Bug 294811 – sci-biology/shrimp fails to build

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Diego Elio Pettenò (RETIRED) 2009-11-27 11:46:44 UTC]

Portage 2.1.7.6 (default/linux/x86/10.0, gcc-4.4.2-asneeded, glibc-2.11-r0, 2.6.32-rc8 i686)
=================================================================
System uname: Linux-2.6.32-rc8-i686-Quad-Core_AMD_Opteron-tm-_Processor_2350-with-gentoo-2.0.1
Timestamp of tree: Sun, 22 Nov 2009 13:30:01 +0000
distcc 3.1 i686-pc-linux-gnu [disabled]
ccache version 2.4 [enabled]
app-shells/bash:     4.0_p35
dev-java/java-config: 1.3.7-r1, 2.1.9-r1
dev-lang/python:     2.6.2-r2, 3.1.1-r1
dev-python/pycrypto: 2.0.1-r8
dev-util/ccache:     2.4-r8
dev-util/cmake:      2.6.4-r2
sys-apps/baselayout: 2.0.1
sys-apps/openrc:     0.5.2-r2
sys-apps/sandbox:    2.1
sys-devel/autoconf:  2.13, 2.65
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2, 1.11
sys-devel/binutils:  2.20
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.6a
virtual/os-headers:  2.6.30-r1
ACCEPT_KEYWORDS="x86 ~x86"
ACCEPT_LICENSE="*"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O2 -pipe"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /opt/openfire/resources/security/ /opt/openjms/config /usr/lib/ccs/conf /usr/lib/fax /usr/share/X11/xkb /usr/share/bufrtables /usr/share/config /usr/share/qpsmtpd/plugins /var/bind /var/lib/hsqldb /var/phxd /var/qmail/alias /var/qmail/control /var/spool/fax/etc /var/spool/torque /var/vpopmail/etc"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/eselect/postgresql /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c /etc/udev/rules.d"
CXXFLAGS="-O2 -pipe"
DISTDIR="/var/cache/distfiles"
FEATURES="assume-digests ccache distlocks fixpackages news parallel-fetch protect-owned sandbox sfperms split-log strict test test-fail-continue unmerge-orphans userfetch"
GENTOO_MIRRORS="http://ftp.uni-erlangen.de/pub/mirrors/gentoo"
INSTALL_MASK="  /usr/share/doc  /usr/share/info"
LDFLAGS="-Wl,-O1"
MAKEOPTS="-j14"
PKGDIR="/var/spool/portage/packages"
PORTAGE_COMPRESS=""
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/var/cache/portage/tree-tinderbox"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="acl berkdb bzip2 cli cracklib crypt cups dri fortran gdbm gpm iconv ipv6 java5 java6 modules mudflap ncurses nls nostatic nptl nptlonly openmp pam pcre perl pppd python qt3support readline reflection ruby session spl ssl sysfs tcpd unicode x86 xorg 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 mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias auth_digest" ELIBC="glibc" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" 
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, LANG, LC_ALL, LINGUAS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY

[Comment 1 Diego Elio Pettenò (RETIRED) 2009-11-27 11:46:58 UTC]

Created attachment 211309 [details]
Build log

[Comment 2 Martin Mokrejš 2009-12-07 23:19:59 UTC]

Same here on ~amd64 and ~x86. I also tested shrimp-1.3.1 and has same problem.

[Comment 3 Martin Mokrejš 2009-12-08 00:00:49 UTC]

Have emailed upstream about this.

[Comment 4 Martin Mokrejš 2009-12-08 20:18:42 UTC]

Created attachment 212490 [details, diff]
stdint_h.patch

I received proposal from upstream and it works! ;-)

[Comment 5 Martin Mokrejš 2009-12-08 20:19:45 UTC]

Created attachment 212492 [details, diff]
shrimp-1.3.0.ebuild.patch

Please provide also 1.3.1.ebuild, basically just copy the patched 1.3.0 under a new name. Thanks.

[Comment 6 Andrey Kislyuk (RETIRED) 2009-12-09 18:52:27 UTC]

Fixed in tree, thanks for your help. Please test.

[Comment 7 Martin Mokrejš 2009-12-11 00:45:40 UTC]

(In reply to comment #6)
> Fixed in tree, thanks for your help. Please test.
> 

1.3.1 compiles fine on ~amd64 and ~x86. Thanks.