I have currebntly on ~x86 the following version: * sci-biology/seaview Latest version available: 20071113 Latest version installed: 20071113 Size of files: 152 kB Homepage: http://pbil.univ-lyon1.fr/software/seaview.html The site offers to download ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/seaview.linuxPC.tgz but it contains a string "Version 3.2". Maybe somebody coudl hack the ebuild to check for the version number in the HTML webpage and based on that download the .tgz file? Anyway, please bump the version in portage. Thanks.
Created attachment 172083 [details] seaview-3.2.ebuild Working ebuild but would be wise to make it detect CXXFLAGS and LDFLAGS needed for FLTK using fltk-config, see comments in the ebuild. Please drop the $PN-$timestamp and use $PN-$PV as proposed by this ebuild. The release have finally a release version number, see ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/
Created attachment 191806 [details] seaview-4.0.ebuild The current source archive lacks some of the formerly present files: * dobin: seaview_align.sh does not exist * doins: protein.mase does not exist * doins: seaview.help does not exist * doins: seaview.xpm does not exist * doins: seaview.desktop does not exist These are not crucial. Second, pdflib suport is disabled by default. Have asked upstream on both issues. Finally, added DEPEND on sci-biology/phyml. Please commit to science overlay if not ~x86 and ~amd64. Thanks.
Answer from upstream: <quote> > * dobin: seaview_align.sh does not exist this file is no longer necessary > * doins: protein.mase does not exist this example file has been replaced by example.nxs > * doins: seaview.help does not exist this help file has been replaced by seaview.html > * doins: seaview.xpm does not exist yes it is in the archive > * doins: seaview.desktop does not exist I have no idea of what is this file </quote> Based on that I will attach a working ebuild. Somehow the source archive currently lacks example.nxs but who cares. The ebuild is ready to install it once it appears in the tar.gz file. Andrey, I think it is ready to go into testing.
Created attachment 192510 [details] seaview-4.0.ebuild Except the following the ebuild is fine: >>> Install seaview-4.0 into /var/tmp/portage/sci-biology/seaview-4.0/image/ category sci-biology install: cannot stat `example.nxs': No such file or directory !!! doins: example.nxs does not exist >>> Completed installing seaview-4.0 into /var/tmp/portage/sci-biology/seaview-4.0/image/ * QA Notice: file does not exist: * * doins: example.nxs does not exist >>> Installing (1 of 1) sci-biology/seaview-4.0 Newly, it used pdf USE flag to detect whether postscript (upstream default) or pdf output files will be written. Tested with pdflib 6 and 7 on ~x86.
From: Manolo Gouy I just want to draw your attention to some licensing issues concerning seaview. It uses some code from PHYLIP which is copyright University of Washington (not GPL) as follows: ================================================== (c) Copyright 1980-2008. University of Washington. All rights reserved. Permission is granted to reproduce, perform, and modify these programs and documentation files. Permission is granted to distribute or provide access to these programs provided that this copyright notice is not removed, the programs are not integrated with or called by any product or service that generates revenue, and that your distribution of these documentation files and programs are free. Any modified versions of these materials that are distributed or accessible shall indicate that they are based on these programs. Institutions of higher education are granted permission to distribute this material to their students and staff for a fee to recover distribution costs. Permission requests for any other distribution of these program should be directed to license (at) u.washington.edu . ================================================== So distribution is authorized only if it does not generate revenue. Somebody please "fix" the LICENSE line in the ebuild. ;-)
From upstream: I added file example.nxs to the archive a few days ago, so get it anew from ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/seaview.tar.gz
Created attachment 192559 [details] seaview-4.0.ebuild Upstream improved the Makefile in the sources. Except maybe the LICENSE issue it can go into the tree.
Thank you, I'll get this in ASAP :)
Rats! I have installed glibc-2.10 and I think I'm hitting issues related to fltk/glibc-2.10 bugs.
Regarding the licensing issue, with version 4.0 happened the change. From my communication with upstream: <quote> >> ... until I was asked by Debian people for a PostScript version compatible >> with GPL code. > > Maybe that is why seaview is under Gentoo Linux tagged as being covered > by a "public domain" license? But you emailed me about the PHYML licence, > right? > Yes, seaview used to be all GPL, but it now contains some code from PhyML, which is GPL, so does not cause license change, and also from PHYLIP which is not GPL. The Debian seaview distribution, currently under preparation, will thus be moved to the non-free category. </quote>
Created attachment 198105 [details] seaview-4.1.ebuild I note that seaview has unhappily been removed from portage. Upstream has smaller issues than before, and this e-build is cleaner than it had been. Changes I made were: 1. archive URL changed 2. added xft USE flag 3. replaced sci-biology/muscle with sci-libs/libmuscle. Muscle probably needs both to be slotted and to have a virtual, since muscle 4.0 has arrived in rough shape. 4. re-added desktop of old 2007 ebuild 5. html help added 6. man page is shipped now Compiled and runs for me using unstable fltk:2.
Taking bug.
Joel, Martin, Thank you for your input. For the moment I am unable to proceed since the upstream website is offline.
(In reply to comment #11) > Created an attachment (id=198105) [edit] > seaview-4.1.ebuild Joel, thanks for the improved ebuild. I have problems on ~x86, though. :( > 3. replaced sci-biology/muscle with sci-libs/libmuscle. Muscle probably needs > both to be slotted and to have a virtual, since muscle 4.0 has arrived in > rough shape. # emerge =sci-biology/seaview-4.1 * IMPORTANT: 1 news items need reading for repository 'gentoo'. * Use eselect news to read news items. Calculating dependencies... done! [ebuild N ] sci-libs/libmuscle-3.7-r1 USE="-doc" [ebuild N ] sci-biology/seaview-4.1 USE="pdf xft" [blocks B ] sci-biology/muscle ("sci-biology/muscle" is blocking sci-libs/libmuscle-3.7-r1) * Error: The above package list contains packages which cannot be * installed at the same time on the same system. ('ebuild', '/', 'sci-libs/libmuscle-3.7-r1', 'merge') pulled in by sci-libs/libmuscle required by ('ebuild', '/', 'sci-biology/seaview-4.1', 'merge') ('installed', '/', 'sci-biology/muscle-3.7', 'nomerge') pulled in by sci-biology/muscle required by world
I dropped the 3 DEPENDencies on clustalw, phyml and libmuscle to be able to get further. I believe these are just RDEPENDencies anyway. However, I get stuck here: >>> Emerging (1 of 1) sci-biology/seaview-4.1 from unknown repo * seaview_4.1.tar.gz RMD160 SHA1 SHA256 size ;-) ... [ ok ] * checking ebuild checksums ;-) ... [ ok ] * checking auxfile checksums ;-) ... [ ok ] * checking miscfile checksums ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking seaview_4.1.tar.gz to /var/tmp/portage/sci-biology/seaview-4.1/work >>> Source unpacked in /var/tmp/portage/sci-biology/seaview-4.1/work >>> Compiling source in /var/tmp/portage/sci-biology/seaview-4.1/work ... i686-pc-linux-gnu-g++ -c -DUSE_XFT -I/usr/include -I/usr/include/freetype2 -DFLTK1 -Dunix -O2 -march=pentium4 -mmmx -msse -msse2 -pipe -fno-strict-aliasing -ggdb -I/usr/include/fltk-1.1 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_THREAD_SAFE -D_REENTRANT -Icsrc -I. -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -I/usr/include custom.cxx i686-pc-linux-gnu-g++ -c -DUSE_XFT -I/usr/include -I/usr/include/freetype2 -DFLTK1 -Dunix -O2 -march=pentium4 -mmmx -msse -msse2 -pipe -fno-strict-aliasing -ggdb -I/usr/include/fltk-1.1 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_THREAD_SAFE -D_REENTRANT -Icsrc -I. -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -I/usr/include use_mase_files.cxx use_mase_files.cxx: In function ‘int output_next_res_from_region(char*, int, list_segments**, int*, FILE*, int, int)’: use_mase_files.cxx:828: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result use_mase_files.cxx: In function ‘void inform_prog_dir(const char*)’: use_mase_files.cxx:1516: error: invalid conversion from ‘const char*’ to ‘char*’ use_mase_files.cxx: In function ‘const char* extract_dirname(const char*)’: use_mase_files.cxx:1752: error: invalid conversion from ‘const char*’ to ‘char*’ make: *** [use_mase_files.o] Error 1 * * ERROR: sci-biology/seaview-4.1 failed. * Call stack: * ebuild.sh, line 49: Called src_compile * environment, line 842: Called die Isn't this a problem with my too new glibc? I have glibc-2.10.1-r0 and this is ~x86 machine.
seaview-4.1 committed to main tree. Please test! I have removed keywords for seaview-20071113 since I'm not planning to maintain it and its version number gets ordered incorrectly. Thanks for contributing and sorry about the delay.
FYI it didn't work for me with fltk:2, if you can make it work I'd appreciate it
Yup, USE="-xft" works fine. I've been trying a long time to get it to build with recent fltk.
(In reply to comment #18) > Yup, USE="-xft" works fine. I've been trying a long time to get it to build > with recent fltk. > Does that mean I should change it to something like DEPEND="x11-libs/fltk xft? ( x11-libs/fltk:1.1[-noxft] )" ?
That's a good idea :)
I still have them problem to compile 4.1 on ~x86 as in comment #15. The ebuiled forced me to downgrade to x11-libs/fltk-1.1.7-r3 bug I cannot get it compiled (have opened bug #288332). So far I have x11-libs/fltk-2.0_pre6786-r1. Finally, I tried x11-libs/fltk-1.1.9-r1 and I could install it but some some reason the seaview ebuild still wants to install fltk-1.1.7-r3. Why? # emerge -pv =sci-biology/seaview-4.1 These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild UD] x11-libs/fltk-1.1.7-r3 [1.1.9-r1] USE="opengl -debug% -noxft% (-doc%) (-examples%) (-games%) (-threads%*) (-xft%*) (-xinerama%*)" 0 kB [ebuild UD] sci-biology/seaview-4.1 [20071113] USE="pdf%* xft%*" 0 kB Total: 2 packages (2 downgrades), Size of downloads: 0 kB
(In reply to comment #21) > I still have them problem to compile 4.1 on ~x86 as in comment #15. Sorry, this maybe not, I had to figure out I had a local copy of the seaview-4.1.ebuild from Joel in /usr/local/..., so cannot say at the moment as am stuck with the fltk-1.1.7-3 issue.
