| Summary: | sci-chemistry/pdb-extract-1.700 - ./src/ndb_htmllib.C:2325: error: ???NDB_MSG_ERR??? was not declared in this scope | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Justin Lecher (RETIRED) <jlec> |
| Component: | New packages | Assignee: | Gentoo Chemistry-Related Packages <sci-chemistry> |
| Status: | RESOLVED FIXED | ||
| Severity: | normal | CC: | dilfridge, flameeyes, qa |
| Priority: | High | Keywords: | EBUILD, InOverlay |
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| URL: | http://sw-tools.pdb.org/apps/PDB_EXTRACT/index.html | ||
| Whiteboard: | [sci overlay] | ||
| Package list: | Runtime testing required: | --- | |
| Bug Depends on: | 249933 | ||
| Bug Blocks: | |||
| Attachments: |
/tmp/build.log
/tmp/emerge.info |
||
|
Description
Justin Lecher (RETIRED)
2008-11-10 08:38:22 UTC
Created attachment 171276 [details]
/tmp/build.log
build.log
Created attachment 171278 [details]
/tmp/emerge.info
emerge.info
This shows up when sci-libs/cifparse-obj-7.025 is installed, because it installes the ndb_misclib.h not in /usr/include/rcsb, but in /usr/include/cifparse-obj. (In reply to comment #3) > This shows up when sci-libs/cifparse-obj-7.025 is installed, because it > installes the ndb_misclib.h not in /usr/include/rcsb, but in > /usr/include/cifparse-obj. > Thanks for tracking this down. Unfortunately, even after fixing the includes, pdb-extract doesn't seem to compile against cifparse-obj-7.025 due to missing member functions etc. I guess it is time for a version bump ;) Best, Markus (In reply to comment #4) > Thanks for tracking this down. Unfortunately, even after fixing > the includes, pdb-extract doesn't seem to compile against cifparse-obj-7.025 > due to missing member functions etc. I guess it is time for a version bump ;) > The path is set in one of the patches, but still after correcting this, there are huge number of missing include to fix. Shall I write the bump? (In reply to comment #5) > The path is set in one of the patches, but still after correcting this, there > are huge number of missing include to fix. Shall I write the bump? > That would be great, thanks in advance! I am currently in the middle of preparing for a conference and won't have much time to do it myself until I return. I had a brief look at the most recent version available (3.004) last night but it looks like their makefile(s) are pretty badly broken and will probably need quite a bit of massaging. cheers, Markus (In reply to comment #6) > I had a brief look at the most recent version available (3.004) last night > but it looks like their makefile(s) are pretty badly broken and will probably > need quite a bit of massaging. Yeah, their whole setup is really a mess. Thanks to both of you for dealing with it. (In reply to comment #4) > Thanks for tracking this down. Unfortunately, even after fixing > the includes, pdb-extract doesn't seem to compile against cifparse-obj-7.025 > due to missing member functions etc. I guess it is time for a version bump ;) No good news, even the newest version doesn't compile against cifparse-obj-7.025 due to missing headers which are included in the v6* package. Had some time to have a closer look. Tryed to build the already suplied libs from sci-libs/cifparse-obj which are duplicated. Focusing on the mein app, but it won't compile fine. Will do some more "massages". Thanks, Justin! I tryed hard to get it to work but without succes. Only building pdb-extract with the shipped cifsparse works. As it is basicaly the version 7.025, what do you think about using the included cifsparse and block the cifsparse package? I would probably change the cifparse package to use the version from the pdbextract tarball. (In reply to comment #12) > I would probably change the cifparse package to use the version from the > pdbextract tarball. > Sorry, didn't comment this bug. I had success with the "massages" bug 249933. We can build against latest cifparse the latest pdb-extract. fix is in sci overlay *** Bug 248342 has been marked as a duplicate of this bug. *** @sci-chemistry team: The only reason why I'm not last-riting this right now is that I don want to bother tracking down the reverse dependencies. If you got a fix in the sci overlay *import it in the tree*. This bug is at least year-old and I'm tired of this kind of stuff. (In reply to comment #16) > @sci-chemistry team: > > The only reason why I'm not last-riting this right now is that I don want to > bother tracking down the reverse dependencies. > > If you got a fix in the sci overlay *import it in the tree*. This bug is at > least year-old and I'm tired of this kind of stuff. > Could someone of the sci team please do that. The recruiters still need time to set me up, so I am not able to fix this myself in near future. (In reply to comment #17) > (In reply to comment #16) > > @sci-chemistry team: > > > > The only reason why I'm not last-riting this right now is that I don want to > > bother tracking down the reverse dependencies. > > > > If you got a fix in the sci overlay *import it in the tree*. This bug is at > > least year-old and I'm tired of this kind of stuff. > > > > Could someone of the sci team please do that. The recruiters still need time to > set me up, so I am not able to fix this myself in near future. > Hi Justin, Thanks much for the 3.004 ebuild and I've just added it to the main tree. Everything seems to work fine AFAICT. We should push 3.004 into stable as soon as the 30 day waiting period is over. cheers, Markus *** Bug 339494 has been marked as a duplicate of this bug. *** |