[EMBOSS] Problems installing EMBASSY / PHYLIPNEW

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Thu Jul 9 11:33:59 UTC 2009 

Hmmm.  My sys admin says....

I can find:
libXaw-devel.x86_64 : X.Org X11 libXaw development package
libXaw.x86_64 : X.Org X11 libXaw runtime library
libXaw.i386 : X.Org X11 libXaw runtime library
libXaw-devel.i386 : X.Org X11 libXaw development package

Have I got compatibility issues here?


-----Original Message-----
From: jason zhang [mailto:jasonzhang2002 at gmail.com]
Sent: Mon 06/07/2009 5:35 PM
To: michael watson (IAH-C)
Cc: emboss at lists.open-bio.org
Subject: Re: [EMBOSS] Problems installing EMBASSY / PHYLIPNEW
 
Hi, Michael
I did this in my fedora server : yum install libXaw libXaw-compat 
libXaw-devel to resolve this.

-jason

michael watson (IAH-C) wrote:
> Hello
>
>  
>
> I did this on a test server a few weeks ago and wrote a script and it
> worked.
>
>  
>
> Now I come to the production server - well, I get some errors.  Same OS,
> same tar balls.  Very frustrating.  Can anyone help?
>
>  
>
> I have PHYLIPNEW-3.67 unpacked in EMBOSS-6.0.1/embassy/PHYLIPNEW-3.67.
> In that directory, I run configure and then make
>
>  
>
> I get a variety of errors, but this time it's:
>
>  
>
> Making all in src
>
> make[1]: Entering directory
> `/home/bioinfvm/EMBOSS-6.0.1/embassy/PHYLIPNEW-3.67/src'
>
> gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
> -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"PHYLIPNEW\"
> -DVERSION=\"3.67\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
> -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1
> -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1
> -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1
> -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1
> -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1
> -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_STRDUP=1 -DHAVE_STRSTR=1
> -DHAVE_STRCHR=1 -DHAVE_ERAND48=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1
> -DPLD_png=1 -I. -I../include -I../../../ajax -I../../../nucleus
> -I../../../plplot  -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64
> -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE  -DLENDIAN -DNO_AUTH  -O2
> -D__amd64__ -MT clique.o -MD -MP -MF .deps/clique.Tpo -c -o clique.o
> clique.c
>
> mv -f .deps/clique.Tpo .deps/clique.Po
>
> gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
> -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"PHYLIPNEW\"
> -DVERSION=\"3.67\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
> -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1
> -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1
> -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1
> -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1
> -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1
> -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_STRDUP=1 -DHAVE_STRSTR=1
> -DHAVE_STRCHR=1 -DHAVE_ERAND48=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1
> -DPLD_png=1 -I. -I../include -I../../../ajax -I../../../nucleus
> -I../../../plplot  -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64
> -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE  -DLENDIAN -DNO_AUTH  -O2
> -D__amd64__ -MT disc.o -MD -MP -MF .deps/disc.Tpo -c -o disc.o disc.c
>
> mv -f .deps/disc.Tpo .deps/disc.Po
>
> gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
> -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"PHYLIPNEW\"
> -DVERSION=\"3.67\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
> -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1
> -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1
> -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1
> -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1
> -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1
> -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_STRDUP=1 -DHAVE_STRSTR=1
> -DHAVE_STRCHR=1 -DHAVE_ERAND48=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1
> -DPLD_png=1 -I. -I../include -I../../../ajax -I../../../nucleus
> -I../../../plplot  -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64
> -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE  -DLENDIAN -DNO_AUTH  -O2
> -D__amd64__ -MT phylip.o -MD -MP -MF .deps/phylip.Tpo -c -o phylip.o
> phylip.c
>
> mv -f .deps/phylip.Tpo .deps/phylip.Po
>
> /bin/sh ../libtool --tag=CC   --mode=link gcc  -O2 -D__amd64__   -o
> fclique clique.o disc.o phylip.o ../../../nucleus/libnucleus.la
> ../../../ajax/libajax.la ../../../plplot/libeplplot.la -L/usr/lib64
> -lX11  -lXaw -lXt -lm  -lgd -lpng -lz -lm
>
> mkdir .libs
>
> gcc -O2 -D__amd64__ -o .libs/fclique clique.o disc.o phylip.o
> ../../../nucleus/.libs/libnucleus.so ../../../ajax/.libs/libajax.so
> ../../../plplot/.libs/libeplplot.so -L/usr/lib64 -lX11 -lXaw -lXt -lgd
> -lpng -lz -lm  -Wl,--rpath -Wl,/usr/local/lib
>
> /usr/bin/ld: cannot find -lXaw
>
> collect2: ld returned 1 exit status
>
> make[1]: *** [fclique] Error 1
>
> make[1]: Leaving directory
> `/home/bioinfvm/EMBOSS-6.0.1/embassy/PHYLIPNEW-3.67/src'
>
> make: *** [all-recursive] Error 1
>
>  
>
> Any help would be appreciated.
>
>  
>
> Thanks
>
> Mick
>
>  
>
> Head of Bioinformatics
> Institute for Animal Health
> Compton
> Berks
> RG20 7NN
> 01635 578411 
>
>  
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