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Installing coot from subversion ( on ubuntu)From $1Table of contentsYou are currently comparing two old versions - only when you are comparing against the latest version can you revert. Return to version archive. Combined revision comparisonUPdated notes on installing are at this page also on this wiki First download the subversion trunk from google code as stated on the google code Coot Source page svn checkout http://coot.googlecode.com/svn/trunk/ coot-read-only This creates a directory coot-read-only whereever you issued the above command Install the packages as described at this page and in the README . On ubuntu you would use the "sudo apt-get install patch From a fresh ubuntu install, you also need to install: patch m4 g++ libxext6-dev libc6-dev libglu1-mesa-dev mesa-common-dev swig libgtk2.0-dev ( added to list in README ) libgnomecanvas2-dev (added to list in README)
After this please us ethe simple autobuild script as describes at the ccp4 wiki: Briefly: export AUTOBUILD_INSTALLED=${HOME}/autobuild/coot
export AUTOBUILD_BUILD=${HOME}/autobuild/
export LOGS=$AUTOBUILD_BUILD/logs
export NIGHTLY_DEST_DIR=$AUTOBUILD_BUILD
export STABLE_DEST_DIR=$AUTOBUILD_BUILD
export build_coot_prerelease=1
bash build-it-gtk2-simple python > build.log
If all goes well coot responds:hari@charlie:~/coot-read-only$ bash build-it-gtk2-simple python > build3.log
This installs a coot binary into the directory mentioned in the AUTOBUILD_BUILD directory in the subdirectory AUTOBUILD_BUILD=${HOME}/autobuild/
In my case coot is installed in the $HOME/autobuild/coot-Linux-x86_64-ubuntu-8.04.2-gtk2-python/bin
Regular updatesAfter the initial build . to update coot regularly. change diorectories into the coot-read-only directory into which you checkedout the tree ( in step one above) - svn checkout http://coot.googlecode.com/svn/trunk/ coot-read-only
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V
cd into this directory
and issue the command (svn update)
svn update You should see me@mymachine:~/coot-read-only$ svn update U src/c-interface-preferences.cc U src/callbacks.c U bldnotes U coot-gtk2.glade Updated to revision 1936. Now you can just re-run the build as indicated above bash build-it-gtk2-simple python > build.log
Trouble shooting regular updatesEvery once in a while . the automatic update indicated above fails . Because something has changed and you need to re-compile everything . for eg. you may see a message such as error: cannot open Packages index using db3 - No such file or directory (2) error: cannot open Packages database in /var/lib/rpm rpm: To install rpm packages on Debian systems, use alien. See README.Debian. error: cannot open Packages index using db3 - No such file or directory (2) error: cannot open Packages database in /var/lib/rpm rpm: To install rpm packages on Debian systems, use alien. See README.Debian. error: cannot open Packages index using db3 - No such file or directory (2) error: cannot open Packages database in /var/lib/rpm --02:14:24-- http://www.ysbl.york.ac.uk/~emsley/build-logs/build-notes => `build-notes' Resolving www.ysbl.york.ac.uk... 144.32.72.243 Connecting to www.ysbl.york.ac.uk|144.32.72.243|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 7,039 (6.9K) [text/plain] 100%[====================================>] 7,039 --.--K/s 02:14:25 (58.94 KB/s) - `build-notes' saved [7039/7039] ./build-it-gtk2-simple: line 1084: domainname: command not found sh: glib-config: not found sh: glib-config: not found sh: glib-config: not found guile-config - Guile version 1.8.5 Python 2.6 BUILDING coot: version coot-0.6-pre-1-revision-1936, python=yes --02:14:28-- http://www.ysbl.york.ac.uk/~emsley/software/pre-release/coot-0.6-pre-1-revision-1936.tar.gz => `/home/hari/autobuild//sources/coot-0.6-pre-1-revision-1936.tar.gz' Resolving www.ysbl.york.ac.uk... 144.32.72.243 Connecting to www.ysbl.york.ac.uk|144.32.72.243|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 10,841,622 (10M) [application/x-gzip] 100%[====================================>] 10,841,622 636.85K/s ETA 00:00 02:14:46 (613.58 KB/s) - `/home/hari/autobuild//sources/coot-0.6-pre-1-revision-1936.tar.gz' saved [10841622/10841622] BUILDING coot: version coot-0.6-pre-1-revision-1936, python=yes coot build failed, exiting.
The coot build logs that hep you troubleshoot this are located in $AUTOBUILD_BUILD/logs and more importantly in the $AUTOBUILD_BUILD/logs/gtk2-gcc-4.2.4_and_g++-4.2.4/16-coot.txt
SO look for the 16-coot.txt in the $AUTOBUILD_BUILD directory hari@hj-ubuntu41:~/autobuild$ cd $AUTOBUILD_BUILD hari@hj-ubuntu41:~/autobuild$ find ./* -name "16-coot.txt" ./logs/gtk2-gcc-4.2.4_and_g++-4.2.4/16-coot.txt And the bottom of that file may contain the reason for the failed build me@myubuntu41:~/autobuild$ tail -f ./logs/gtk2-gcc-4.2.4_and_g++-4.2.4/16-coot.txt checking for pkg-config... /usr/bin/pkg-config checking for GtkGLExt - version >= 1.0.0... yes (version 1.2.0) checking for GLUT... yes checking for MMDB... yes checking for SSMLib... /home/hari/autobuild/coot-pre-release-gtk2-python checking for Clipper... no Error locating Clipper - a CNS-enabled version of Clipper (2.1-090210-ac or later) is required now need to update libtool here /home/hari/autobuild/hj-ubuntu41_2009-03-26__T06_14_24/coot-0.6-pre-1 make: *** No targets specified and no makefile found. Stop. make failed. You can see here that a "CNS enabled clipper version was not available. So you need to force the build script to recompile cns Lts find out what convinces the script you have clipper in the first place . Look at the script(build-it-gtk2-simple) and you will see that it looks for two files $install_top_dir/include/clipper/ccp4/ccp4_mtz_io.h OR $install_top_dir/include/clipper/contrib/sfscale.h
Delete either of those files to force a clipper rebuild. ( For some reason messing with the build_clipper variable in this script does not seem to force building clipper) so we look for the ccp4_mtz_io.h file in the $AUTOBUILD_BUILD directory and delete it me@myubuntu41:~/autobuild$ find ./* -name ccp4_mtz_io.h ./coot-pre-release-gtk2-python/include/clipper/ccp4/ccp4_mtz_io.h ./hj-ubuntu41_2009-02-06__T12_53_46/clipper-2.1/clipper/ccp4/ccp4_mtz_io.h hari@hj-ubuntu41:~/autobuild$ echo $AUTOBUILD_INSTALLED /home/hari/autobuild/coot
rm $AUTOBUILD_BUILD/coot-pre-release-gtk2-python/include/clipper/ccp4/ccp4_mtz_io.h Then we re-run the build script. This time it forces a selective rebuild of only clipper and this should satisfy the coot build and it should proceed without any problems after that so in the coot-read-only directory we re-run build-it-gtk2-simple python > build.log ANd this should hopefully complete as above and tell you that the build was successfull. Of course you could always change the $AUTOBUILD_BUILD and $AUTOBUILD_INSTALLED directory above to a whole "fresk" new directory and rebuild everything from scratch as you did above to make sure all the libraries are updated . But this workaround ( courtesy Bernhard lokhamp) does help get around the failure due to a clipper library update Version from 21:10, 6 Feb 2009UPdated notes on installing are at this page also on this wiki First download the subversion trunk from google code as stated on the google code Coot Source page svn checkout http://coot.googlecode.com/svn/trunk/ coot-read-only This creates a directory coot-read-only whereever you issued the above command Install the packages as described at this page and in the README . On ubuntu you would use the "sudo apt-get install patch From a fresh ubuntu install, you also need to install: patch m4 g++ libxext6-dev libc6-dev libglu1-mesa-dev mesa-common-dev swig libgtk2.0-dev ( added to list in README ) libgnomecanvas2-dev (added to list in README)
After this please us ethe simple autobuild script as describes at the ccp4 wiki: Briefly: export AUTOBUILD_INSTALLED=${HOME}/autobuild/coot
export AUTOBUILD_BUILD=${HOME}/autobuild/
export LOGS=$AUTOBUILD_BUILD/logs
export NIGHTLY_DEST_DIR=$AUTOBUILD_BUILD
export STABLE_DEST_DIR=$AUTOBUILD_BUILD
export build_coot_prerelease=1
bash build-it-gtk2-simple python > build.log
If all goes well coot responds:hari@charlie:~/coot-read-only$ bash build-it-gtk2-simple python > build3.log
This installs a coot binary into the directory mentioned in the AUTOBUILD_BUILD directory in the subdirectory AUTOBUILD_BUILD=${HOME}/autobuild/
In my case coot is installed in the $HOME/autobuild/coot-Linux-x86_64-ubuntu-8.04.2-gtk2-python/bin
Version as of 06:52, 26 Mar 2009UPdated notes on installing are at this page also on this wiki First download the subversion trunk from google code as stated on the google code Coot Source page svn checkout http://coot.googlecode.com/svn/trunk/ coot-read-only This creates a directory coot-read-only whereever you issued the above command Install the packages as described at this page and in the README . On ubuntu you would use the "sudo apt-get install patch From a fresh ubuntu install, you also need to install: patch m4 g++ libxext6-dev libc6-dev libglu1-mesa-dev mesa-common-dev swig libgtk2.0-dev ( added to list in README ) libgnomecanvas2-dev (added to list in README)
After this please us ethe simple autobuild script as describes at the ccp4 wiki: Briefly: export AUTOBUILD_INSTALLED=${HOME}/autobuild/coot
export AUTOBUILD_BUILD=${HOME}/autobuild/
export LOGS=$AUTOBUILD_BUILD/logs
export NIGHTLY_DEST_DIR=$AUTOBUILD_BUILD
export STABLE_DEST_DIR=$AUTOBUILD_BUILD
export build_coot_prerelease=1
bash build-it-gtk2-simple python > build.log
If all goes well coot responds:hari@charlie:~/coot-read-only$ bash build-it-gtk2-simple python > build3.log
This installs a coot binary into the directory mentioned in the AUTOBUILD_BUILD directory in the subdirectory AUTOBUILD_BUILD=${HOME}/autobuild/
In my case coot is installed in the $HOME/autobuild/coot-Linux-x86_64-ubuntu-8.04.2-gtk2-python/bin
Regular updatesAfter the initial build . to update coot regularly. change diorectories into the coot-read-only directory into which you checkedout the tree ( in step one above) - svn checkout http://coot.googlecode.com/svn/trunk/ coot-read-only
|
V
cd into this directory
and issue the command (svn update)
svn update You should see me@mymachine:~/coot-read-only$ svn update U src/c-interface-preferences.cc U src/callbacks.c U bldnotes U coot-gtk2.glade Updated to revision 1936. Now you can just re-run the build as indicated above bash build-it-gtk2-simple python > build.log
Trouble shooting regular updatesEvery once in a while . the automatic update indicated above fails . Because something has changed and you need to re-compile everything . for eg. you may see a message such as error: cannot open Packages index using db3 - No such file or directory (2) error: cannot open Packages database in /var/lib/rpm rpm: To install rpm packages on Debian systems, use alien. See README.Debian. error: cannot open Packages index using db3 - No such file or directory (2) error: cannot open Packages database in /var/lib/rpm rpm: To install rpm packages on Debian systems, use alien. See README.Debian. error: cannot open Packages index using db3 - No such file or directory (2) error: cannot open Packages database in /var/lib/rpm --02:14:24-- http://www.ysbl.york.ac.uk/~emsley/build-logs/build-notes => `build-notes' Resolving www.ysbl.york.ac.uk... 144.32.72.243 Connecting to www.ysbl.york.ac.uk|144.32.72.243|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 7,039 (6.9K) [text/plain] 100%[====================================>] 7,039 --.--K/s 02:14:25 (58.94 KB/s) - `build-notes' saved [7039/7039] ./build-it-gtk2-simple: line 1084: domainname: command not found sh: glib-config: not found sh: glib-config: not found sh: glib-config: not found guile-config - Guile version 1.8.5 Python 2.6 BUILDING coot: version coot-0.6-pre-1-revision-1936, python=yes --02:14:28-- http://www.ysbl.york.ac.uk/~emsley/software/pre-release/coot-0.6-pre-1-revision-1936.tar.gz => `/home/hari/autobuild//sources/coot-0.6-pre-1-revision-1936.tar.gz' Resolving www.ysbl.york.ac.uk... 144.32.72.243 Connecting to www.ysbl.york.ac.uk|144.32.72.243|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 10,841,622 (10M) [application/x-gzip] 100%[====================================>] 10,841,622 636.85K/s ETA 00:00 02:14:46 (613.58 KB/s) - `/home/hari/autobuild//sources/coot-0.6-pre-1-revision-1936.tar.gz' saved [10841622/10841622] BUILDING coot: version coot-0.6-pre-1-revision-1936, python=yes coot build failed, exiting.
The coot build logs that hep you troubleshoot this are located in $AUTOBUILD_BUILD/logs and more importantly in the $AUTOBUILD_BUILD/logs/gtk2-gcc-4.2.4_and_g++-4.2.4/16-coot.txt
SO look for the 16-coot.txt in the $AUTOBUILD_BUILD directory hari@hj-ubuntu41:~/autobuild$ cd $AUTOBUILD_BUILD hari@hj-ubuntu41:~/autobuild$ find ./* -name "16-coot.txt" ./logs/gtk2-gcc-4.2.4_and_g++-4.2.4/16-coot.txt And the bottom of that file may contain the reason for the failed build me@myubuntu41:~/autobuild$ tail -f ./logs/gtk2-gcc-4.2.4_and_g++-4.2.4/16-coot.txt checking for pkg-config... /usr/bin/pkg-config checking for GtkGLExt - version >= 1.0.0... yes (version 1.2.0) checking for GLUT... yes checking for MMDB... yes checking for SSMLib... /home/hari/autobuild/coot-pre-release-gtk2-python checking for Clipper... no Error locating Clipper - a CNS-enabled version of Clipper (2.1-090210-ac or later) is required now need to update libtool here /home/hari/autobuild/hj-ubuntu41_2009-03-26__T06_14_24/coot-0.6-pre-1 make: *** No targets specified and no makefile found. Stop. make failed. You can see here that a "CNS enabled clipper version was not available. So you need to force the build script to recompile cns Lts find out what convinces the script you have clipper in the first place . Look at the script(build-it-gtk2-simple) and you will see that it looks for two files $install_top_dir/include/clipper/ccp4/ccp4_mtz_io.h OR $install_top_dir/include/clipper/contrib/sfscale.h
Delete either of those files to force a clipper rebuild. ( For some reason messing with the build_clipper variable in this script does not seem to force building clipper) so we look for the ccp4_mtz_io.h file in the $AUTOBUILD_BUILD directory and delete it me@myubuntu41:~/autobuild$ find ./* -name ccp4_mtz_io.h ./coot-pre-release-gtk2-python/include/clipper/ccp4/ccp4_mtz_io.h ./hj-ubuntu41_2009-02-06__T12_53_46/clipper-2.1/clipper/ccp4/ccp4_mtz_io.h hari@hj-ubuntu41:~/autobuild$ echo $AUTOBUILD_INSTALLED /home/hari/autobuild/coot
rm $AUTOBUILD_BUILD/coot-pre-release-gtk2-python/include/clipper/ccp4/ccp4_mtz_io.h Then we re-run the build script. This time it forces a selective rebuild of only clipper and this should satisfy the coot build and it should proceed without any problems after that so in the coot-read-only directory we re-run build-it-gtk2-simple python > build.log ANd this should hopefully complete as above and tell you that the build was successfull. Of course you could always change the $AUTOBUILD_BUILD and $AUTOBUILD_INSTALLED directory above to a whole "fresk" new directory and rebuild everything from scratch as you did above to make sure all the libraries are updated . But this workaround ( courtesy Bernhard lokhamp) does help get around the failure due to a clipper library update |