[Bioperl-l] Problem installing bioperl-ext

[Jason Stajich]

Be warned that the bioperl-ext that is on CPAN is not as up-to-date 
with all the alignment stuff that is in the CVS version.

libsw.a is being built as part of this package.

You need to run ranlib as the error message is saying.
Try:
  ranlib Bio/Ext/Align/libs/libsw.a

-jason


On Sep 20, 2004, at 1:58 PM, Thomas J Keller wrote:

> Problem installing bioperl-ext
>
> Greetings,
> I can't seem to sort out this error. I was missing the os.h header 
> file from the io_lib dir (long list below). But even after copying 
> that over from io_lib-1.8.12, I still get an error both by hand and 
> the CPAN shell:
> ..
> LD_RUN_PATH="" MACOSX_DEPLOYMENT_TARGET=10.3 cc  -bundle -undefined 
> dynamic_lookup -L/usr/local/lib Align.o  -o 
> ./blib/arch/auto/Bio/Ext/Align/Align.bundle libs/libsw.a  -lm
> ld: archive: libs/libsw.a has no table of contents, add one with 
> ranlib(1) (can't load from it)
> make[1]: *** [../blib/arch/auto/Bio/Ext/Align/Align.bundle] Error 1
> make: *** [subdirs] Error 2
>   /usr/bin/make  -- NOT OK
> Running make test
>   Can't test without successful make
> Running make install
>   make had returned bad status, install seems impossible
>
> Looks like I'm missing libsw.a
> Where would I get that?
>
> Thanks,
> Tom Keller
>
> Tom Keller, Ph.D.
> http://www.ohsu.edu/research/core
> kellert at ohsu.edu
> 503-494-2442
>
> $ ll /usr/local/include/io_lib/
> total 224
> drwxr-xr-x  25 root  staff   850B 20 Sep 10:24 .
> drwxr-xr-x  25 root  staff   850B 12 Aug 12:10 ..
> -rw-r--r--   1 root  staff     6K 12 Aug 12:10 Read.h
> -rw-r--r--   1 root  staff     1K 12 Aug 12:10 abi.h
> -rw-r--r--   1 root  staff     1K 12 Aug 12:10 alf.h
> -rw-r--r--   1 root  staff     1K 12 Aug 12:10 array.h
> -rw-r--r--   1 root  staff     2K 12 Aug 12:10 compress.h
> -rw-r--r--   1 root  staff     6K 12 Aug 12:10 compression.h
> -rw-r--r--   1 root  staff   683B 12 Aug 12:10 error.h
> -rw-r--r--   1 root  staff     6K 12 Aug 12:10 expFileIO.h
> -rw-r--r--   1 root  staff   645B 12 Aug 12:10 fpoint.h
> -rw-r--r--   1 root  staff     2K 12 Aug 12:10 mach-io.h
> -rw-r--r--   1 root  staff     2K 12 Aug 12:10 misc.h
> -rw-r--r--   1 root  staff     1K 12 Aug 12:10 open_trace_file.h
> -rw-r--r--   1 root  staff     3K 20 Sep 10:24 os.h
> -rw-r--r--   1 root  staff     1K 12 Aug 12:10 plain.h
> -rw-r--r--   1 root  staff    10K 12 Aug 12:10 scf.h
> -rw-r--r--   1 root  staff   760B 12 Aug 12:10 scf_extras.h
> -rw-r--r--   1 root  staff     2K 12 Aug 12:10 seqIOABI.h
> -rw-r--r--   1 root  staff   152B 12 Aug 12:10 seqIOCTF.h
> -rw-r--r--   1 root  staff     1K 12 Aug 12:10 tar_format.h
> -rw-r--r--   1 root  staff     1K 12 Aug 12:10 traceType.h
> -rw-r--r--   1 root  staff     3K 12 Aug 12:10 translate.h
> -rw-r--r--   1 root  staff   781B 12 Aug 12:10 xalloc.h
> -rw-r--r--   1 root  staff     3K 12 Aug 12:10 ztr.h
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--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/
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