I am package masking "app-sci/ncbi-tools" (all versions) because of the following issues: - No check for compilation success. The merge process would take place even if compilation failed, resulting in a broken setup. - The NCBI Toolkit (libraries and headers for application development) is not installed. Only the NCBI applications (sequin, entrez, blast...) are. It is thus impossible to compile applications based on the NCBI toolkit application framework (such as njplot, phylo_win, clustalx, etc.). - More than 80 % of the documentation (including all 58 man pages) is missing. - Shared data is installed in "/usr/var". This directory does not exist in the FHS, and I do not think "var" is appropriate since the data is not variable (updating a blast database is part of the system management process, the database is not modified during system operation unless I am mistaken). I think this static data should go in "/usr/share". - It is not correct to force the usage of a skel file (and to require existing users' accounts to be modified) when it is not absolutely necessary. In the present case, setting the "NCBI" variable in an env file to point to a system-wide config file would be a lot better. - The ebuild does not honor "CFLAGS" or "CC". It is correct to filter some flags if they are known to cause problems, but not to leave the developer's flags in place, especially since it is possible to compile this package with optimized flags without problem as long as they are not aggressive. I am working on a new ebuild, but I still wanted to post this on Bugzilla to avoid silently changing a package for which there is a maintainer. I'll wait for sediener's OK before commiting anything (but I really felt I had to mask the package).
Created attachment 40822 [details] ncbi-tools/ncbi-tools-20040616.ebuild This ebuild fixes the problems I mentionned. It is also an updated version of the NCBI toolkit.
Created attachment 40823 [details] 21ncbi
Created attachment 40824 [details] ncbirc
Sounds good but I am having trouble locating "ncbi-tools-20040616.tar.gz". None of the mirrors I connect to seemto have it. Additionally, I went to http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit.section.release_notes and found that ncbi-tools 2004-07-08 is available. Is this the same ncbi-tools?
Hi Greg, The july 8th release is for the NCBI C++ toolkit, not the classic C toolkit. Latest release for the later toolkit is june 16th (unless I am mistaken). I plan to look into the C++ toolkit later, but I have no time for this right now. I am pretty sure there is some overlapping functionnality in the two packages, but I will have to learn more about them before considering the C++ toolkit for inclusion in Portage. Thanks for the tip anyway. You will not find the ncbi-toolkit archive on the Gentoo mirrors since I have not uploaded it yet. You can download it from the NCBI FTP server: "ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/ncbi.tar.gz" (rename it to ncbi-tools-20040616.tar.gz and put it in your distfiles directory). I will post the SDK documentation here. Just copy it to your distfiles directory if you want to have developer documentation installed. Cheers,
Created attachment 40887 [details] ncbi-tools-sdk-doc.tar.bz2 - SDK documentation
Looks good to me, I was just getting back into looking at my packages after an absence for a while. Go ahead and submit if you feel it's ready. I had tried to deal with some of these things previously (CFLAGS, NCBI variable, etc) but ran into so many problems that I just gave up. If someone would have thrown a bug at me I would have looked back into them... - Steve
Thanks, sediener. I commited the new version to CVS (with small changes). I will unmask the package in a few hours when I am sure the SDK documentation archive has hit the Gentoo mirrors. The only remaining problem is we no longer have a "x86" "ncbi-tools" since it would be too much work (for me at least) to backport the fixes to the old versions. I do not think this is problematic anyway, since no stable package depends on "ncbi-tools".
It is problematic to stable users who suddenly had a package disappear (Their emerge -u world may break, but not sure on that), but there's not much we can do about it.
I think I found the problem in ncbi-tools-20070826/work/ncbi/platform/linux64.ncbi.mk could someone please add the following patch to portage? Thanks. patch file: --- linux64.ncbi.mk 2008-03-16 03:30:08.000000000 +0100 +++ ncbi/platform/linux64.ncbi.mk 2008-03-16 03:29:33.000000000 +0100 @@ -15,13 +15,13 @@ NCBI_ALTLIB = /home/coremake/ncbi/altlib #will work only when you have Motif installed! NCBI_VIBFLAG = -I/usr/X11R6/include -L/usr/X11R6/lib64 -L/usr/X11R6/lib -DWIN_MOTIF NCBI_VIBLIBS = -lXmu -lXm -lXt -lSM -lICE -lXext -lXp -lX11 -ldl #warning! If you have only dynamic version of Motif or Lesstif #you should delete -Wl,-Bstatic sentence from the next line: -NCBI_DISTVIBLIBS = -L/usr/X11R6/lib64 -L/usr/X11R6/lib -lXmu -Wl,-Bstatic -lXm -Wl,-Bdynamic -lXt -lSM -lICE -lXext -lXp -lX11 -ldl +NCBI_DISTVIBLIBS = -L/usr/X11R6/lib64 -L/usr/X11R6/lib -lXmu -lXm -lXt -lSM -lICE -lXext -lXp -lX11 -ldl NCBI_OTHERLIBS = -lm NCBI_RANLIB = ranlib # Used by makedis.csh NCBI_MT_OTHERLIBS = -lpthread NCBI_OTHERLIBS_MT = $(NCBI_MT_OTHERLIBS) -lm NCBI_THREAD_OBJ = ncbithr.o
(In reply to comment #11) > I think I found the problem in > ncbi-tools-20070826/work/ncbi/platform/linux64.ncbi.mk > could someone please add the following patch to portage? Thanks. > Hi Till, Thanks much for the patch. Could you please be a bit more specific as to what "problem" your patch is addressing? Thanks, Markus
It is to avoid an compilation error due to static linking to openmotiv on amd64 systems I actually found the right bug now and posted a working patch and ebuild there: Bug #195251 sorry for the confusion.
Thanks for the clarification :) cheers, Markus
