Hi,
I've experienced the same problem with applying update.7.
It looks like it is a problem with the patch; I've tried this on our local
cluster (Rocks 5.3 - Essentially RedHat) and on my MacBook (MacOS 10.7.5).
In both cases, the patch failed to apply:
$ ./update_amber --update
Preparing to apply updates... please wait.
Downloading updates for AmberTools 14
Downloading AmberTools 14/update.7 (192.92 KB)
Downloading: [::::::::::::::::::::::::::::::::::::::::::::::::::] 100.0%
Done.
Applying AmberTools 14/update.7
instance: .patches/AmberTools14_Unapplied_Patches/update.7 failed to apply.
No changes made from this patch
--Marc
On 27 July 2014 17:35, Marek Maly <marek.maly.ujep.cz> wrote:
> Hello,
>
> I just tried to reinstall whole Amber14 package because I found out that
> there
> is the new AmberTools patch (7).
>
> Unfortunately the automatic patching mechanism failed to apply this patch
> and
> consequently failed whole Amber14 installation process.
>
> Please see below. My previous Amber14 installation (AT patches up to 6,
> Amb14 patches up to 3)
> was without any problems.
> My OS is CentOS release 6.5 (2.6.32-431.el6.x86_64), I used gnu compilers
> to compile Amber14 ( gcc version 4.4.7 20120313 (Red Hat 4.4.7-4) (GCC) ).
>
> Thanks in advance for any helpful information,
>
> Best wishes,
>
> Marek
>
> *****RELEVANT TEXT FROM THE TERMINAL*****
> *****RELEVANT TEXT FROM THE TERMINAL*****
> *****RELEVANT TEXT FROM THE TERMINAL*****
>
> Preparing to apply updates... please wait.
> Downloading updates for AmberTools 14
> Downloading AmberTools 14/update.1 (282.66 KB)
> Downloading: [::::::::::::::::::::::::::::::::::::::::::::::::::] 100.0%
> Done.
> Applying AmberTools 14/update.1.bz2
> Downloading AmberTools 14/update.2 (47.60 KB)
> Applying AmberTools 14/update.2
> Downloading AmberTools 14/update.3 (17.66 KB)
> Applying AmberTools 14/update.3
> Downloading AmberTools 14/update.4 (12.07 KB)
> Applying AmberTools 14/update.4
> Downloading AmberTools 14/update.5 (1742.96 KB)
> Downloading: [::::::::::::::::::::::::::::::::::::::::::::::::::] 100.0%
> Done.
> Applying AmberTools 14/update.5
> Downloading AmberTools 14/update.6 (197.91 KB)
> Downloading: [::::::::::::::::::::::::::::::::::::::::::::::::::] 100.0%
> Done.
> Applying AmberTools 14/update.6
> Downloading AmberTools 14/update.7 (192.92 KB)
> Downloading: [::::::::::::::::::::::::::::::::::::::::::::::::::] 100.0%
> Done.
> Applying AmberTools 14/update.7
> PatchingError: .patches/AmberTools14_Unapplied_Patches/update.7 failed to
> apply. No changes made from this patch
> Automatic patching failed! Check the errors before re-configuring
> .
> .
>
> ----------------------------------------------------------------------------------
> After I pressed "y" cca 3 times as the reaction to repeated questions
> about the patching (remaining AT 7 and Amber patches 1,2,3) Amber
> installation crashed with text written below.
>
> ----------------------------------------------------------------------------------
>
>
> Applying AmberTools 14/update.7
> PatchingError: .patches/AmberTools14_Unapplied_Patches/update.7 failed to
> apply. No changes made from this patch
> Automatic patching failed! Check the errors before re-configuring
> Makefile:3: config.h: AdresåŠnebo soubor neexistuje
> make: *** No rule to make target `config.h'. Stop.
>
> *****CONTENT OF THE configure FILE*****
> *****CONTENT OF THE configure FILE*****
> *****CONTENT OF THE configure FILE*****
>
> #!/bin/sh
>
> error() {
> echo "Configure failed due to the errors above!"
> exit 1
> }
>
> # Check for --no-updates in any position
> updates="yes"
> requested_help="no"
> for var in "$."; do
> case "$var" in
> --no-updates)
> echo "Skipping check for Amber updates"; updates="no";;
> -h|-H|--h|--he|--hel|--help|-help)
> updates="no"; requested_help="yes";;
> --full|--full-h|--full-he|--full-hel|--full-help)
> updates="no"; requested_help="yes";;
> esac
> done
>
> # No arguments means we ask for help
> if [ $# -eq 0 ]; then
> requested_help="yes"
> updates="no"
> fi
>
> if [ "$updates" = "yes" ]; then
> # Tell people we're checking for updates, since this could take a
> # couple seconds, especially if ambermd.org is down
> echo "Checking for updates..."
>
> # Check to see if there are any updates available. This will print a
> message
> # giving how many patches are available for Amber and AmberTools
> ./update_amber --check-updates
>
> # The return code of the above command tells us what happened. Return 1
> for
> # an error, and return 2 if there are patches available
> ret_code=$?
>
> if [ $ret_code -eq 2 ]; then
> printf "There are patches available. Do you want to apply them now?
> [y/N]"
> echo " (Recommended Y) "
> read answer
> ans=`echo $answer | awk '{print substr($1,1,1)}'`
>
> if [ "$ans" = "y" -o "$ans" = "Y" ]; then
> # Since patch_amber may patch itself and quit before applying all
> patches,
> # continue to check for updates and update the tree until they
> have all
> # been applied.
> while [ $ret_code -eq 2 ]
> do
> ./update_amber --update
> if [ $? -ne 0 ]; then
> echo "Automatic patching failed! Check the errors before
> re-configuring"
> exit 1
> fi
> ./update_amber --check-updates 2>&1 > /dev/null
> ret_code=$?
> done
> else
> echo "NOT updating your tree and continuing anyway."
> fi
> elif [ $ret_code -eq 1 ]; then
> echo "Check for updates failed."
> fi
> fi
>
> # Simple redirection to carry out the configure script inside
> AmberTools/src
>
> (cd AmberTools/src && ./configure2 $.) || error
>
> # Bail out if we just got the usage statement
> if [ "$requested_help" = "yes" ]; then
> exit 0
> fi
>
> ln -sf AmberTools/src/config.h .
>
> # Make clean here
>
> echo "Cleaning the src directories. This may take a few moments."
> make clean > /dev/null 2>&1
> echo "Configure complete."
>
> *****CONTENT OF THE update_amber FILE*****
> *****CONTENT OF THE update_amber FILE*****
> *****CONTENT OF THE update_amber FILE*****
>
> #!/usr/bin/env python
> """ The driver for the updater """
>
> import os
> import sys
> from updateutils import main
> from updateutils.exceptions import AmberUpdaterError, PatchingUpdater
>
> if __name__ == '__main__':
> # Some startup stuff, see if AMBERHOME is set correctly and/or make
> sure that
> # appdir
> appdir = os.path.abspath(os.path.split(sys.argv[0])[0])
> amberhome = os.getenv('AMBERHOME')
> if amberhome is None or appdir != os.path.realpath(amberhome):
> sys.stderr.write('Warning: AMBERHOME [%s] differs from expected
> [%s].\n' %
> (amberhome, appdir))
> sys.stderr.write(' No changes will be made until this is
> fixed\n')
> else:
> main.ALLOW_UPDATES = True
> os.chdir(appdir)
> app = main.MainUpdater()
> try:
> app.mainloop()
> except PatchingUpdater:
> app.finalize()
> sys.stderr.write('\n\nupdater.py has found a patch to itself... I am
> '
> 'quitting now so\nfuture updates will apply with the fixed
> script.'
> '\n\nRun this script again to get all updates.\n\n')
> sys.exit(0)
> except AmberUpdaterError:
> err = sys.exc_info()[1]
> sys.stderr.write('%s: %s\n' % (type(err).__name__, err))
> app.finalize()
> sys.exit(1)
> app.finalize(normal=True)
> if app.num_updates > 0:
> sys.exit(2)
> sys.exit(0)
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> --
> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
> http://www.opera.com/mail/
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jul 28 2014 - 05:00:02 PDT
