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/
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Received on Sun Jul 27 2014 - 10:00:02 PDT
