I did everything on my desktop, where, in my .bshrc I had already set,
and activated:
# For AmberTools12
export AMBERHOME=/usr/local/amber12
export PATH=$PATH/:$AMBERHOME/bin
I extracted the folder amber12 from the tarball into my home. Then
copied into /usr/local, and done what I wrote.
Following your kind advice, I deleted everything, extracted the folder
amber12 from the tarball into /usr/local. The, the installation went
on without problems.
Thanks again
francesco
On Fri, Sep 28, 2012 at 2:29 PM, Jason Swails <jason.swails.gmail.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri Sep 28 2012 - 11:00:02 PDT
