Re: [ccp4bb] ARP/wARP install on 6.2.0 RHEL 6?
Hello, I'm one of the ARP/wARP developers. Sorry for the slow reply - this is down to time differences. I'll install RHEL6 and try the ARP/wARP install and then report back. This may take a day or so though. My suspicion, based on previous bug reports, is that this problem is related to the TCL installation. The UnpackTaskArchive subroutine is part of the CCP4 API: http://www.ccp4.ac.uk/ccp4bin/viewcvs/*checkout*/ccp4/ccp4i/help/programmers/progdocs/install_utils.html#UnpackTaskArchive We've found that the behaviour of this call is dependent on TCL versions and that we have problems installing on 64bit fink (OSX) because the version of TCL. When I download and install CCP4 onto Ubuntu or SUSE I get a big package (1GB) that contains CCP4 and a compatible version of TCL. The CCP4 installation then adds the following calls to my .bashrc: source /home/saul/ccp4-linux-6.2.0/setup-scripts/sh/ccp4.setup source /home/saul/ccp4-linux-6.2.0/setup-scripts/sh/ccp4-others.setup The ccp4-others.setup pulls in the correct TCL environment. Is your installation of CCP4 similar? Thanks for reporting this problem - it will hopefully improve future versions of ARP/wARP. Saul Hazledine On Jul 28, 2011, at 2:31 AM, Jonathan Kay wrote: Hi all, I have a RHEL 6 x86_64 machine I recently installed CCP4-6.2.0 onto; the install went through fine, but when I went to install the ARP/wARP GUI (via System Administration - Install/uninstall task), I received the following error in the shell window I started ccp4i from: UnpackTaskArchive: uncompress failed to create /tmp/user/install_ARP_wARP_CCP4I6/ARP_wARP_CCP4I6.tar ExamineTaskArchive: failed to unpack temporary copy of /usr/local/arp_warp_7.1/ARP_wARP_CCP4I6.tar.gz /tmp is not at all full and has plenty of inodes left. (running the install.sh from the arp_warp_7.1 directory doesn't install it either) I have searched around for some solutions, but haven't found anything really relevant. The odd thing I have another x86_64 machine running RHEL 5 that I can do the exact same install method and it works (and using the install.sh from arp_warp_7.1/ works too), so I wonder if something changed with RHEL6 that might be causing problems? Anyone have any suggestions? Thanks! Jonathan
Re: [ccp4bb] ARP/wARP install on 6.2.0 RHEL 6?
Hello, My reply is in the text below: On Jul 28, 2011, at 6:00 AM, ccp4 wrote: A plea from West Australia too. I was sitting with someone yesterday who was trying to install it on a Mac , and finding it a nightmare. We're working on improving this. I believe the main issue is that CCP4 has become more user friendly and installs from a DMG, while the ARP/waRP 7.1 install is still showing its Unix command line roots. He finally got it set up as a local installation, whereupon it promtly failed. We use Macs a lot here with few problems (and various versions of CCP4) so my first suspicion is that this might be an install problem. The message said See refmac-last.log but that told us nothing, and indeed refmac seemed to have worked.. Would it be possible to send me the install.log that is created in the ARP/wARP install directory? Also, the refmac-last.log that will be created in the directory where ARP/wARP was working? Its probably best if the remaining communication is done by direct email. I'm sorry for the trouble that you are having. I hope we can fix the problem and prevent it happening to others in future. Saul Hazledine
Re: [ccp4bb] ARP/wARP install on 6.2.0 RHEL 6?
Dear all, I had no problem with Arp/wARP, but I didn't reinstall. Assume ccp4 sits in /installation/directory/ccp4 and arp in /installation/directory/arp_warp_7.1. The new ccp4 doesn't recognize the existing arp because the task interface is not installed. I run ./install.sh in /installation/directory/arp_warp_7.1, and five seconds later, all is good. I hope this is of help for someone. Andreas On 28/07/2011 4:35, Ethan Merritt wrote: On Wednesday, 27 July 2011, you wrote: Hi Jonathan, seems to be a UW centered day today on the BB (Eric, Jan, you, me). Have the permissions changed ? I assume you are installing as root ? Wouldn't be surprised if Ethan replies soon :-) Sure. I hit the same problem trying to install Arp/wARP on Mandriva. The specific error message you quote comes because the install script fails to create the temp directory before trying to unpack into it. You can fix that by creating the directory by hand first. Unfortunately, that doesn't help very much. The next thing that happens is that the ccp4i installer complains that the tarball is not recognized as a ccp4i install tarball. I gave up at that point. Ethan Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Jul 27, 2011, at 20:31, Jonathan Kayjp...@u.washington.edu wrote: Hi all, I have a RHEL 6 x86_64 machine I recently installed CCP4-6.2.0 onto; the install went through fine, but when I went to install the ARP/wARP GUI (via System Administration - Install/uninstall task), I received the following error in the shell window I started ccp4i from: UnpackTaskArchive: uncompress failed to create /tmp/user/install_ARP_wARP_CCP4I6/ARP_wARP_CCP4I6.tar ExamineTaskArchive: failed to unpack temporary copy of /usr/local/arp_warp_7.1/ARP_wARP_CCP4I6.tar.gz /tmp is not at all full and has plenty of inodes left. (running the install.sh from the arp_warp_7.1 directory doesn't install it either) I have searched around for some solutions, but haven't found anything really relevant. The odd thing I have another x86_64 machine running RHEL 5 that I can do the exact same install method and it works (and using the install.sh from arp_warp_7.1/ works too), so I wonder if something changed with RHEL6 that might be causing problems? Anyone have any suggestions? Thanks! Jonathan -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
Re: [ccp4bb] ARP/wARP install on 6.2.0 RHEL 6?
Hi, 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. Wei-Chun We've found that the behaviour of this call is dependent on TCL versions and that we have problems installing on 64bit fink (OSX) because the version of TCL. When I download and install CCP4 onto Ubuntu or SUSE I get a big package (1GB) that contains CCP4 and a compatible version of TCL. The CCP4 installation then adds the following calls to my .bashrc: source /home/saul/ccp4-linux-6.2.0/setup-scripts/sh/ccp4.setup source /home/saul/ccp4-linux-6.2.0/setup-scripts/sh/ccp4-others.setup The ccp4-others.setup pulls in the correct TCL environment. Is your installation of CCP4 similar? Thanks for reporting this problem - it will hopefully improve future versions of ARP/wARP. Saul Hazledine
Re: [ccp4bb] ARP/wARP install on 6.2.0 RHEL 6?
My two cents: I am installing arp/warp on my Mac since ages and it works ;-) The only thing you need to make sure is that you grab ownership of the /usr/local directory to you as a user, if you installed ccp4 from dmg. If you do this by eg sudo chown -R me.mygroup $CCP4 Then install.sh should work for arp/warp Package type installation for arp/warp is also possible technically, and it can be made available in the next release if it is agreed between developers that from now we will support system-specific installations and not only an all-in-one package as till now. A. Sent from my iPad On 28 Jul 2011, at 10:06, Saul Hazledine s.hazled...@embl-hamburg.de wrote: Hello, My reply is in the text below: On Jul 28, 2011, at 6:00 AM, ccp4 wrote: A plea from West Australia too. I was sitting with someone yesterday who was trying to install it on a Mac , and finding it a nightmare. We're working on improving this. I believe the main issue is that CCP4 has become more user friendly and installs from a DMG, while the ARP/waRP 7.1 install is still showing its Unix command line roots. He finally got it set up as a local installation, whereupon it promtly failed. We use Macs a lot here with few problems (and various versions of CCP4) so my first suspicion is that this might be an install problem. The message said See refmac-last.log but that told us nothing, and indeed refmac seemed to have worked.. Would it be possible to send me the install.log that is created in the ARP/wARP install directory? Also, the refmac-last.log that will be created in the directory where ARP/wARP was working? Its probably best if the remaining communication is done by direct email. I'm sorry for the trouble that you are having. I hope we can fix the problem and prevent it happening to others in future. Saul Hazledine
[ccp4bb] ARP/wARP install on 6.2.0 RHEL 6?
Hi all, I have a RHEL 6 x86_64 machine I recently installed CCP4-6.2.0 onto; the install went through fine, but when I went to install the ARP/wARP GUI (via System Administration - Install/uninstall task), I received the following error in the shell window I started ccp4i from: UnpackTaskArchive: uncompress failed to create /tmp/user/install_ARP_wARP_CCP4I6/ARP_wARP_CCP4I6.tar ExamineTaskArchive: failed to unpack temporary copy of /usr/local/arp_warp_7.1/ARP_wARP_CCP4I6.tar.gz /tmp is not at all full and has plenty of inodes left. (running the install.sh from the arp_warp_7.1 directory doesn't install it either) I have searched around for some solutions, but haven't found anything really relevant. The odd thing I have another x86_64 machine running RHEL 5 that I can do the exact same install method and it works (and using the install.sh from arp_warp_7.1/ works too), so I wonder if something changed with RHEL6 that might be causing problems? Anyone have any suggestions? Thanks! Jonathan
Re: [ccp4bb] ARP/wARP install on 6.2.0 RHEL 6?
Hi Jonathan, seems to be a UW centered day today on the BB (Eric, Jan, you, me). Have the permissions changed ? I assume you are installing as root ? Wouldn't be surprised if Ethan replies soon :-) Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Jul 27, 2011, at 20:31, Jonathan Kay jp...@u.washington.edu wrote: Hi all, I have a RHEL 6 x86_64 machine I recently installed CCP4-6.2.0 onto; the install went through fine, but when I went to install the ARP/wARP GUI (via System Administration - Install/uninstall task), I received the following error in the shell window I started ccp4i from: UnpackTaskArchive: uncompress failed to create /tmp/user/install_ARP_wARP_CCP4I6/ARP_wARP_CCP4I6.tar ExamineTaskArchive: failed to unpack temporary copy of /usr/local/arp_warp_7.1/ARP_wARP_CCP4I6.tar.gz /tmp is not at all full and has plenty of inodes left. (running the install.sh from the arp_warp_7.1 directory doesn't install it either) I have searched around for some solutions, but haven't found anything really relevant. The odd thing I have another x86_64 machine running RHEL 5 that I can do the exact same install method and it works (and using the install.sh from arp_warp_7.1/ works too), so I wonder if something changed with RHEL6 that might be causing problems? Anyone have any suggestions? Thanks! Jonathan
Re: [ccp4bb] ARP/wARP install on 6.2.0 RHEL 6?
On Wednesday, 27 July 2011, you wrote: Hi Jonathan, seems to be a UW centered day today on the BB (Eric, Jan, you, me). Have the permissions changed ? I assume you are installing as root ? Wouldn't be surprised if Ethan replies soon :-) Sure. I hit the same problem trying to install Arp/wARP on Mandriva. The specific error message you quote comes because the install script fails to create the temp directory before trying to unpack into it. You can fix that by creating the directory by hand first. Unfortunately, that doesn't help very much. The next thing that happens is that the ccp4i installer complains that the tarball is not recognized as a ccp4i install tarball. I gave up at that point. Ethan Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Jul 27, 2011, at 20:31, Jonathan Kay jp...@u.washington.edu wrote: Hi all, I have a RHEL 6 x86_64 machine I recently installed CCP4-6.2.0 onto; the install went through fine, but when I went to install the ARP/wARP GUI (via System Administration - Install/uninstall task), I received the following error in the shell window I started ccp4i from: UnpackTaskArchive: uncompress failed to create /tmp/user/install_ARP_wARP_CCP4I6/ARP_wARP_CCP4I6.tar ExamineTaskArchive: failed to unpack temporary copy of /usr/local/arp_warp_7.1/ARP_wARP_CCP4I6.tar.gz /tmp is not at all full and has plenty of inodes left. (running the install.sh from the arp_warp_7.1 directory doesn't install it either) I have searched around for some solutions, but haven't found anything really relevant. The odd thing I have another x86_64 machine running RHEL 5 that I can do the exact same install method and it works (and using the install.sh from arp_warp_7.1/ works too), so I wonder if something changed with RHEL6 that might be causing problems? Anyone have any suggestions? Thanks! Jonathan
Re: [ccp4bb] ARP/wARP install on 6.2.0 RHEL 6?
A plea from West Australia too. I was sitting with someone yesterday who was trying to install it on a Mac , and finding it a nightmare. He finally got it set up as a local installation, whereupon it promtly failed. The message said See refmac-last.log but that told us nothing, and indeed refmac seemed to have worked.. Can someone - either CCP4 or arp-warp people check this out? Eleanor On Wed, 27 Jul 2011 20:35:50 -0700, Ethan Merritt merr...@u.washington.edu wrote: On Wednesday, 27 July 2011, you wrote: Hi Jonathan, seems to be a UW centered day today on the BB (Eric, Jan, you, me). Have the permissions changed ? I assume you are installing as root ? Wouldn't be surprised if Ethan replies soon :-) Sure. I hit the same problem trying to install Arp/wARP on Mandriva. The specific error message you quote comes because the install script fails to create the temp directory before trying to unpack into it. You can fix that by creating the directory by hand first. Unfortunately, that doesn't help very much. The next thing that happens is that the ccp4i installer complains that the tarball is not recognized as a ccp4i install tarball. I gave up at that point. Ethan Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Jul 27, 2011, at 20:31, Jonathan Kay jp...@u.washington.edu wrote: Hi all, I have a RHEL 6 x86_64 machine I recently installed CCP4-6.2.0 onto; the install went through fine, but when I went to install the ARP/wARP GUI (via System Administration - Install/uninstall task), I received the following error in the shell window I started ccp4i from: UnpackTaskArchive: uncompress failed to create /tmp/user/install_ARP_wARP_CCP4I6/ARP_wARP_CCP4I6.tar ExamineTaskArchive: failed to unpack temporary copy of /usr/local/arp_warp_7.1/ARP_wARP_CCP4I6.tar.gz /tmp is not at all full and has plenty of inodes left. (running the install.sh from the arp_warp_7.1 directory doesn't install it either) I have searched around for some solutions, but haven't found anything really relevant. The odd thing I have another x86_64 machine running RHEL 5 that I can do the exact same install method and it works (and using the install.sh from arp_warp_7.1/ works too), so I wonder if something changed with RHEL6 that might be causing problems? Anyone have any suggestions? Thanks! Jonathan
Re: [ccp4bb] ARP/wARP install on 6.2.0 RHEL 6?
... strange, I have not seen any problems installing ARPwARP 7.1 on a new CCP6-6.2.0 install on - linux centos - os-x snow leopard, here I initially ran into write permissions issues and wound up changing the ownership of the /Applications/ccp4-6.2.0 directory Cheers Jan On Jul 27, 2011, at 9:00 PM, ccp4 wrote: A plea from West Australia too. I was sitting with someone yesterday who was trying to install it on a Mac , and finding it a nightmare. He finally got it set up as a local installation, whereupon it promtly failed. The message said See refmac-last.log but that told us nothing, and indeed refmac seemed to have worked.. Can someone - either CCP4 or arp-warp people check this out? Eleanor On Wed, 27 Jul 2011 20:35:50 -0700, Ethan Merritt merr...@u.washington.edu wrote: On Wednesday, 27 July 2011, you wrote: Hi Jonathan, seems to be a UW centered day today on the BB (Eric, Jan, you, me). Have the permissions changed ? I assume you are installing as root ? Wouldn't be surprised if Ethan replies soon :-) Sure. I hit the same problem trying to install Arp/wARP on Mandriva. The specific error message you quote comes because the install script fails to create the temp directory before trying to unpack into it. You can fix that by creating the directory by hand first. Unfortunately, that doesn't help very much. The next thing that happens is that the ccp4i installer complains that the tarball is not recognized as a ccp4i install tarball. I gave up at that point. Ethan Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Jul 27, 2011, at 20:31, Jonathan Kay jp...@u.washington.edu wrote: Hi all, I have a RHEL 6 x86_64 machine I recently installed CCP4-6.2.0 onto; the install went through fine, but when I went to install the ARP/wARP GUI (via System Administration - Install/uninstall task), I received the following error in the shell window I started ccp4i from: UnpackTaskArchive: uncompress failed to create /tmp/user/install_ARP_wARP_CCP4I6/ARP_wARP_CCP4I6.tar ExamineTaskArchive: failed to unpack temporary copy of /usr/local/arp_warp_7.1/ARP_wARP_CCP4I6.tar.gz /tmp is not at all full and has plenty of inodes left. (running the install.sh from the arp_warp_7.1 directory doesn't install it either) I have searched around for some solutions, but haven't found anything really relevant. The odd thing I have another x86_64 machine running RHEL 5 that I can do the exact same install method and it works (and using the install.sh from arp_warp_7.1/ works too), so I wonder if something changed with RHEL6 that might be causing problems? Anyone have any suggestions? Thanks! Jonathan -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com
