153766 2006-11-01 17:12 0000 Stabilisation request for EMBOSS 4.0.0 and related packages 2006-12-10 11:05:27 0000 1 1 1 Unclassified Gentoo Linux Applications unspecified All Linux RESOLVED FIXED P2 normal --- 1 ribosome@gentoo.org ribosome@gentoo.org sci-biology@gentoo.org sparc@gentoo.org ribosome@gentoo.org 2006-11-01 17:12:07 0000 I would like all supporting arches to please stabilise EMBOSS 4.0.0 and related packages. These were already stabilised on x86. On amd64, ppc64: sci-biology/prosite-19.36 sci-biology/rebase-610 sci-biology/aaindex-9.1 sci-biology/cutg-151 sci-biology/emboss-4.0.0 On ppc, ppc-macos: sci-biology/prosite-19.36 sci-biology/rebase-610 sci-biology/aaindex-9.1 sci-biology/cutg-151 sci-biology/emboss-4.0.0 sci-biology/embassy-domainatrix-0.1.0-r1 sci-biology/embassy-domalign-0.1.0-r1 sci-biology/embassy-domsearch-0.1.0-r1 sci-biology/embassy-emnu-1.05-r3 sci-biology/embassy-esim4-1.0.0-r3 sci-biology/embassy-hmmer-2.3.2 sci-biology/embassy-memenew-0.1.0 sci-biology/embassy-mse-1.0.0-r3 sci-biology/embassy-phylipnew-3.6b sci-biology/embassy-signature-0.1.0-r1 sci-biology/embassy-structure-0.1.0-r1 sci-biology/embassy-topo-1.0.0-r3 sci-biology/embassy-4.0.0 On sparc: None of these packages were ever stable on sparc, but I know they work perfectly at least on the (limited) sparc hardware I have access to. If you are interested in supporting EMBOSS in the stable branch, the following packages should be stabilised. Otherwise, feel free to remove your team from CC. In all cases, you really need to remove emboss from use.mask in the sparc profiles, but I will open another report for that. sci-biology/primer3-1.0.0 sci-biology/aaindex-9.1 sci-biology/cutg-151 sci-biology/prints-38.0 sci-biology/prosite-19.36 sci-biology/rebase-610 sci-biology/transfac-3.2 sci-biology/emboss-4.0.0 nixnut@gentoo.org 2006-11-02 10:39:20 0000 Do you have some test cases for these packages please? ribosome@gentoo.org 2006-11-02 13:51:15 0000 Created an attachment (id=101091) Small test suite for EMBOSS on Gentoo Sure. Here is a small test suite. If you think something more involved is necessary, just tell me, but I am pretty confident that if this runs correctly and produces correct results, your EMBOSS installation is fine. grobian@gentoo.org 2006-11-02 14:35:47 0000 ppc-macos fully moved into prefix nixnut@gentoo.org 2006-11-03 05:29:01 0000 Ok, the test script runs ok. Output seems ok as far as I can figure it out. ppc done kugelfang@gentoo.org 2006-11-04 07:48:15 0000 Created an attachment (id=101225) Output of emboss test-script Olivier: I presume the attached output is not what it should look like, is it? This is on amd64, please advise. je_fro@gentoo.org 2006-11-04 15:25:12 0000 Created an attachment (id=101248) output from test script Here's my output on amd64...I'm not sure what's wrong with yours. What character encoding are you using? corsair@gentoo.org 2006-11-15 05:09:00 0000 ppc64 stable thedude0001@gmx.de 2006-11-18 06:57:55 0000 Created an attachment (id=102270) Another emboss test suite output Let's add a third test on amd64, looks ok, so the problem seems to be on your end, Kugelfang... Emerges fine for me and seems to work ok. Portage 2.1.1-r1 (default-linux/amd64/2006.1/desktop, gcc-4.1.1, glibc-2.4-r4, 2.6.18-suspend2-Dudebox-Edition x86_64) ================================================================= System uname: 2.6.18-suspend2-Dudebox-Edition x86_64 AMD Athlon(tm) 64 Processor 3200+ Gentoo Base System version 1.12.6 Last Sync: Sat, 18 Nov 2006 05:00:01 +0000 distcc 2.18.3 x86_64-pc-linux-gnu (protocols 1 and 2) (default port 3632) [enabled] ccache version 2.3 [enabled] app-admin/eselect-compiler: [Not Present] dev-java/java-config: 1.3.7, 2.0.30 dev-lang/python: 2.4.3-r4 dev-python/pycrypto: 2.0.1-r5 dev-util/ccache: 2.3 dev-util/confcache: [Not Present] sys-apps/sandbox: 1.2.17 sys-devel/autoconf: 2.13, 2.60 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2 sys-devel/binutils: 2.16.1-r3 sys-devel/gcc-config: 1.3.13-r4 sys-devel/libtool: 1.5.22 virtual/os-headers: 2.6.11-r2 ACCEPT_KEYWORDS="amd64" AUTOCLEAN="yes" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=k8 -msse3 -Os -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/X11/xkb /usr/share/config /var/qmail/alias /var/qmail/control /var/vpopmail/domains /var/vpopmail/etc" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /etc/java-config/vms/ /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c" CXXFLAGS="-march=k8 -msse3 -Os -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="autoconfig ccache collision-protect distcc distlocks metadata-transfer multilib-strict parallel-fetch sandbox sfperms strict test" GENTOO_MIRRORS="ftp://linux.rz.ruhr-uni-bochum.de/gentoo-mirror/ ftp:///ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/" LDFLAGS="-Wl,-O1" MAKEOPTS="-j4" PKGDIR="/usr/portage/packages" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude='/distfiles' --exclude='/local' --exclude='/packages'" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage_overlay" SYNC="rsync://server/gentoo-portage" USE="amd64 X alsa apache2 berkdb bitmap-fonts cairo cdr cli cracklib crypt cups dbus dlloader dri dvd dvdr eds elibc_glibc emboss encode esd fam firefox fortran gcj gdbm gif gpm gstreamer gtk gtk2 hal iconv imap input_devices_keyboard input_devices_mouse isdnlog jpeg kde kdeenablefinal kdehiddenvisibility kernel_linux libg++ mad mikmod mp3 mpeg mysql ncurses nls nptl nptlonly objc objc++ ogg oss pam pcre perl png ppds pppd python qt3 quicktime readline reflection sdl session spell spl sqlite ssl tcpd test truetype truetype-fonts type1-fonts udev unicode userland_GNU video_cards_radeon vorbis xml xorg xv zlib" Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LINGUAS, PORTAGE_RSYNC_EXTRA_OPTS blubb@gentoo.org 2006-11-20 12:58:49 0000 amd64 done ribosome@gentoo.org 2006-12-10 11:05:27 0000 All arches done. Thanks to everyone. 101091 2006-11-02 13:51 0000 Small test suite for EMBOSS on Gentoo emboss-test.sh text/plain IyEvYmluL2Jhc2gKCiMgQ29weXJpZ2h0IDE5OTktMjAwNiBHZW50b28gRm91bmRhdGlvbgojIERp c3RyaWJ1dGVkIHVuZGVyIHRoZSB0ZXJtcyBvZiB0aGUgR05VIEdlbmVyYWwgUHVibGljIExpY2Vu c2UgdjIKCiMgZW1ib3NzLXRlc3Quc2ggLSBBIHNtYWxsIHRlc3Qgc3VpdGUgZm9yIEVNQk9TUyA0 LjAuMCBvbiBHZW50b28KIyBPbGl2aWVyIEZpc2V0dGUgPHJpYm9zb21lQGdlbnRvby5vcmc+IDIw MDYtMTEtMDIKCnNvdXJjZSAiL3NiaW4vZnVuY3Rpb25zLnNoIgoKZWluZm8gIkVNQk9TUyB2ZXJz aW9uIChmcm9tIFwiZW1ib3NzdmVyc2lvblwiKTogJChlbWJvc3N2ZXJzaW9uIC1hdXRvKSIKCmVj aG8KZWluZm8gIlVzZSBcInNlcXJldFwiIHRvIHN0b3JlIGEgc2VxdWVuY2UgaW4gR2VuQmFuayBm b3JtYXQsIGluIGxvd2VyY2FzZS4iCmVpbmZvICJBZGQgYSB0aXRsZSB1c2luZyBcImRlc2NzZXFc IiBhbmQgY29udmVydCB0byBGYXN0YSBmb3JtYXQuIFByaW50IGl0IgplaW5mbyAib24gc2NyZWVu IGluIEVNQkwgZm9ybWF0LiIKZWNobwpzZXFyZXQgLWF1dG8gLXNsb3dlciAicmF3OjpzdGRpbiIg ImdlbmJhbms6OnBoaWt6LWx5cy5nYiIgPDwtIEVPRgoJQVRHQUFBR1RBVFRBQ0dDQUFBR0dDR0FU 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