'emerge emboss' fails with: ... >>> Downloading 'ftp://ftp.tu-clausthal.de/pub/linux/gentoo/distfiles/emboss-6.3.1_p4-upstream.patch.gz' --2011-09-19 16:48:35-- ftp://ftp.tu-clausthal.de/pub/linux/gentoo/distfiles/emboss-6.3.1_p4-upstream.patch.gz Connecting to 10.101.10.254:3128... connected. Proxy request sent, awaiting response... 404 Not Found 2011-09-19 16:48:35 ERROR 404: Not Found. >>> Downloading 'ftp://ftp.easynet.nl/mirror/gentoo/distfiles/emboss-6.3.1_p4-upstream.patch.gz' --2011-09-19 16:48:35-- ftp://ftp.easynet.nl/mirror/gentoo/distfiles/emboss-6.3.1_p4-upstream.patch.gz Connecting to 10.101.10.254:3128... connected. Proxy request sent, awaiting response... 503 Service Unavailable 2011-09-19 16:48:35 ERROR 503: Service Unavailable. >>> Downloading 'ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-4.gz' --2011-09-19 16:48:35-- ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-4.gz Connecting to 10.101.10.254:3128... connected. Proxy request sent, awaiting response... 404 Not Found 2011-09-19 16:48:37 ERROR 404: Not Found. !!! Couldn't download 'emboss-6.3.1_p4-upstream.patch.gz'. Aborting. * Fetch failed for 'sci-biology/emboss-6.3.1_p4-r1', Log file: * '/var/tmp/portage/sci-biology/emboss-6.3.1_p4-r1/temp/build.log' >>> Failed to emerge sci-biology/emboss-6.3.1_p4-r1, Log file:
Created attachment 287021 [details] /var/tmp/portage/sci-biology/emboss-6.3.1_p4-r1/temp/build.log
I will bump it.
Hi Justin, two days later I can't find emboss-6.4 neither in the portage tree nor in the science overlay. Regards Juergen
Probably There were some reallife things which hinders me from fixing that. Do you like to propose a patch?
Created attachment 287575 [details] emboss-6.3.1_p4-r1.ebuild with changed URL The attached ebuild emerged emboss-6.3.1_p4-r1 and helped to reemerge the depending packages after libpng upgrade to libpng-1.5.4.
Thanks Juergen. I added you patch to the overlay. It will take another week or so for the bump. But it is on my list.
Hi Justin, I suppose that you changed the title of the bug. I think that the new title does not really reflect the problem of the bug. Regards Juergen
(In reply to comment #7) > Hi Justin, > > I suppose that you changed the title of the bug. I think that the new title > does not really reflect the problem of the bug. > > Regards Juergen But it would be a fix. I add your change until the bump is fixed.
Hi, All, The urgency of this just increased for me because of the disappearance of libpng14 and libLASi.so.0 from portage. The emboss components, whether the ones recently masked by Justin or the really old ones, are now unbuildable for me, even with plplot-5.9.9 masked, because the patches no longer work. My workaround has been to keep libpng14 and lasi 1.0 around for now.
Version 6.6.0 now in science overlay (thanks, Justin!), but fails to find a patch file: * Cannot find $EPATCH_SOURCE! Value for $EPATCH_SOURCE is: * * /var/tmp/portage/sci-biology/emboss-6.6.0/work/emboss-6.6.0-upstream.patch * ( emboss-6.6.0-upstream.patch )
No Joel, that was me who committed the broken ebuild. My apologies. I have dropped the KEYWORDS for now, added the patch, and much more. See the Changelog in the overlay. Maybe you will be lucky to get through the 3-4 issues I faced with 6.6.0. ;) However, I tried to cleanup a bit the 6.3.1-p4-r1 ebuild there aiming to shrink down the number of libraries being linked into resulting binaries (bug #394425).
AFAIR there was put some effort into the emboss ebuild and eclass. 6.6.0 is in the tree now. Therefore I believe this bug is obsolete and can be closed. Please correct me if I am wrong, otherwise I will close this in the next few days.
