[Bioperl-l] staden package building problem

[Aaron J. Mackey]

Unfortunately, I think you need to ask the staden package developers,  
as the source of your errors doesn't have anything to do with BioPerl.

But, it looks like a symlink is trying to be made over an existing  
file; I'd suggest investigating this, and possibly starting over with  
a clean slate.

-Aaron

On Jun 6, 2005, at 3:45 AM, xuying wrote:

> Hi all:
>     When I was compiling the staden package, it aborted with the  
> follow messages.
> ............
> Makefile:73: warning: overriding commands for target `clean'
> mk/global.mk:256: warning: ignoring old commands for target `clean'
> Makefile:88: warning: overriding commands for target `depend'
> mk/global.mk:515: warning: ignoring old commands for target `depend'
> Makefile:128: warning: overriding commands for target `distsrc'
> mk/global.mk:494: warning: ignoring old commands for target `distsrc'
> cd Misc && make   all
> make[1]: Entering directory `/home/xuying/staden-src-1-5-3/src/Misc'
> make[1]: Nothing to be done for `all'.
> make[1]: Leaving directory `/home/xuying/staden-src-1-5-3/src/Misc'
> cd io_lib && make   all
> make[1]: Entering directory `/home/xuying/staden-src-1-5-3/src/io_lib'
> Makefile:129: dependencies: No such file or directory
> Makefile:161: warning: overriding commands for target `distsrc'
> ../mk/global.mk:494: warning: ignoring old commands for target  
> `distsrc'
> cc -L../lib/linux-binaries  -shared -o ../lib/linux-binaries/ 
> libread.so  read/linux-binaries/Read.o read/linux-binaries/ 
> translate.o read/linux-binaries/scf_extras.o utils/linux-binaries/ 
> find.o utils/linux-binaries/mach-io.o utils/linux-binaries/ 
> traceType.o utils/linux-binaries/read_alloc.o utils/linux-binaries/ 
> compress.o utils/linux-binaries/open_trace_file.o scf/linux- 
> binaries/read_scf.o scf/linux-binaries/write_scf.o scf/linux- 
> binaries/misc_scf.o exp_file/linux-binaries/expFileIO.o plain/linux- 
> binaries/seqIOPlain.o abi/linux-binaries/fpoint.o abi/linux- 
> binaries/seqIOABI.o alf/linux-binaries/seqIOALF.o ctf/linux- 
> binaries/ctfCompress.o ctf/linux-binaries/seqIOCTF.o ztr/linux- 
> binaries/compression.o ztr/linux-binaries/ztr_translate.o ztr/linux- 
> binaries/ztr.o  -lz   -lmisc
> cd progs && make
> make[2]: Entering directory `/home/xuying/staden-src-1-5-3/src/ 
> io_lib/progs'
> Makefile:84: dependencies: No such file or directory
> make[2]: Nothing to be done for `all'.
> make[2]: Leaving directory `/home/xuying/staden-src-1-5-3/src/ 
> io_lib/progs'
> make[1]: Leaving directory `/home/xuying/staden-src-1-5-3/src/io_lib'
> cd tk_utils && make   all
> make[1]: Entering directory `/home/xuying/staden-src-1-5-3/src/ 
> tk_utils'
> Makefile:123: warning: overriding commands for target `distsrc'
> ../mk/global.mk:494: warning: ignoring old commands for target  
> `distsrc'
> ln -s ../licence/boxes.h .
> ln: `./boxes.h': File exists
> make[1]: *** [.links] Error 1
> make[1]: Leaving directory `/home/xuying/staden-src-1-5-3/src/ 
> tk_utils'
> make: *** [tk_utils] Error 2
>
>
> What's the problem? I just installed the exact external package  
> required manually. Please help!!!
>
>
> Best Regards!
>
>
> 　　　　　　　　xuying
> 　　　　　　　　xuying at sibs.ac.cn
> 　　　　　　　　　　2005-06-06
>
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>

--
Aaron J. Mackey, Ph.D.
Project Manager, ApiDB Bioinformatics Resource Center
Penn Genomics Institute, University of Pennsylvania
email:  amackey at pcbi.upenn.edu
office: 215-898-1205
fax:    215-746-6697
postal: Penn Genomics Institute
         Goddard Labs 212
         415 S. University Avenue
         Philadelphia, PA  19104-6017