42 root-ccp4-6.3.0-5 drwxr-xr-x3 root admin 102 Nov 13 2011 suitesparse-3.1.0-1 Do you have any idea? ccp4-6.2.0-102 was successfully built so its directories in /sw/src/fink.build were deleted. That's normal. If no, that is OK. Thanks, Shih-Kai Chou What do you get from ls -l /sw/src/fink.build/ccp4-6.3.0-5/ccp4-6.3.0/lib/libccp4/data/ ? -- Alexander Hansen, Ph.D. Fink User Liaison My package updates: http://finkakh.wordpress.com/ -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_123012 ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] the problem with installing ccp4
On Sun, 13 Jan 2013 16:24:43 -0700, Alexander Hansen alexanderk.han...@gmail.com wrote: Putting this on the list, because this is not MY package. On 1/13/13 11:31 AM, Shih-Kai Chou wrote: So far, I think my problem is not fixed. (no one mail to me) I didn't reproduce your problem, no. I tried to realized it on my own way although I am not good at Linux and programming language. Because It says : cd data/ ( the path is /sw/lib/ccp4-6.2.0//data ) (In your case, I think it is ccp4-6.3.0 ?) ./fontpack At line 12 .. I just cd there, and execute it (./fontpack) to see what is information it will give me! At line 14 of file /sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/lib/data/fontpack.f (unit = 11, file = 'font84.dat') Fortran runtime error: Cannot write to file opened for READ It _shouldn't_ say /sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/lib/data/fontpack.f--apparently this got set during the build and probably needs to be fixed. However, this probably isn't relevant, since you're comparing files from two different versions of the package. I don't know anything about this package or its confusing build system, but I do see two places in ccp4.info that do hard-code non-constant paths. line 298: perl -pi.bak -e 's|/src/fink.build/ccp4-%v-%r|/opt|g' bin/clipper-config line 307: perl -pi.bak -e 's|/src/fink.build/ccp4-%v-%r/ccp4-%v/lib|/lib/ccp4-%v|g' lib/**/*.la It is not valid to assume the path to the build-dir (the src/fink.build part there). I assume those lines have the fink prefix first (/sw/src/fink.build for example), so one should be using something related to the %b token. If one is hacking .la files that are actually generated by libtool (rather than a custom-written script that simulates some features of it) and you're getting build-dir paths in it, the *actual* problem is in the makefiles or use of libtool. Modern libtool knows the difference between build dir and eventual runtime dir and especially knows to use the latter for .la. dan -- Daniel Macks dma...@netspace.org -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122412 ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] the problem with installing ccp4
Hi, I get : ( ls -l /sw/src/fink.build/ccp4-6.3.0-5/ccp4-6.3.0/lib/libccp4/data ) -rwxr-xr-x 1 fink-bld fink-bld1791 Mar 7 2012 README -rwxr-xr-x 1 fink-bld fink-bld 53152 Jan 8 2009 atomsf.lib -rwxr-xr-x 1 fink-bld fink-bld 51863 Jul 24 1996 atomsf_neutron.lib -rwxr-xr-x 1 fink-bld fink-bld 521160 May 19 1992 font84.ascii -rw-r--r-- 1 fink-bld fink-bld 0 Jan 4 18:29 font84.dat -rwxr-xr-x 1 fink-bld fink-bld 13624 Jan 4 18:29 fontpack -rwxr-xr-x 1 fink-bld fink-bld 518 May 12 2005 fontpack.f -rw-r--r-- 1 fink-bld fink-bld4272 Jan 4 17:42 fontpack.o -rw-r--r-- 1 fink-bld fink-bld 0 Jan 4 18:29 fort.10 -rwxr-xr-x 1 fink-bld fink-bld 323020 Mar 7 2012 syminfo.lib -rwxr-xr-x 1 fink-bld fink-bld 75406 Aug 5 2009 symop.lib Thanks, Shih-Kai Chou On Mon, Jan 14, 2013 at 7:24 AM, Alexander Hansen alexanderk.han...@gmail.com wrote: Putting this on the list, because this is not MY package. On 1/13/13 11:31 AM, Shih-Kai Chou wrote: Hi, So far, I think my problem is not fixed. (no one mail to me) I didn't reproduce your problem, no. I tried to realized it on my own way although I am not good at Linux and programming language. Because It says : cd data/ ( the path is /sw/lib/ccp4-6.2.0//data ) (In your case, I think it is ccp4-6.3.0 ?) ./fontpack At line 12 .. I just cd there, and execute it (./fontpack) to see what is information it will give me! At line 14 of file /sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/lib/data/fontpack.f (unit = 11, file = 'font84.dat') Fortran runtime error: Cannot write to file opened for READ It _shouldn't_ say /sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/lib/data/fontpack.f--apparently this got set during the build and probably needs to be fixed. However, this probably isn't relevant, since you're comparing files from two different versions of the package. Very similar message but a little different! I gauss the difference comes from the different fontpack.f file, one is 6.2.0 and the other is 6.3.0. The error above looks like it's because you're trying to write files a directory where you don't have write permissions, as opposed to your reported error in ccp-6.3.0-5: ./fontpack At line 12 of file data/fontpack.f (unit = 10, file = 'fort.10') Fortran runtime error: End of file I find a strange thing : It says /sw/src/fink.build/ (I did not edit the file there!) Then, I cd /sw/src/fink.buid/ and ls ccp4-6.3.0-5root-ccp4-6.3.0-5 suitesparse-3.1.0-1 no ccp4-6.2.0-102 How about ls -al total 0 ... drwxr-xr-x4 fink-bld fink-bld136 Jan 12 00:26 ccp4-6.3.0-5 drwxr-xr-x4 fink-bld fink-bld136 Jan 12 00:42 root-ccp4-6.3.0-5 drwxr-xr-x3 root admin 102 Nov 13 2011 suitesparse-3.1.0-1 Do you have any idea? ccp4-6.2.0-102 was successfully built so its directories in /sw/src/fink.build were deleted. That's normal. If no, that is OK. Thanks, Shih-Kai Chou What do you get from ls -l /sw/src/fink.build/ccp4-6.3.0-5/ccp4-6.3.0/lib/libccp4/data/ ? -- Alexander Hansen, Ph.D. Fink User Liaison My package updates: http://finkakh.wordpress.com/ -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122412___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] the problem with installing ccp4
On Sun, 13 Jan 2013 20:28:59 -0500, Daniel Macks dma...@netspace.org wrote:
On Sun, 13 Jan 2013 16:24:43 -0700, Alexander Hansen
alexanderk.han...@gmail.com wrote:
Putting this on the list, because this is not MY package.
On 1/13/13 11:31 AM, Shih-Kai Chou wrote:
So far, I think my problem is not fixed. (no one mail to me)
I didn't reproduce your problem, no.
I tried to realized it on my own way although I am not good at Linux and
programming language.Because It says : cd data/ ( the
path is /sw/lib/ccp4-6.2.0//data ) (In your case, I think
it is ccp4-6.3.0 ?)
./fontpack
At line 12 ..I just cd there, and execute it
(./fontpack) to see what is information
it will give me!
At line 14 of file
/sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/lib/data/fontpack.f (unit =
11, file = 'font84.dat')
Fortran runtime error: Cannot write to file opened for READ
It _shouldn't_ say
/sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/lib/data/fontpack.f--apparently
this got set during the build and probably needs to be fixed.
However, this probably isn't relevant, since you're comparing files from
two different versions of the package. I don't know anything about
this package or its confusing build system, but I do see two places
in ccp4.info that do hard-code non-constant paths. line 298: perl
-pi.bak -e 's|/src/fink.build/ccp4-%v-%r|/opt|g' bin/clipper-config
line 307: perl -pi.bak -e
's|/src/fink.build/ccp4-%v-%r/ccp4-%v/lib|/lib/ccp4-%v|g' lib/**/*.la
It is not valid to assume the path to the build-dir (the
src/fink.build part there). I assume those lines have the fink
prefix first (/sw/src/fink.build for example), so one should be
using something related to the %b token. If one is hacking .la files
that are actually generated by libtool (rather than a custom-written
script that simulates some features of it) and you're getting
build-dir paths in it, the *actual* problem is in the makefiles or
use of libtool. Modern libtool knows the difference between build
dir and eventual runtime dir and especially knows to use the
latter for .la.
Couldn't even get that far. First, missing BuildDepends:libiconv-dev
(no big deal). Then 6K lines of linker errors (no, seriously!) because
I'm on 10.6/i386 and the .info hardcodes /usr/bin/{gcc,g++} which use
the x86_64 arch instead. Need to use just gcc and g++ because fink
does some behind-the-scenes magic to make the compiler use the right
arch for how the user has fink configured, whereas hardcoding uses
whatever apple decides is best this week.
dan
--
Daniel Macks
dma...@netspace.org
--
Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
MVPs and experts. SALE $99.99 this month only -- learn more at:
http://p.sf.net/sfu/learnmore_122412
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[Fink-users] the problem with installing ccp4
Hi, I use : fink selfupdate fink update-all for ccp4 : .. wall clock time: 4 minutes 9.43 seconds (249.43 seconds total) cd exe cp phaser $CCP4/bin/. cd $CCP4 # rapper manual install if [[ -x src/rapper/bin/rapper ]]; then cp src/rapper/bin/rapper $CCP4/bin/. cp src/rapper/lib/libcord.1.0.3.dylib $CCP4/lib/libcord.1.dylib cp src/rapper/lib/libgc.1.0.3.dylib $CCP4/lib/libgc.1.dylib cp src/rapper/lib/libxml2.2.dylib $CCP4/lib/libxml2.2.dylib /bin/rm -rf src/rapper/lib/*.dylib mkdir -p share/rapper cp src/rapper/LOOP/params.xml share/rapper/. cp -R src/rapper/data share/rapper/. fi * export DYLD_LIBRARY_PATH=$CLIB* * cd $CLIB/libccp4* * gfortran -m64 -fno-second-underscore -O2 -fno-second-underscore -L$CLIB -o data/fontpack data/fontpack.o -lccp4f -lccp4c* * cd data* * ./fontpack* *At line 12 of file data/fontpack.f (unit = 10, file = 'fort.10')* *Fortran runtime error: End of file* Backtrace for this error: + 0 libgfortran.3.dylib 0x0001029d1e93 _gfortrani_show_backtrace + 35 ### execution of /tmp/fink.2HF5a failed, exit code 2 ### execution of /tmp/fink.Ih6Jf failed, exit code 2 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-ccp4-6.3.0-5 (Reading database ... 309886 files and directories currently installed.) Removing fink-buildlock-ccp4-6.3.0-5 ... Reading buildlock packages... /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/gpp4-dev_1.2.0-31_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/ssm-dev_0.1-31_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/mmdb-dev_1.23.2-31_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/clipper_2.1-31_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/clipper-dev_2.1-31_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/languages/python_2.7.3-1_darwin-x86_64.deb Selecting previously deselected package gpp4-dev. (Reading database ... 309885 files and directories currently installed.) Unpacking gpp4-dev (from .../gpp4-dev_1.2.0-31_darwin-x86_64.deb) ... Selecting previously deselected package ssm-dev. Unpacking ssm-dev (from .../ssm-dev_0.1-31_darwin-x86_64.deb) ... Selecting previously deselected package mmdb-dev. Unpacking mmdb-dev (from .../mmdb-dev_1.23.2-31_darwin-x86_64.deb) ... Selecting previously deselected package clipper. Unpacking clipper (from .../clipper_2.1-31_darwin-x86_64.deb) ... Selecting previously deselected package clipper-dev. Unpacking clipper-dev (from .../clipper-dev_2.1-31_darwin-x86_64.deb) ... Selecting previously deselected package python. Unpacking python (from .../python_2.7.3-1_darwin-x86_64.deb) ... Setting up gpp4-dev (1.2.0-31) ... Clearing dependency_libs of .la files being installed Setting up ssm-dev (0.1-31) ... Clearing dependency_libs of .la files being installed Setting up mmdb-dev (1.23.2-31) ... Clearing dependency_libs of .la files being installed Setting up clipper (2.1-31) ... Setting up clipper-dev (2.1-31) ... Clearing dependency_libs of .la files being installed Setting up python (2.7.3-1) ... .. Package manager version: 0.34.4 Distribution version: selfupdate-rsync Wed Jan 9 23:24:23 2013, 10.6, x86_64 Trees: local/main stable/main stable/crypto unstable/main unstable/crypto Xcode.app: 3.2.6 Xcode command-line tools: 3.2.6 ccp4-6.3.0-5 is set to build with only one job. Thanks, Shih-Kai Chou -- Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery and much more. Keep your Java skills current with LearnJavaNow - 200+ hours of step-by-step video tutorials by Java experts. SALE $49.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122612 ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] the problem with installing ccp4
On 1/9/13 9:41 AM, Shih-Kai Chou wrote: Hi, I use : fink selfupdate fink update-all for ccp4 : .. wall clock time: 4 minutes 9.43 seconds (249.43 seconds total) cd exe cp phaser $CCP4/bin/. cd $CCP4 # rapper manual install if [[ -x src/rapper/bin/rapper ]]; then cp src/rapper/bin/rapper $CCP4/bin/. cp src/rapper/lib/libcord.1.0.3.dylib $CCP4/lib/libcord.1.dylib cp src/rapper/lib/libgc.1.0.3.dylib $CCP4/lib/libgc.1.dylib cp src/rapper/lib/libxml2.2.dylib $CCP4/lib/libxml2.2.dylib /bin/rm -rf src/rapper/lib/*.dylib mkdir -p share/rapper cp src/rapper/LOOP/params.xml share/rapper/. cp -R src/rapper/data share/rapper/. fi * export DYLD_LIBRARY_PATH=$CLIB* * cd $CLIB/libccp4* * gfortran -m64 -fno-second-underscore -O2 -fno-second-underscore -L$CLIB -o data/fontpack data/fontpack.o -lccp4f -lccp4c* * cd data* * ./fontpack* *At line 12 of file data/fontpack.f (unit = 10, file = 'fort.10')* *Fortran runtime error: End of file* Backtrace for this error: + 0 libgfortran.3.dylib 0x0001029d1e93 _gfortrani_show_backtrace + 35 snip .. Package manager version: 0.34.4 Distribution version: selfupdate-rsync Wed Jan 9 23:24:23 2013, 10.6, x86_64 Trees: local/main stable/main stable/crypto unstable/main unstable/crypto Xcode.app: 3.2.6 Xcode command-line tools: 3.2.6 ccp4-6.3.0-5 is set to build with only one job. Thanks, Shih-Kai Chou What do you get from the following command: which gfortran -- Alexander Hansen, Ph.D. Fink User Liaison My package updates: http://finkakh.wordpress.com/ -- Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery and much more. Keep your Java skills current with LearnJavaNow - 200+ hours of step-by-step video tutorials by Java experts. SALE $49.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122612 ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] the problem with installing ccp4
Hi, which gfortran /sw/bin/gfortran Actually, I have installed another fortran compiler! (I think that is the newest fortran compiler called gfortran, so I do it.) But I forgot which directory is the one I installed? It looks like the new gfortran I installed replaced the fink one! Thanks, Shih-Kai Chou On Thu, Jan 10, 2013 at 7:38 AM, Alexander Hansen alexanderk.han...@gmail.com wrote: On 1/9/13 9:41 AM, Shih-Kai Chou wrote: Hi, I use : fink selfupdate fink update-all for ccp4 : .. wall clock time: 4 minutes 9.43 seconds (249.43 seconds total) cd exe cp phaser $CCP4/bin/. cd $CCP4 # rapper manual install if [[ -x src/rapper/bin/rapper ]]; then cp src/rapper/bin/rapper $CCP4/bin/. cp src/rapper/lib/libcord.1.0.3.dylib $CCP4/lib/libcord.1.dylib cp src/rapper/lib/libgc.1.0.3.dylib $CCP4/lib/libgc.1.dylib cp src/rapper/lib/libxml2.2.dylib $CCP4/lib/libxml2.2.dylib /bin/rm -rf src/rapper/lib/*.dylib mkdir -p share/rapper cp src/rapper/LOOP/params.xml share/rapper/. cp -R src/rapper/data share/rapper/. fi * export DYLD_LIBRARY_PATH=$CLIB* * cd $CLIB/libccp4* * gfortran -m64 -fno-second-underscore -O2 -fno-second-underscore -L$CLIB -o data/fontpack data/fontpack.o -lccp4f -lccp4c* * cd data* * ./fontpack* *At line 12 of file data/fontpack.f (unit = 10, file = 'fort.10')* *Fortran runtime error: End of file* Backtrace for this error: + 0 libgfortran.3.dylib 0x0001029d1e93 _gfortrani_show_backtrace + 35 snip .. Package manager version: 0.34.4 Distribution version: selfupdate-rsync Wed Jan 9 23:24:23 2013, 10.6, x86_64 Trees: local/main stable/main stable/crypto unstable/main unstable/crypto Xcode.app: 3.2.6 Xcode command-line tools: 3.2.6 ccp4-6.3.0-5 is set to build with only one job. Thanks, Shih-Kai Chou What do you get from the following command: which gfortran -- Alexander Hansen, Ph.D. Fink User Liaison My package updates: http://finkakh.wordpress.com/ -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] the problem with installing ccp4
Normally fink's gfortran shouldn't get overwritten (unless you switch versions within Fink), but let's verify that with the following command: /sw/bin/gfortran --version Also, let's verify the PATH which is being used in your build: fink dumpinfo -ePATH ccp4 On 1/9/13 7:18 PM, Shih-Kai Chou wrote: Hi, which gfortran /sw/bin/gfortran Actually, I have installed another fortran compiler! (I think that is the newest fortran compiler called gfortran, so I do it.) But I forgot which directory is the one I installed? It looks like the new gfortran I installed replaced the fink one! Thanks, Shih-Kai Chou On Thu, Jan 10, 2013 at 7:38 AM, Alexander Hansen alexanderk.han...@gmail.com mailto:alexanderk.han...@gmail.com wrote: On 1/9/13 9:41 AM, Shih-Kai Chou wrote: Hi, I use : fink selfupdate fink update-all for ccp4 : .. wall clock time: 4 minutes 9.43 seconds (249.43 seconds total) cd exe cp phaser $CCP4/bin/. cd $CCP4 # rapper manual install if [[ -x src/rapper/bin/rapper ]]; then cp src/rapper/bin/rapper $CCP4/bin/. cp src/rapper/lib/libcord.1.0.3.dylib $CCP4/lib/libcord.1.dylib cp src/rapper/lib/libgc.1.0.3.dylib $CCP4/lib/libgc.1.dylib cp src/rapper/lib/libxml2.2.dylib $CCP4/lib/libxml2.2.dylib /bin/rm -rf src/rapper/lib/*.dylib mkdir -p share/rapper cp src/rapper/LOOP/params.xml share/rapper/. cp -R src/rapper/data share/rapper/. fi * export DYLD_LIBRARY_PATH=$CLIB* * cd $CLIB/libccp4* * gfortran -m64 -fno-second-underscore -O2 -fno-second-underscore -L$CLIB -o data/fontpack data/fontpack.o -lccp4f -lccp4c* * cd data* * ./fontpack* *At line 12 of file data/fontpack.f (unit = 10, file = 'fort.10')* *Fortran runtime error: End of file* Backtrace for this error: + 0 libgfortran.3.dylib 0x0001029d1e93 _gfortrani_show_backtrace + 35 snip .. Package manager version: 0.34.4 Distribution version: selfupdate-rsync Wed Jan 9 23:24:23 2013, 10.6, x86_64 Trees: local/main stable/main stable/crypto unstable/main unstable/crypto Xcode.app: 3.2.6 Xcode command-line tools: 3.2.6 ccp4-6.3.0-5 is set to build with only one job. Thanks, Shih-Kai Chou What do you get from the following command: which gfortran -- Alexander Hansen, Ph.D. Fink User Liaison My package updates: http://finkakh.wordpress.com/ -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712 ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] the problem with installing ccp4
Hi, Thank you. /sw/bin/gfortran --version GNU Fortran (GCC) 4.7.2 Copyright (C) 2012 Free Software Foundation, Inc. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING fink dumpinfo -ePATH ccp4 PATH=/sw/var/lib/fink/path-prefix-clang:/sw/bin:/sw/sbin:/bin:/usr/bin:/sbin:/usr/sbin:/usr/X11R6/bin:/sw/share/xtal/ccp4-6.2.0/etc:/sw/share/xtal/ccp4-6.2.0/bin:/sw/share/xtal/ccp4-6.2.0/ccp4i/bin:/sw/share/xtal/ccp4-6.2.0/share/dbccp4i/bin:/sw/share/xtal/ccp4-6.2.0/share/XIAROOT/xia2/Applications:/sw/share/tinker/bin Thanks, Shih-Kai Chou On Thu, Jan 10, 2013 at 10:34 AM, Alexander Hansen alexanderk.han...@gmail.com wrote: Normally fink's gfortran shouldn't get overwritten (unless you switch versions within Fink), but let's verify that with the following command: /sw/bin/gfortran --version Also, let's verify the PATH which is being used in your build: fink dumpinfo -ePATH ccp4 On 1/9/13 7:18 PM, Shih-Kai Chou wrote: Hi, which gfortran /sw/bin/gfortran Actually, I have installed another fortran compiler! (I think that is the newest fortran compiler called gfortran, so I do it.) But I forgot which directory is the one I installed? It looks like the new gfortran I installed replaced the fink one! Thanks, Shih-Kai Chou On Thu, Jan 10, 2013 at 7:38 AM, Alexander Hansen alexanderk.han...@gmail.com mailto:alexanderk.han...@gmail.com wrote: On 1/9/13 9:41 AM, Shih-Kai Chou wrote: Hi, I use : fink selfupdate fink update-all for ccp4 : .. wall clock time: 4 minutes 9.43 seconds (249.43 seconds total) cd exe cp phaser $CCP4/bin/. cd $CCP4 # rapper manual install if [[ -x src/rapper/bin/rapper ]]; then cp src/rapper/bin/rapper $CCP4/bin/. cp src/rapper/lib/libcord.1.0.3.dylib $CCP4/lib/libcord.1.dylib cp src/rapper/lib/libgc.1.0.3.dylib $CCP4/lib/libgc.1.dylib cp src/rapper/lib/libxml2.2.dylib $CCP4/lib/libxml2.2.dylib /bin/rm -rf src/rapper/lib/*.dylib mkdir -p share/rapper cp src/rapper/LOOP/params.xml share/rapper/. cp -R src/rapper/data share/rapper/. fi * export DYLD_LIBRARY_PATH=$CLIB* * cd $CLIB/libccp4* * gfortran -m64 -fno-second-underscore -O2 -fno-second-underscore -L$CLIB -o data/fontpack data/fontpack.o -lccp4f -lccp4c* * cd data* * ./fontpack* *At line 12 of file data/fontpack.f (unit = 10, file = 'fort.10')* *Fortran runtime error: End of file* Backtrace for this error: + 0 libgfortran.3.dylib 0x0001029d1e93 _gfortrani_show_backtrace + 35 snip .. Package manager version: 0.34.4 Distribution version: selfupdate-rsync Wed Jan 9 23:24:23 2013, 10.6, x86_64 Trees: local/main stable/main stable/crypto unstable/main unstable/crypto Xcode.app: 3.2.6 Xcode command-line tools: 3.2.6 ccp4-6.3.0-5 is set to build with only one job. Thanks, Shih-Kai Chou What do you get from the following command: which gfortran -- Alexander Hansen, Ph.D. Fink User Liaison My package updates: http://finkakh.wordpress.com/ -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] the problem with installing ccp4
Those look normal. I will check whether I can replicate your failure on a 10.6 setup with the same Xcode. On 1/9/13 7:40 PM, Shih-Kai Chou wrote: Hi, Thank you. /sw/bin/gfortran --version GNU Fortran (GCC) 4.7.2 Copyright (C) 2012 Free Software Foundation, Inc. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING fink dumpinfo -ePATH ccp4 PATH=/sw/var/lib/fink/path-prefix-clang:/sw/bin:/sw/sbin:/bin:/usr/bin:/sbin:/usr/sbin:/usr/X11R6/bin:/sw/share/xtal/ccp4-6.2.0/etc:/sw/share/xtal/ccp4-6.2.0/bin:/sw/share/xtal/ccp4-6.2.0/ccp4i/bin:/sw/share/xtal/ccp4-6.2.0/share/dbccp4i/bin:/sw/share/xtal/ccp4-6.2.0/share/XIAROOT/xia2/Applications:/sw/share/tinker/bin Thanks, Shih-Kai Chou On Thu, Jan 10, 2013 at 10:34 AM, Alexander Hansen alexanderk.han...@gmail.com mailto:alexanderk.han...@gmail.com wrote: Normally fink's gfortran shouldn't get overwritten (unless you switch versions within Fink), but let's verify that with the following command: /sw/bin/gfortran --version Also, let's verify the PATH which is being used in your build: fink dumpinfo -ePATH ccp4 On 1/9/13 7:18 PM, Shih-Kai Chou wrote: Hi, which gfortran /sw/bin/gfortran Actually, I have installed another fortran compiler! (I think that is the newest fortran compiler called gfortran, so I do it.) But I forgot which directory is the one I installed? It looks like the new gfortran I installed replaced the fink one! Thanks, Shih-Kai Chou On Thu, Jan 10, 2013 at 7:38 AM, Alexander Hansen alexanderk.han...@gmail.com mailto:alexanderk.han...@gmail.com mailto:alexanderk.han...@gmail.com mailto:alexanderk.han...@gmail.com wrote: On 1/9/13 9:41 AM, Shih-Kai Chou wrote: Hi, I use : fink selfupdate fink update-all for ccp4 : .. wall clock time: 4 minutes 9.43 seconds (249.43 seconds total) cd exe cp phaser $CCP4/bin/. cd $CCP4 # rapper manual install if [[ -x src/rapper/bin/rapper ]]; then cp src/rapper/bin/rapper $CCP4/bin/. cp src/rapper/lib/libcord.1.0.3.dylib $CCP4/lib/libcord.1.dylib cp src/rapper/lib/libgc.1.0.3.dylib $CCP4/lib/libgc.1.dylib cp src/rapper/lib/libxml2.2.dylib $CCP4/lib/libxml2.2.dylib /bin/rm -rf src/rapper/lib/*.dylib mkdir -p share/rapper cp src/rapper/LOOP/params.xml share/rapper/. cp -R src/rapper/data share/rapper/. fi * export DYLD_LIBRARY_PATH=$CLIB* * cd $CLIB/libccp4* * gfortran -m64 -fno-second-underscore -O2 -fno-second-underscore -L$CLIB -o data/fontpack data/fontpack.o -lccp4f -lccp4c* * cd data* * ./fontpack* *At line 12 of file data/fontpack.f (unit = 10, file = 'fort.10')* *Fortran runtime error: End of file* Backtrace for this error: + 0 libgfortran.3.dylib 0x0001029d1e93 _gfortrani_show_backtrace + 35 snip .. Package manager version: 0.34.4 Distribution version: selfupdate-rsync Wed Jan 9 23:24:23 2013, 10.6, x86_64 Trees: local/main stable/main stable/crypto unstable/main unstable/crypto Xcode.app: 3.2.6 Xcode command-line tools: 3.2.6 ccp4-6.3.0-5 is set to build with only one job. Thanks, Shih-Kai Chou What do you get from the following command: which gfortran -- Alexander Hansen, Ph.D. Fink User Liaison My package updates: http://finkakh.wordpress.com/ -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
