Re: [ccp4bb] Newbie Installation Question- Solved
I can launch the program after installing the newest package from the Website Thank you all, yuri On Mon, 1 Aug 2011 17:01:47 +, ronan.kee...@stfc.ac.uk wrote: > Dear Yuri, > > Are you still encountering problems with this? I've made the changes to the CCP4 download site so that the path to the tcltk distribution is set correctly on installation. You might want to download the latest version from our website again if you are still having problems. > > Let me know if you need help. > > Best wishes, > > Ronan > > Ronan Keegan > > CCP4 Group > > FROM: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] ON BEHALF OF Yuri > SENT: 30 July 2011 01:02 > TO: ccp4bb > SUBJECT: Re: [ccp4bb] Newbie Installation Question > > I downloaded the package for RHEL5. My default shell is sh. But I can change environments. I have progrmas that I must run in tcsh. > > I tried sourcing sh and csh setups. With the csh setup, after I changed the PATH in the ccp4.setup file (originally set to usr/local/bin), I type ccp4 and I get no error. I am a bit at loss > > with the sh setup I tried sourcing and I get a "command not found" message, which leads me to think I am not succeding in sourcing it. > > Someone mentioned something about some files are not readable... > > I tried running the executables in the /bin directory but nothing happens... > > Thank you > > On Fri, 29 Jul 2011 13:53:49 -0700, Iain Kerr wrote: > >> What is the output when you try to launch ccp4i ? Are there any error messages ? Problems with Tcl/Tk will usually return an error about not being able to locate a specific library. >> >> Can you launch the programs independent of the GUI ? eg. if you go to where the executables are (CCP4/ccp4-6.2.0/bin) >> >> > ./mtzdump >> >> You should see some output giving the program version etc. and a list of keyword options. If so, the installation is probably OK and as Ed suggested it could be an environment problem. Why don't you outline the specific steps you've taken so far during installation and environment set up - what shell are you using ? did you download the source code or binaries ? what Tcl/Tk version are you using and where did you get it from ? >> >> I can help with this, off the board and then if we find a solution you can post it on the BB. >> >> Iain >> >> On 7/29/2011 12:37 PM, Yuri wrote: >> >> I tried that too ... no success >> >> On Fri, 29 Jul 2011 15:28:58 -0400, Ed Pozharski wrote: >> >> On Fri, 2011-07-29 at 20:08 +0100, Yuri wrote: >> >> Dear all, >> I have just downloaded and installed the ccp4-6.2.0. >> It says all I should do next is source the /setup-scripts/csh/ccp4.setup file... I have done that, but I cannot launch the program... >> Any help is welcome...(it is probably something really stupid on my part...) >> Best, >> >> It is most likely that your default shell is bash and you are trying to >> source tsch script, which naturally fails. >> Try /setup-scripts/sh/ccp4.setup instead. > > -- > > Yuri Pompeu -- Yuri Pompeu
Re: [ccp4bb] Newbie Installation Question
There is another potential problem in the ccp4.setup-sh file: the lines if test "LD_LIBRARY_PATH"; then and if test "DYLD_LIBRARY_PATH"; then (which always evaluate to true) should be if test "$LD_LIBRARY_PATH"; then and if test "$DYLD_LIBRARY_PATH"; then Otherwise you end up with LD_LIBRARY_PATH settings that could contain a dangling "...:" - not sure if that could mess up your environment? Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
Re: [ccp4bb] Newbie Installation Question
On 07/30/11 04:05, Weiergräber, Oliver H. wrote: I also observed the tcltk path problem... I am not sure that it is the tcltk path he's talking about, it could be the execution path. I think a look at the ccp4.setup file is needed to figure out what went wrong. From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Yuri [yuri.pom...@ufl.edu] Sent: Saturday, July 30, 2011 2:02 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Newbie Installation Question I downloaded the package for RHEL5. My default shell is sh. But I can change environments. I have progrmas that I must run in tcsh. I tried sourcing sh and csh setups. With the csh setup, after I changed the PATH in the ccp4.setup file (originally set to usr/local/bin), I type ccp4 and I get no error. I am a bit at loss with the sh setup I tried sourcing and I get a "command not found" message, which leads me to think I am not succeding in sourcing it. Someone mentioned something about some files are not readable... I tried running the executables in the /bin directory but nothing happens... Thank you On Fri, 29 Jul 2011 13:53:49 -0700, Iain Kerr wrote: What is the output when you try to launch ccp4i ? Are there any error messages ? Problems with Tcl/Tk will usually return an error about not being able to locate a specific library. Can you launch the programs independent of the GUI ? eg. if you go to where the executables are (CCP4/ccp4-6.2.0/bin) ./mtzdump You should see some output giving the program version etc. and a list of keyword options. If so, the installation is probably OK and as Ed suggested it could be an environment problem. Why don't you outline the specific steps you've taken so far during installation and environment set up - what shell are you using ? did you download the source code or binaries ? what Tcl/Tk version are you using and where did you get it from ? I can help with this, off the board and then if we find a solution you can post it on the BB. Iain On 7/29/2011 12:37 PM, Yuri wrote: I tried that too ... no success On Fri, 29 Jul 2011 15:28:58 -0400, Ed Pozharski wrote: On Fri, 2011-07-29 at 20:08 +0100, Yuri wrote: Dear all, I have just downloaded and installed the ccp4-6.2.0. It says all I should do next is source the /setup-scripts/csh/ccp4.setup file... I have done that, but I cannot launch the program... Any help is welcome...(it is probably something really stupid on my part...) Best, It is most likely that your default shell is bash and you are trying to source tsch script, which naturally fails. Try /setup-scripts/sh/ccp4.setup instead. -- Yuri Pompeu Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Newbie Installation Question
Quoting you: "I type ccp4 and I get no error", what happens if you type "ccp4i" (followed by carriage return) ? Yuri wrote: I downloaded the package for RHEL5. My default shell is sh. But I can change environments. I have progrmas that I must run in tcsh. I tried sourcing sh and csh setups. With the csh setup, after I changed the PATH in the ccp4.setup file (originally set to usr/local/bin), I type ccp4 and I get no error. I am a bit at loss with the sh setup I tried sourcing and I get a "command not found" message, which leads me to think I am not succeding in sourcing it. Someone mentioned something about some files are not readable... I tried running the executables in the /bin directory but nothing happens... Thank you On Fri, 29 Jul 2011 13:53:49 -0700, Iain Kerr wrote: What is the output when you try to launch ccp4i ? Are there any error messages ? Problems with Tcl/Tk will usually return an error about not being able to locate a specific library. Can you launch the programs independent of the GUI ? eg. if you go to where the executables are (CCP4/ccp4-6.2.0/bin) > ./mtzdump You should see some output giving the program version etc. and a list of keyword options. If so, the installation is probably OK and as Ed suggested it could be an environment problem. Why don't you outline the specific steps you've taken so far during installation and environment set up - what shell are you using ? did you download the source code or binaries ? what Tcl/Tk version are you using and where did you get it from ? I can help with this, off the board and then if we find a solution you can post it on the BB. Iain On 7/29/2011 12:37 PM, Yuri wrote: I tried that too ... no success On Fri, 29 Jul 2011 15:28:58 -0400, Ed Pozharski wrote: On Fri, 2011-07-29 at 20:08 +0100, Yuri wrote: Dear all, I have just downloaded and installed the ccp4-6.2.0. It says all I should do next is source the /setup-scripts/csh/ccp4.setup file... I have done that, but I cannot launch the program... Any help is welcome...(it is probably something really stupid on my part...) Best, It is most likely that your default shell is bash and you are trying to source tsch script, which naturally fails. Try /setup-scripts/sh/ccp4.setup instead. -- Yuri Pompeu
Re: [ccp4bb] Newbie Installation Question
I also observed the tcltk path problem when installing ccp4-6.2.0 on EL5 (CentOS 5 in this case). It happens if root is using tcsh instead of bash. Notably, it must be a new bug introduced with the *revised* 6.2.0 packages. The initial version (the one with the file permission problem) generated the correct path for tcltk binaries in ccp4.setup, as did all other ccp4 versions I installed in recent years on the same OS. After fixing this, however, I did not notice any further problems. Regards, Oliver From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Yuri [yuri.pom...@ufl.edu] Sent: Saturday, July 30, 2011 2:02 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Newbie Installation Question I downloaded the package for RHEL5. My default shell is sh. But I can change environments. I have progrmas that I must run in tcsh. I tried sourcing sh and csh setups. With the csh setup, after I changed the PATH in the ccp4.setup file (originally set to usr/local/bin), I type ccp4 and I get no error. I am a bit at loss with the sh setup I tried sourcing and I get a "command not found" message, which leads me to think I am not succeding in sourcing it. Someone mentioned something about some files are not readable... I tried running the executables in the /bin directory but nothing happens... Thank you On Fri, 29 Jul 2011 13:53:49 -0700, Iain Kerr wrote: What is the output when you try to launch ccp4i ? Are there any error messages ? Problems with Tcl/Tk will usually return an error about not being able to locate a specific library. Can you launch the programs independent of the GUI ? eg. if you go to where the executables are (CCP4/ccp4-6.2.0/bin) > ./mtzdump You should see some output giving the program version etc. and a list of keyword options. If so, the installation is probably OK and as Ed suggested it could be an environment problem. Why don't you outline the specific steps you've taken so far during installation and environment set up - what shell are you using ? did you download the source code or binaries ? what Tcl/Tk version are you using and where did you get it from ? I can help with this, off the board and then if we find a solution you can post it on the BB. Iain On 7/29/2011 12:37 PM, Yuri wrote: I tried that too ... no success On Fri, 29 Jul 2011 15:28:58 -0400, Ed Pozharski wrote: On Fri, 2011-07-29 at 20:08 +0100, Yuri wrote: Dear all, I have just downloaded and installed the ccp4-6.2.0. It says all I should do next is source the /setup-scripts/csh/ccp4.setup file... I have done that, but I cannot launch the program... Any help is welcome...(it is probably something really stupid on my part...) Best, It is most likely that your default shell is bash and you are trying to source tsch script, which naturally fails. Try /setup-scripts/sh/ccp4.setup instead. -- Yuri Pompeu Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt
Re: [ccp4bb] Newbie Installation Question
I downloaded the package for RHEL5. My default shell is sh. But I can change environments. I have progrmas that I must run in tcsh. I tried sourcing sh and csh setups. With the csh setup, after I changed the PATH in the ccp4.setup file (originally set to usr/local/bin), I type ccp4 and I get no error. I am a bit at loss with the sh setup I tried sourcing and I get a "command not found" message, which leads me to think I am not succeding in sourcing it. Someone mentioned something about some files are not readable... I tried running the executables in the /bin directory but nothing happens... Thank you On Fri, 29 Jul 2011 13:53:49 -0700, Iain Kerr wrote: > What is the output when you try to launch ccp4i ? Are there any error messages ? Problems with Tcl/Tk will usually return an error about not being able to locate a specific library. > > Can you launch the programs independent of the GUI ? eg. if you go to where the executables are (CCP4/ccp4-6.2.0/bin) > >> ./mtzdump > > You should see some output giving the program version etc. and a list of keyword options. If so, the installation is probably OK and as Ed suggested it could be an environment problem. Why don't you outline the specific steps you've taken so far during installation and environment set up - what shell are you using ? did you download the source code or binaries ? what Tcl/Tk version are you using and where did you get it from ? > > I can help with this, off the board and then if we find a solution you can post it on the BB. > > Iain > > On 7/29/2011 12:37 PM, Yuri wrote: > >> I tried that too ... no success >> >> On Fri, 29 Jul 2011 15:28:58 -0400, Ed Pozharski wrote: >> >>> On Fri, 2011-07-29 at 20:08 +0100, Yuri wrote: >>> Dear all, I have just downloaded and installed the ccp4-6.2.0. It says all I should do next is source the /setup-scripts/csh/ccp4.setup file... I have done that, but I cannot launch the program... Any help is welcome...(it is probably something really stupid on my part...) Best, >>> >>> It is most likely that your default shell is bash and you are trying to >>> source tsch script, which naturally fails. >>> Try /setup-scripts/sh/ccp4.setup instead. -- Yuri Pompeu
Re: [ccp4bb] Newbie Installation Question
yes, I noticed the default was TCLTK /usr/local/bin. I think it should be /usr/local/username.../tcltkplusplus/bin Even after editing this it doesnt launch. the command not found message is gone though On Fri, 29 Jul 2011 22:02:22 +0200, Wei-Chun Kao wrote: > Hi, > where did you install CCP4? from the path of your setup-script it seems like to be in the root (/) ? It looks like the problem I posted some days before but probably being buried in the middle of the other thread. Since it's more related to this topic so I paste it again, hoping that it can solve your question. > I recently found the problem that after finishing the installation of CCP4-6.2.0 on RHEL5, if the installation destination is not the default path (/usr/local/), the ccp4.setup for csh wouldn't take the customized TCLTK path correctly. No matter if I used sh or csh to install the CCP4 package. This would result in programs using wish failed to start (e.g., ccp4i) from csh. Perhaps it's also related to the issue in this thread. > > The way to solve this problem is to manually edit the ccp4.setup for csh and correct the TCLTK path. If you have no idea you can just copy the correct one in the ccp4.setup for sh. > Wei-Chun > > On Fri, Jul 29, 2011 at 9:08 PM, Yuri wrote: > >> Dear all, >> I have just downloaded and installed the ccp4-6.2.0. >> It says all I should do next is source the /setup-scripts/csh/ccp4.setup file... I have done that, but I cannot launch the program... >> Any help is welcome...(it is probably something really stupid on my part...) >> Best, > > -- > > Wei-Chun Kao, MSc. > TEL: +49-761-203-5277 > Institute for Biochemistry and Molecular Biology > Albert-Ludwigs-Universitaet Freiburg im Breisgau > Stefan-Meier-Str. 17 > D-79104 Freiburg im Breisgau > Germany -- Yuri Pompeu Links: -- [1] mailto:yuri.pom...@ufl.edu
Re: [ccp4bb] Newbie Installation Question
Hi, where did you install CCP4? from the path of your setup-script it seems like to be in the root (/) ? It looks like the problem I posted some days before but probably being buried in the middle of the other thread. Since it's more related to this topic so I paste it again, hoping that it can solve your question. I recently found the problem that after finishing the installation of CCP4-6.2.0 on RHEL5, if the installation destination is not the default path (/usr/local/), the ccp4.setup for csh wouldn't take the customized TCLTK path correctly. No matter if I used sh or csh to install the CCP4 package. This would result in programs using wish failed to start (e.g., ccp4i) from csh. Perhaps it's also related to the issue in this thread. The way to solve this problem is to manually edit the ccp4.setup for csh and correct the TCLTK path. If you have no idea you can just copy the correct one in the ccp4.setup for sh. Wei-Chun On Fri, Jul 29, 2011 at 9:08 PM, Yuri wrote: > Dear all, > I have just downloaded and installed the ccp4-6.2.0. > It says all I should do next is source the /setup-scripts/csh/ccp4.setup > file... I have done that, but I cannot launch the program... > Any help is welcome...(it is probably something really stupid on my > part...) > Best, > -- Wei-Chun Kao, MSc. TEL: +49-761-203-5277 Institute for Biochemistry and Molecular Biology Albert-Ludwigs-Universitaet Freiburg im Breisgau Stefan-Meier-Str. 17 D-79104 Freiburg im Breisgau Germany
Re: [ccp4bb] Newbie Installation Question
I tried that too ... no success On Fri, 29 Jul 2011 15:28:58 -0400, Ed Pozharski wrote: On Fri, 2011-07-29 at 20:08 +0100, Yuri wrote: Dear all, I have just downloaded and installed the ccp4-6.2.0. It says all I should do next is source the /setup-scripts/csh/ccp4.setup file... I have done that, but I cannot launch the program... Any help is welcome...(it is probably something really stupid on my part...) Best, It is most likely that your default shell is bash and you are trying to source tsch script, which naturally fails. Try /setup-scripts/sh/ccp4.setup instead. -- Yuri Pompeu
Re: [ccp4bb] Newbie Installation Question
On Fri, 2011-07-29 at 20:08 +0100, Yuri wrote: > Dear all, > I have just downloaded and installed the ccp4-6.2.0. > It says all I should do next is source the /setup-scripts/csh/ccp4.setup > file... I have done that, but I cannot launch the program... > Any help is welcome...(it is probably something really stupid on my part...) > Best, It is most likely that your default shell is bash and you are trying to source tsch script, which naturally fails. Try /setup-scripts/sh/ccp4.setup instead. -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs
Re: [ccp4bb] Newbie Installation Question
I've had problems too. Some of the files are non-readable, so you need to do a sudo chmod -R a+r * to make them readable. Also it looks like the libraries changed a bit (at least for ADP). Bernie On Fri, July 29, 2011 2:08 pm, Yuri wrote: > Dear all, > I have just downloaded and installed the ccp4-6.2.0. > It says all I should do next is source the /setup-scripts/csh/ccp4.setup > file... I have done that, but I cannot launch the program... > Any help is welcome...(it is probably something really stupid on my > part...) > Best, >
[ccp4bb] Newbie Installation Question
Dear all, I have just downloaded and installed the ccp4-6.2.0. It says all I should do next is source the /setup-scripts/csh/ccp4.setup file... I have done that, but I cannot launch the program... Any help is welcome...(it is probably something really stupid on my part...) Best,
