233046 – sci-biology/clustalx-1.83-r2 fails to build (missing xpm dep?)

Bug 233046 - sci-biology/clustalx-1.83-r2 fails to build (missing xpm dep?)

Summary: sci-biology/clustalx-1.83-r2 fails to build (missing xpm dep?)

Status:	RESOLVED FIXED

Alias:	None

Product:	Gentoo Linux
Classification:	Unclassified
Component:	New packages (show other bugs)
Hardware:	All Linux

Importance:	High normal (vote)
Assignee:	Olivier Fisette (RETIRED)

URL:
Whiteboard:
Keywords:

Depends on:
Blocks:

Reported:	2008-07-26 21:10 UTC by Evil Compile Person
Modified:	2008-08-26 15:06 UTC (History)
CC List:	1 user (show)

See Also:
Package list:
Runtime testing required:	---

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Description Evil Compile Person 2008-07-26 21:10:54 UTC

i686-pc-linux-gnu-gcc -o clustalx interface.o sequence.o showpair.o malign.o util.o trees.o gcgcheck.o prfalign.o pairalign.o calcgapcoeff.o calcprf1.o calcprf2.o calctree.o readmat.o alnscore.o random.o  xutils.o xmenu.o xcolor.oxdisplay.o xscore.o clustalx.o -lm -O2 -march=i686 -pipe -L/usr/lib -L/usr/X11R6/lib -lvibrant -lncbi -lXm -lXmu -lXpm -lXt -lX11 -lm
/usr/lib/gcc/i686-pc-linux-gnu/4.1.2/../../../../i686-pc-linux-gnu/bin/ld: cannot find -lXpm
collect2: ld returned 1 exit status
make: *** [clustalx] Error 1
 *
 * ERROR: sci-biology/clustalx-1.83-r2 failed.

Portage 2.1.4.4 (default-linux/x86/2007.0, gcc-4.1.2, glibc-2.6.1-r0, 2.6.20-vs2.2.0-gentoo i686)                                                         
=================================================================            
System uname: 2.6.20-vs2.2.0-gentoo i686 Intel(R) Pentium(R) D CPU 3.20GHz   
Timestamp of tree: Wed, 23 Jul 2008 11:15:01 +0000                           
app-shells/bash:     3.2_p33                                                 
dev-lang/python:     2.5.2-r5                                                
sys-apps/baselayout: 1.12.11.1                                               
sys-apps/sandbox:    1.2.18.1-r2                                             
sys-devel/autoconf:  2.61-r2                                                 
sys-devel/automake:  1.10.1                                                  
sys-devel/binutils:  2.18-r3                                                 
sys-devel/gcc-config: 1.4.0-r4                                               
sys-devel/libtool:   1.5.26                                                  
virtual/os-headers:  2.6.17-r2                                               
ACCEPT_KEYWORDS="x86"                                                        
CBUILD="i686-pc-linux-gnu"                                                   
CFLAGS="-O2 -march=i686 -pipe"                                               
CHOST="i686-pc-linux-gnu"                                                    
CONFIG_PROTECT="/etc"                                                        
CONFIG_PROTECT_MASK="/etc/env.d /etc/gconf /etc/revdep-rebuild /etc/terminfo /etc/udev/rules.d"                                                           
CXXFLAGS="-O2 -march=i686 -pipe"                                             
DISTDIR="/usr/portage/distfiles"                                             
FEATURES="buildpkg distlocks metadata-transfer sandbox sfperms strict unmerge-orphans userfetch"                                                          
GENTOO_MIRRORS="http://mirror.switch.ch/mirror/gentoo/"                      
PKGDIR="/usr/portage/packages"                                               
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="/usr/portage"                                                       
SYNC="rsync://rsync.de.gentoo.org/gentoo-portage"
USE="X acl berkdb cli cracklib crypt cups dri fortran gcj gdbm gpm iconv ipv6 isdnlog midi mudflap ncurses nls nptl nptlonly objc openmp pam pcre perl pppd python readline reflection session spl ssl 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 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 envexpires 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" 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 cirruscyrix dummy fbdev glint i128 i740 i810 imstt mach64 mga neomagic nsc nv r128radeon rendition s3 s3virge savage siliconmotion sis sisusb tdfx tga tridenttseng v4l vesa vga via vmware voodoo"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, LINGUAS, MAKEOPTS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY

Comment 1 Jeffrey Gardner (RETIRED) gentoo-dev

2008-07-27 16:40:16 UTC

I cannot reproduce the failure.


Portage 2.2_rc3 (default-linux/amd64/2007.0/desktop, gcc-4.3.1,
glibc-2.8_p20080602-r0, 2.6.26-gentoo x86_64)
=================================================================
System uname:
Linux-2.6.26-gentoo-x86_64-Intel-R-_Core-TM-2_CPU_6700_@_2.66GHz-with-glibc2.2.5
Timestamp of tree: Sun, 27 Jul 2008 03:23:01 +0000
app-shells/bash:     3.2_p39
dev-java/java-config: 1.3.7, 2.1.6-r1
dev-lang/python:     2.4.4-r13, 2.5.2-r5
dev-python/pycrypto: 2.0.1-r6
sys-apps/baselayout: 2.0.0
sys-apps/openrc:     0.2.5
sys-apps/sandbox:    1.2.18.1-r3
sys-devel/autoconf:  2.13, 2.62-r1
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2,
1.10.1-r1
sys-devel/binutils:  2.18-r3
sys-devel/gcc-config: 1.4.0-r4
sys-devel/libtool:   2.2.4
virtual/os-headers:  2.6.25-r4
ACCEPT_KEYWORDS="amd64 ~amd64"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=core2 -mtune=core2 -O2 -pipe -fomit-frame-pointer"
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/kde/4.0/env /usr/kde/4.0/share/config
/usr/kde/4.0/shutdown /usr/share/config /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/
/etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild
/etc/terminfo /etc/texmf/web2c /etc/udev/rules.d"
CXXFLAGS="-march=core2 -mtune=core2 -O2 -pipe -fomit-frame-pointer"
DISTDIR="/usr/portage/distfiles"
FEATURES="collision-protect cvs digest distlocks multilib-strict parallel-fetch
preserve-libs sandbox sfperms strict unmerge-orphans userfetch"
GENTOO_MIRRORS="ftp://mirror.iawnet.sandia.gov/pub/gentoo
http://distfiles.gentoo.org
http://www.ibiblio.org/pub/Linux/distributions/gentoo"
LDFLAGS="-Wl,-O1,--hash-style=gnu,--sort-common,--as-needed"
LINGUAS="en en_US"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
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="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage/layman/je_fro
/usr/local/portage/layman/science"
SYNC="rsync://rsync.namerica.gentoo.org/gentoo-portage"
USE="X a52 aac acpi alsa amd64 apbs async automount bash-completion
bitmap-fonts blas branding bzip2 cairo cdio cdr chardet cli cracklib crypt
cscope cups custom-optimization dbus directfb divx djvu dlloader dri dts dvd
dvdnav dvdr dvdread dvi emboss encode exif fam fbcon ffmpeg fftw firefox flac
fontconfig foomaticdb fortran fortran95 gdbm gif glibc-omitfp gmedia gnutls
gphoto2 gpm gs gsl gstreamer gtk h323 hal hdf iconv ieee1394 ifc imagemagick
inotify int64 isdnlog ithreads java jce jfs joystick jpeg jpeg2k kde
kdehiddenvisibility lapack libnotify libwww logitech-mouse logrotate mad
maildir matroska midi mikmod mjpeg mmap mmx mng modplug mopac7 motif mp2 mp3
mp4 mpeg mpi mplayer mpqc mudflap musepack musicbrainz mysql ncurses netcdf
network newspr nfs nls no-old-linux no_wxgtk1 noamazon nosendmail nptl nptlonly
nsplugin nvidia nvtv offensive ogg openbabel opengl openmp pam pcre pdf perl
pertty plotutils png postfix ppds pppd python qt3 qt3support qt4 quicktime rar
readline realmedia reflection reiserfs roe rtc ruby samba sdl seamonkey session
shaders smp snmp spell spl sse sse2 ssl ssse3 startup-notification subtitles
subversion svg syslog t1lib tcl tcpd theora threads tiff tk transcode truetype
truetype-fonts type1-fonts udev unicode usb v4l v4l2 vcd vim-with-x
visualization vorbis wavpack webdav wma wmf wmp x264 xchattext xfs xgetdefault
xinetd xml xmpi xorg xpm xscreensaver xulrunner xv xvid xvmc zlib"
ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci 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"
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" ELIBC="glibc"
INPUT_DEVICES="evdev joystick keyboard mouse vmmouse wacom" KERNEL="linux"
LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses
text" LINGUAS="en en_US" USERLAND="GNU" VIDEO_CARDS="fbdev nv nvidia v4l v4l2
vesa vga vmware"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL,
PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

Comment 2 Olivier Fisette (RETIRED) gentoo-dev

2008-08-26 15:06:25 UTC

Added missing libXpm dependency. Thanks for reporting.