[Bioperl-l] OS X bioperl, staden/read, install problems

[Marcelino Suzuki]

Aaron. Your suggestion worked, but I had to do some tweeking, since  
editing the file Bio/SeqIO/staden/read.pm on the directory that I  
untared from current_ext_stable.tar resulted in no errrors for 'make  
test' and 'make install' but I still got errors running a test file.  I  
edited read.pm as suggested and in  
/Library/Perl/5.8.1/Bio/SeqIO/staden/read.pm the ran the make in that  
directory.  I have no errors so I assume it is finally installed.

This was really quite a puzzle so I hope the following will help  
someone else who is trying to install bioperl-ext under OSX (I guess  
the same is true for other systems).

For someone else is trying to install bioperl-ext :
	
I did not have Inline so:

	sudo perl -MCPAN -e 'install Inline'

then I installed the staden io_lib 1.8.11 that is at  
ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/io_lib/   after untaring in  
/usr/local

	cd /usr/local/io_lib-1.8.11
	./configure
	sudo make
	sudo make install

no problems at all under OSX Panther

After numerous suggestions from the web I moved both os.h and config.h  
from  /usr/local/io_lib-1.8.11 to /usr/local/include/io_lib.  I edited  
os.h to remove the "<:" and ">" around config.h.

Then I untared in /usr/local the current_ext_stable.tar from the  
bioperl distribution, and:

	cd /usr/local/bioperl-ext-1.4
	
++++ I edited (following Aaron Mackey's suggestion)  
/usr/local/bioperl-ext-1.4/Bio/SeqIO/staden/read.pm and added the -lz  
option to LIBS in line 81, then

	ranlib /usr/local/lib/libread.a
	perl Makefile.pl IOLIB_LIB=/usr/local/lib  
IOLIB_INC=/usr/local/include/io_lib
	make
	
I got an error message and did
	
	ranlib /usr/local/bioperl-ext-1.4/Bio/Ext/Align/libs/libsw.a
	make
	make test
	make install

No errors so I ran a test and still got the same old error:

	The extension 'Bio::SeqIO::staden::read' is not properly installed in  
path:
   '/Library/Perl/5.8.1'

I repeated everything after ++++ above in the directory /Library/Perl

The 'make test' did not work, but now I don't get the error running my  
perl test script
	
Interestingly I tried to install the whole thing the exact same way on  
my powerbook, and I am having yet a different type of error:

like in http://bioperl.org/pipermail/bioperl-l/2004-January/014481.htm


	Marcelino






On Jan 5, 2005, at 6:28 PM, Aaron J. Mackey wrote:

>
> Try editing Bio/SeqIO/staden/read.pm to include "-lz" in LIBS
>
> -Aaron
>
> Marcelino Suzuki wrote:
>
>>     Well,  I tried all I could, but I keep getting the same error as   
>> srikanth patury:
>> http://bioperl.org/pipermail/bioperl-guts-l/2004-June/016855.html
>>     Got to the point I got no errors in the make step of bioperl-ext
>>     I installed io_lib (1.8.11)
>>     I copied os.h and config.h to /usr/local/include/io_lib
>>     I changed os.h to remove the "<:" and ">" around config.h
>>     I ranlib /usr/local/lib/libread.a
>>     after an error message I also
>>     ranlib /usr/local/bioperl-ext-1.4/Bio/Ext/Align/libs/libsw.a
>>     Is there any other thing that needs to be done.
>>     I am using perl 5.8.1
>>     Thanks
>>     Marcelino suzuki
>>     suzuki at cbl dot umces dot edu
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
======================================================================== 
====
             oOOOOo           			Marcelino Suzuki,  Assistant Professor
           oOOO            Chesapeake Biological Lab - Univ of Maryland  
Center Environm Science
        oOOOOOo.          		PO Box 38, One Williams St Solomons, MD 20688
     .oOOOOOOOOOo.                      suzuki at cbl.umces.edu  -   
http://cbl.umces.edu
   .oOOOOOOOOOOOOOOooo..    	 Ph 410-326-7291   FAX 410-326-7341
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