[EMBOSS] More on EMBOSS install on OS X: refuses to overwrite X11

Thu Mar 31 02:23:21 UTC 2005

Many thanks to all who suggested fixes for an OS X emboss install.
Not having time to mix and match, I tried them all. After a few failed  
attempts to try them one by one.

I updated to the latest X11SDK in the Xcode1.5 package.
I updated fink to the latest 0.71 version.
and then I tried using fink to install emboss.

It went on for a couple of _hours_, installing a huge number of things  
but then finally dumped me out, complaining that there is an existing  
X11 distribution and telling me to remove it. This is sort of  
obnoxious, since I use my existing X11 for sequence assembly with  
consed, and it works fine and is important to my work. Fink/emboss  
gives me no assurance that it will not screw up what I have working  
already (and which took me no small amount of effort to get working),  
so I am not about to blithely remove my existing X11 without some way  
to know that I will not mess up what is working now.

I thought maybe everything _but_ X11 got installed, but even the first  
example in the tutorial fails:
[dhc017077:~] robin% wossname
tcsh: wossname: Command not found.
[dhc017077:~] robin% man wossname
No manual entry for wossname

So now I cannot tell whether anything at all is working or what to do  
to debug it. Fink seems to have downloaded, compiled and installed  
hundreds of files on my machine but not given me any working programs.  
Very frustrating.

below are the last few lines of installer output.
Any advice on where to go from here appreciated...

robin

************

dpkg-deb: building package `xfree86-shlibs' in  
`/sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/xfree86- 
shlibs_4.4.0-13_darwin-powerpc.deb'.
dpkg -i  
/sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/ 
xfree86_4.4.0-13_darwin-powerpc.deb  
/sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/xfree86- 
shlibs_4.4.0-13_darwin-powerpc.deb
Selecting previously deselected package xfree86.
(Reading database ... 4015 files and directories currently installed.)
Unpacking xfree86 (from .../xfree86_4.4.0-13_darwin-powerpc.deb) ...
WARNING: if you compile X11 applications against this XFree86 release,
you will *not* be able to run them if you decide to revert to Apple's
X11 provided with Panther.

You have an existing X11 installation in /usr/X11R6 and/or /etc/X11.
This package refuses to overwrite these. Remove them, then tell Fink to
install xfree86 again. (The package won't be recompiled.) If you want
to keep your X11 installation, install system-xfree86 resp.  
system-xtools
instead to make this known to Fink's package system.

Press Return to continue.

dpkg: error processing  
/sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/ 
xfree86_4.4.0-13_darwin-powerpc.deb (--install):
  subprocess pre-installation script returned error exit status 1
Selecting previously deselected package xfree86-shlibs.
Unpacking xfree86-shlibs (from  
.../xfree86-shlibs_4.4.0-13_darwin-powerpc.deb) ...

You have an existing X11 installation in /usr/X11R6/lib.
This package refuses to overwrite these. Remove them, then tell Fink to
install xfree86-shlibs again. (The package won't be recompiled.)

Press Return to continue.

dpkg: error processing  
/sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/xfree86- 
shlibs_4.4.0-13_darwin-powerpc.deb (--install):
  subprocess pre-installation script returned error exit status 1
Errors were encountered while processing:

/sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/ 
xfree86_4.4.0-13_darwin-powerpc.deb

/sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/xfree86- 
shlibs_4.4.0-13_darwin-powerpc.deb
### execution of dpkg failed, exit code 1
Failed: can't batch-install packages:  
/sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/ 
xfree86_4.4.0-13_darwin-powerpc.deb  
/sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/xfree86- 
shlibs_4.4.0-13_darwin-powerpc.deb

On Mar 30, 2005, at 11:47 AM, Robin Colgrove wrote:

>
> Hello all,
>
> I am new to the list. Apologies if this is an FAQ. I could not find it  
> in the archives.
> Anyway, I am running OS X 10.3.8 and downloaded the latest EMBOSS,  
> 2.10.0.
> I followed the instruction for installation, ./configure, then
> sudo make
> which goes on for a long time, compiling an lot of things, but then  
> finally fails with:
> [...lots of stuff compiled OK...]
> source='aaindexextract.c' object='aaindexextract.o' libtool=no \
> DEPDIR=.deps depmode=gcc /bin/sh ../depcomp \
> gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"  
> -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\"  
> -DVERSION=\"2.10.0\" -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 -DX_DISPLAY_MISSING=1  
> -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1  
> -DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1  
> -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1  
> -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1  -I. -I. -I../nucleus -I../ajax  
> -I../plplot  -DAJ_MACOSXLF  -DBENDIAN -DNO_AUTH  -O2 -c  
> aaindexextract.c
> /bin/sh ../libtool --tag=CC --mode=link gcc  -O2   -o aaindexextract   
> aaindexextract.o ../nucleus/libnucleus.la ../ajax/libajaxg.la  
> ../ajax/libajax.la ../plplot/libplplot.la -lX11  -lm
> mkdir .libs
> gcc -O2 -o .libs/aaindexextract aaindexextract.o   
> ../nucleus/.libs/libnucleus.dylib ../ajax/.libs/libajaxg.dylib  
> ../ajax/.libs/libajax.dylib ../plplot/.libs/libplplot.dylib -lX11 -lm
> ld: can't locate file for: -lX11
> make[2]: *** [aaindexextract] Error 1
> make[1]: *** [all-recursive] Error 1
> make: *** [all-recursive] Error 1
>
> [...and then exits...]
>
> just to see if it would work, I tried
> sudo make install
> which installed a lot of things but then failed with:
>
> /bin/sh ../libtool --tag=CC --mode=link gcc  -O2   -o aaindexextract   
> aaindexextract.o ../nucleus/libnucleus.la ../ajax/libajaxg.la  
> ../ajax/libajax.la ../plplot/libplplot.la -lX11  -lm
> gcc -O2 -o .libs/aaindexextract aaindexextract.o   
> ../nucleus/.libs/libnucleus.dylib ../ajax/.libs/libajaxg.dylib  
> ../ajax/.libs/libajax.dylib ../plplot/.libs/libplplot.dylib -lX11 -lm
> ld: can't locate file for: -lX11
> make[2]: *** [aaindexextract] Error 1
> make[1]: *** [install-recursive] Error 1
> make: *** [install-recursive] Error 1
>
> Hoping it would work anyway, I tried the tutorial and the first  
> example:
> %wossname
> fails with
> tcsh: wossname: Command not found.
> even though I see:
> /usr/local/share/EMBOSS/acd/wossname.acd
>
> My knowledge of these things is rudimentary, but the error seems to be  
> complaining about not finding X11, but that can't be right, since I  
> have
> X11 1.0 - XFree86 4.3.0
> and have been using it for other programs like Phred/Phrap/Consed.
>
> Does anyone know what this error means and how to fix it?
>
> thanks
>
> robin colgrove
> department of microbiology
> harvard medical school
>