Here is my guess as to what happened:
You wanted AmberTools somewhere, and so you took your existing tree that
you already had lying around and copied the whole directory over while
inside $AMBERHOME, yes? In your existing AmberTools installation, you had
already applied all of these bug fixes (i.e., the installation in your
Debian server).
To fix the problem, just extract a fresh AmberTools12.tar.bz2 tarball
downloaded from the Amber website and go from there. My best guess for an
explanation is provided in the PS.
HTH,
Jason
Here is what is happening (I think): patch_amber.py tracks the applied
patches by storing all of the ones you've already applied in a .patches/
folder. That way, it knows *exactly* what it has applied and what it
hasn't, and has all of the information there to reverse a bugfix if you
want to or to tell you exactly what it has changed. To prevent people from
messing with this directory and ruining their tree for future updates, the
decision was made to make this directory 'hidden' (i.e., with a leading
.). By default, scp and rsync will not copy over hidden files or
directories via the "scp * remote:destination" or "rsync *
remote:destination" -- you have to explicitly include hidden files and
folders -- e.g., "scp * .* remote:destination". Since these patch files
were not copied over, patch_amber.py had no way of knowing that you had
already applied these patches, so it tried applying them again. Only to
find out, as you've noticed, that they've already been applied, so it quit
with error.
While there are a number of things you can do, like copying over the
.patches/ folder from your server (only if I was right in my initial
assumption!), or use the --ignore-fails flag for patch_amber.py; the safest
thing IMO is to just start anew.
On Fri, Sep 28, 2012 at 5:36 AM, Francesco Pietra <chiendarret.gmail.com>wrote:
> I already have AmberTools12 on a Debian amd64 server. Now I wanted to
> have it also on my vintage desktop Debian i386.
>
> At ./configure gnu, problems arose in applying patches:
>
> root.deb32:/usr/local/amber12# ./configure gnu
> Checking for updates...
> AmberTools12 has 24 unapplied patches: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,
> 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24
>
> There are patches available. Do you want to apply them now? [y/n]
> (Recommended Y)
> y
> Determining patches to download for AmberTools12
> Downloading bugfix.1
> Downloading bugfix.2
> Downloading bugfix.3
> Downloading bugfix.4
> Downloading bugfix.5
> Downloading bugfix.6
> Downloading bugfix.7
> Downloading bugfix.8
> Downloading bugfix.9
> Downloading bugfix.10
> Downloading bugfix.11
> Downloading bugfix.12
> Downloading bugfix.13
> Downloading bugfix.14
> Downloading bugfix.15
> Downloading bugfix.16
> Downloading bugfix.17
> Downloading bugfix.18
> Downloading bugfix.19
> Downloading bugfix.20
> Downloading bugfix.21
> Downloading bugfix.22
> Downloading bugfix.23
> Downloading bugfix.24
>
> Applying AmberTools12 patches
> Error or warning during patching process for
> .patches/AmberTools_Unapplied_Patches/bugfix.1:
> Reversed (or previously applied) patch detected! Skipping patch.
> 6 out of 6 hunks ignored -- saving rejects to file
> AmberTools/src/parmed/ParmedTools/ParmedActions.py.rej
> Reversed (or previously applied) patch detected! Skipping patch.
> 1 out of 1 hunk ignored -- saving rejects to file
> AmberTools/src/parmed/ParmedTools/exceptions.py.rej
> Reversed (or previously applied) patch detected! Skipping patch.
> 1 out of 1 hunk ignored -- saving rejects to file
> AmberTools/src/parmed/ParmedTools/gui/_guiactions.py.rej
> Reversed (or previously applied) patch detected! Skipping patch.
> 2 out of 2 hunks ignored -- saving rejects to file
> AmberTools/src/parmed/chemistry/amber/mask.py.rej
> Reversed (or previously applied) patch detected! Skipping patch.
> 1 out of 1 hunk ignored -- saving rejects to file
> AmberTools/src/parmed/chemistry/amber/readparm.py.rej
> Reversed (or previously applied) patch detected! Skipping patch.
> 1 out of 1 hunk ignored -- saving rejects to file
> AmberTools/src/parmed/chemistry/exceptions.py.rej
>
> Automatic patching failed! Check the errors before re-configuring
> root.deb32:/usr/local/amber12#
>
> While its was not clear to me (from examining the indicated files) why
> the problem, does that mean that also bugfixes 2-24 were skipped?
>
> thanks
> francesco pietra
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Sep 28 2012 - 05:30:03 PDT
