As discussed in bug 246255 there is a version bump which is needed. I suggest following ebuild and patches. Please test and report issues.
Created attachment 174315 [details] /mnt/tmpfs/pdb-extract.ebuild.diff dif to the new ebuild
Created attachment 174316 [details] files/respect-cflags-and-fix-install.patch respect-cflags-and-fix-install.patch
Created attachment 174318 [details] files/pdb-extract-3.004-gcc-4.3.patch pdb-extract-3.004-gcc-4.3.patch
Created attachment 174319 [details] files/pdb-extract-3.004-Makefile.patch pdb-extract-3.004-Makefile.patch
After testing I found out that when not having ccp4 installed there is a problem with env variables. Therefor I suggest following patch.
Created attachment 174336 [details] files/pdb-extract-3.004-env.patch pdb-extract-3.004-env.patch
Created attachment 174337 [details] /mnt/tmpfs/pdb-extract-3.004-r1.ebuild.diff pdb-extract-3.004-r1.ebuild.diff
Thanks for working on this needed version bump. Assigning to maintainers.
It will be great to have working sci-chemistry/validation after the version bump, thank you.
(In reply to comment #9) > It will be great to have working sci-chemistry/validation after the version > bump, thank you. > Please open an extra bug for this.
Justin, would you please make sure the bin/extract is renamed to say pdb-extract filename? # equery belongs /usr/bin/extract [ Searching for file(s) /usr/bin/extract in *... ] sci-chemistry/pdb-extract-1.700 (/usr/bin/extract) app-crypt/pkcrack-1.2.2 (/usr/bin/extract) app-text/html-xml-utils-3.7 (/usr/bin/extract) # The /usr/bin/connect is also asking for a trouble but is not used by another package on my computer (which does not mean it is safe). I would say rename both to pdb-$oldfilename.
Sure I have seen this problem too. BUT: The package already contains a second exec which is named pdb_extract. All scripts which you can found for this packages use the executables in this order "extract --> pdb_extract --> pdb_extract_sf". I will think about a solution, because there are some more packages, also the same topic related, which contain a extract exec.
For completeness, currently the ebuild sci-chemistry/pdb-extract-3.004 in overlay does: /usr/bin/extract-pdb /usr/bin/pdb_extract /usr/bin/pdb_extract_sf I do not know why no -r1 exists yet.
I removed all attachments in favour of the files which are in the overlay. http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=tree;f=sci-chemistry/pdb-extract;h=c6f4760b9a756c7e4287913f03ab7e28d8ca894c;hb=HEAD As Martin pointed out the extract binary is renamed to extract-pdb. We have to discuss if this is the best renaming, or we should block the other packages and push their devs to rename. Reason: our package is often used in scripts.
(In reply to comment #13) > For completeness, currently the ebuild sci-chemistry/pdb-extract-3.004 in > overlay does: > > /usr/bin/extract-pdb > /usr/bin/pdb_extract > /usr/bin/pdb_extract_sf > > I do not know why no -r1 exists yet. > was a working revision from my private overlay. I merged it into the base revision. Sorry for not doing the bump with the renaming.
I have never used the extract (now extract-pdb), how about pdb_extract_wrapper? Or you want pdb_extract_script? See http://sw-tools.rcsb.org/apps/PDB_EXTRACT/documentation.html#script
All those renaming are bad by the same argument. html-xml-utils conflict solved in overlay.
I've added 3.004 to the main tree. Thanks a lot for the hard work! cheers, Markus
