[Bioperl-l] error during installation

Du, Peng du at ibio.jp
Sat Jun 16 03:57:09 EDT 2012


Hi everybody, I fixed this problem by replacing 'libs/libsw$(LIB_EXT)'
with '\'-fPIC libs/libsw$(LIB_EXT)\'' in the file
bioperl-ext-14.2/Bio/Ext/Align/Makefile.PL according to one post by a
kind man ^_^. Many thanks to him.
But, when I did make test. Some other errors occurred:

chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..2
Can't load '../blib/arch/auto/Bio/Ext/Align/Align.so' for module
Bio::Ext::Align: ../blib/arch/auto/Bio/Ext/Align/Align.so: undefined
symbol: bp_sw_show_simple_PackAln at /usr/lib/perl/5.14/DynaLoader.pm
line 184.
 at test.pl line 10.
Compilation failed in require at test.pl line 10.
BEGIN failed--compilation aborted at test.pl line 10.
not ok 1
make[1]: *** [test_dynamic] Error 2


Could anybody tell me what I should do next?

Thank you, all your replies will be appreciated~~~


On Sat, Jun 16, 2012 at 12:28 PM, Du, Peng <du at ibio.jp> wrote:
> Hi everybody,
>
> I am a newbie, I encountered a problem while installing bioperl-ext.
> The error message is :
>
>
> /usr/bin/ld: libs/libsw.a(aln.o): relocation R_X86_64_32 against
> `.rodata.str1.8' can not be used when making a shared object;
> recompile with -fPIC
> libs/libsw.a: could not read symbols: Bad value
> collect2: ld returned 1 exit status
>
> I googled some solutions, but all of them are confusing, could you
> tell me where exactly should I add the -fPIC? In the makefile under
> the bioperl-ext-1.4 directory?  I tried to add this to the CCCDLFLAGS,
> CCDLFLAGS, LDDLFLAGS and LDFLAGS in that file. But it still doesn't
> work.
>
> Could you tell me what to do or where could I find the answer?
>
> Thank you very much.
>
> Best Regards,
> Peng
>
> --
>
> Peng Du
> Graduate School of Information Science and Technology, Hokkaido University
> Kita 14 Nishi 9 Kita-ku, Sapporo, Japan  060-0814
> Email: du at ibio.jp Tel: +81 80 3268 9713



-- 

Peng Du
Graduate School of Information Science and Technology, Hokkaido University
Kita 14 Nishi 9 Kita-ku, Sapporo, Japan  060-0814
Email: du at ibio.jp Tel: +81 80 3268 9713



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