Hi all, since wise-2.2.0 still has a buggy pthread support (actually the latest ebuild excludes pthread support), since wise-2.1.23c ebuild has been removed from portage tree (once again), even if it is the stable version (also with full pthread support), since wise-2.4.0 is on EBI ftp since 2005, I've decided to try it. It compiles, even if some more work should be done on documentation (in the same way it has been done on .tex files in wise-2.2.0).
Created attachment 130492 [details] the ebuild
emerge --info Portage 2.1.3.6 (default-linux/x86/no-nptl, gcc-4.1.1, glibc-2.5-r0, 2.6.19-gentoo-r4-smp i686) ================================================================= System uname: 2.6.19-gentoo-r4-smp i686 Intel(R) Xeon(TM) CPU 3.06GHz Gentoo Base System version 1.12.9 Timestamp of tree: Fri, 17 Aug 2007 12:50:01 +0000 dev-java/java-config: 1.3.7, 2.0.31-r3 dev-lang/python: 2.4.4 dev-python/pycrypto: 2.0.1-r5 sys-apps/sandbox: 1.2.18.1 sys-devel/autoconf: 2.13, 2.61 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.9.6-r2, 1.10 sys-devel/binutils: 2.17 sys-devel/gcc-config: 1.3.14 sys-devel/libtool: 1.5.22 virtual/os-headers: 2.6.19.2-r1 ACCEPT_KEYWORDS="x86 ~x86" AUTOCLEAN="yes" CBUILD="i686-pc-linux-gnu" CFLAGS="-march=pentium4 -O2 -fomit-frame-pointer -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/X11/xkb" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /etc/java-config/vms/ /etc/terminfo /etc/texmf/web2c" CXXFLAGS="-march=pentium4 -O2 -fomit-frame-pointer -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="distlocks metadata-transfer sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="http://mirror.switch.ch/ftp/mirror/gentoo http://distfiles.gentoo.org http://www.ibiblio.org/pub/Linux/distributions/gentoo" MAKEOPTS="-j3" 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 --filter=H_**/files/digest-*" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage" SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" USE="X apm arts berkdb bitmap-fonts cli cracklib crypt cups dri eds emboss encode foomaticdb fortran gdbm gif gpm gstreamer gtk gtk2 iconv imlib ipv6 isdnlog jpeg kde ldap libwww mad midi mikmod motif mp3 mpeg mudflap mysql ncurses nls ogg opengl openmp oss pam pcre perl png pppd python qt3 qt4 quicktime readline reflection session spell spl ssl tcpd threads truetype truetype-fonts type1-fonts vorbis x86 xml xorg xv zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mulaw multi null plug rate route share shm softvol" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" VIDEO_CARDS="apm ark chips cirrus cyrix dummy fbdev glint i128 i740 i810 imstt mach64 mga neomagic nsc nv r128 radeon rendition s3 s3virge savage siliconmotion sis sisusb tdfx tga trident tseng v4l vesa vga via vmware voodoo" Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
I forgot to say that this version doesn't compile with glib-2.x. It is a good thing that glib-1.2 can be installed as a slot!
It should be noted that wise-2.4.0 is an alpha version. It is true that pthread support in 2.2.0 is problematic but I believe that might be resolved with a little work (it looks like they never finished adding the code for pthread loop drivers, but there are examples that can be drawn upon). But if 2.4 (even alpha) has the corrected code then its better to go with that). Also, the problem compiling wise (actually HMMer2/sqio.c is due to the recent inclusion of getline() in stdio.h. This conflicts with the getline() function in sqio.c. I will be attaching that file to a new bug report I am filing on it.
Bumped, thanks for your contribution.
