[Bioperl-l] not being able to install Bio-ext-1.4

Wed Jul 2 07:36:24 UTC 2008

Hi

I am having problem installing Bio::Ext-1.4.  I have forced installed BioPerl1.4 and now trying to install Bio::Ext but getting the following errors in Ubuntu. This is not the full list of errors but I am not being able to get all. Can anyone please help me with this. I have been trying the mailing list for quite sometime now.

Align.c:5835: error: array subscript is not an integer
Align.c:5835: error: array subscript is not an integer
Align.c:5835: error: array subscript is not an integer
Align.c:5836: error: array subscript is not an integer
Align.c:5836: error: array subscript is not an integer
Align.c:5836: error: array subscript is not an integer
Align.c:5836: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:5838: error: ‘OP’ has no member named ‘op_private’
Align.c:5838: error: ‘OP’ has no member named ‘op_targ’
Align.c:5842: error: invalid operands to binary +
Align.c:5842: error: ‘IV’ undeclared (first use in this function)
Align.c:5842: error: expected ‘)’ before ‘RETVAL’
Align.c:5842: error: too many arguments to function ‘Perl_sv_setiv’
Align.c:5842: error: ‘SV’ has no member named ‘sv_flags’
Align.c:5844: error: expected ‘;’ before ‘tmpXSoff’
Align.c:5844: error: invalid operands to binary +
Align.c:5844: error: ‘tmpXSoff’ undeclared (first use in this function)
Align.c: In function ‘XS_Bio__Ext__Align__FileSource_filename’:
Align.c:5851: error: function ‘ax’ is initialized like a variable
Align.c:5851: error: invalid lvalue in increment
Align.c:5851: error: function ‘items’ is initialized like a variable
Align.c:5852: warning: comparison between pointer and integer
Align.c:5855: error: array subscript is not an integer
Align.c:5855: error: array subscript is not an integer
Align.c:5855: error: array subscript is not an integer
Align.c:5855: error: array subscript is not an integer
Align.c:5857: error: ‘OP’ has no member named ‘op_private’
Align.c:5857: error: ‘OP’ has no member named ‘op_targ’
Align.c:5865: error: invalid operands to binary +
Align.c:5865: error: ‘SV’ has no member named ‘sv_flags’
Align.c:5867: error: ‘IV’ undeclared (first use in this function)
Align.c:5867: error: expected ‘;’ before ‘tmpXSoff’
Align.c:5867: error: invalid operands to binary +
Align.c:5867: error: ‘tmpXSoff’ undeclared (first use in this function)
Align.c: In function ‘XS_Bio__Ext__Align__FileSource_set_input’:
Align.c:5874: error: function ‘ax’ is initialized like a variable
Align.c:5874: error: invalid lvalue in increment
Align.c:5874: error: function ‘items’ is initialized like a variable
Align.c:5875: warning: comparison between pointer and integer
Align.c:5878: error: array subscript is not an integer
Align.c:5878: error: array subscript is not an integer
Align.c:5878: error: array subscript is not an integer
Align.c:5878: error: array subscript is not an integer
Align.c:5879: error: array subscript is not an integer
Align.c:5879: error: ‘XPVIO’ has no member named ‘xio_ifp’
Align.c:5881: error: ‘OP’ has no member named ‘op_private’
Align.c:5881: error: ‘OP’ has no member named ‘op_targ’
Align.c:5885: error: invalid operands to binary +
Align.c:5885: error: ‘IV’ undeclared (first use in this function)
Align.c:5885: error: expected ‘)’ before ‘RETVAL’
Align.c:5885: error: too many arguments to function ‘Perl_sv_setiv’
Align.c:5885: error: ‘SV’ has no member named ‘sv_flags’
Align.c:5887: error: expected ‘;’ before ‘tmpXSoff’
Align.c:5887: error: invalid operands to binary +
Align.c:5887: error: ‘tmpXSoff’ undeclared (first use in this function)
Align.c: In function ‘XS_Bio__Ext__Align__FileSource_input’:
Align.c:5894: error: function ‘ax’ is initialized like a variable
Align.c:5894: error: invalid lvalue in increment
Align.c:5894: error: function ‘items’ is initialized like a variable
Align.c:5895: warning: comparison between pointer and integer
Align.c:5898: error: array subscript is not an integer
Align.c:5898: error: array subscript is not an integer
Align.c:5898: error: array subscript is not an integer
Align.c:5898: error: array subscript is not an integer
Align.c:5903: error: array subscript is not an integer
Align.c:5907: warning: passing argument 3 of ‘Perl_do_open’ makes pointer from integer without a cast
Align.c:5908: error: array subscript is not an integer
Align.c:5908: warning: passing argument 2 of ‘Perl_gv_stashpv’ makes pointer from integer without a cast
Align.c:5908: warning: passing argument 3 of ‘Perl_sv_setsv_flags’ makes pointer from integer without a cast
Align.c:5910: error: array subscript is not an integer
Align.c:5913: error: ‘IV’ undeclared (first use in this function)
Align.c:5913: error: expected ‘;’ before ‘tmpXSoff’
Align.c:5913: error: invalid operands to binary +
Align.c:5913: error: ‘tmpXSoff’ undeclared (first use in this function)
Align.c: In function ‘XS_Bio__Ext__Align__FileSource_set_format’:
Align.c:5920: error: function ‘ax’ is initialized like a variable
Align.c:5920: error: invalid lvalue in increment
Align.c:5920: error: function ‘items’ is initialized like a variable
Align.c:5921: warning: comparison between pointer and integer
Align.c:5924: error: array subscript is not an integer
Align.c:5924: error: array subscript is not an integer
Align.c:5924: error: array subscript is not an integer
Align.c:5924: error: array subscript is not an integer
Align.c:5925: error: array subscript is not an integer
Align.c:5925: error: array subscript is not an integer
Align.c:5925: error: array subscript is not an integer
Align.c:5927: error: ‘OP’ has no member named ‘op_private’
Align.c:5927: error: ‘OP’ has no member named ‘op_targ’
Align.c:5931: error: invalid operands to binary +
Align.c:5931: error: ‘IV’ undeclared (first use in this function)
Align.c:5931: error: expected ‘)’ before ‘RETVAL’
Align.c:5931: error: too many arguments to function ‘Perl_sv_setiv’
Align.c:5931: error: ‘SV’ has no member named ‘sv_flags’
Align.c:5933: error: expected ‘;’ before ‘tmpXSoff’
Align.c:5933: error: invalid operands to binary +
Align.c:5933: error: ‘tmpXSoff’ undeclared (first use in this function)
Align.c: In function ‘XS_Bio__Ext__Align__FileSource_format’:
Align.c:5940: error: function ‘ax’ is initialized like a variable
Align.c:5940: error: invalid lvalue in increment
Align.c:5940: error: function ‘items’ is initialized like a variable
Align.c:5941: warning: comparison between pointer and integer
Align.c:5944: error: array subscript is not an integer
Align.c:5944: error: array subscript is not an integer
Align.c:5944: error: array subscript is not an integer
Align.c:5944: error: array subscript is not an integer
Align.c:5946: error: ‘OP’ has no member named ‘op_private’
Align.c:5946: error: ‘OP’ has no member named ‘op_targ’
Align.c:5950: error: invalid operands to binary +
Align.c:5950: error: ‘IV’ undeclared (first use in this function)
Align.c:5950: error: expected ‘)’ before ‘RETVAL’
Align.c:5950: error: too many arguments to function ‘Perl_sv_setiv’
Align.c:5950: error: ‘SV’ has no member named ‘sv_flags’
Align.c:5952: error: expected ‘;’ before ‘tmpXSoff’
Align.c:5952: error: invalid operands to binary +
Align.c:5952: error: ‘tmpXSoff’ undeclared (first use in this function)
Align.c: In function ‘XS_Bio__Ext__Align__FileSource_set_type’:
Align.c:5959: error: function ‘ax’ is initialized like a variable
Align.c:5959: error: invalid lvalue in increment
Align.c:5959: error: function ‘items’ is initialized like a variable
Align.c:5960: warning: comparison between pointer and integer
Align.c:5963: error: array subscript is not an integer
Align.c:5963: error: array subscript is not an integer
Align.c:5963: error: array subscript is not an integer
Align.c:5963: error: array subscript is not an integer
Align.c:5964: error: array subscript is not an integer
Align.c:5964: error: array subscript is not an integer
Align.c:5964: error: array subscript is not an integer
Align.c:5966: error: ‘OP’ has no member named ‘op_private’
Align.c:5966: error: ‘OP’ has no member named ‘op_targ’
Align.c:5970: error: invalid operands to binary +
Align.c:5970: error: ‘IV’ undeclared (first use in this function)
Align.c:5970: error: expected ‘)’ before ‘RETVAL’
Align.c:5970: error: too many arguments to function ‘Perl_sv_setiv’
Align.c:5970: error: ‘SV’ has no member named ‘sv_flags’
Align.c:5972: error: expected ‘;’ before ‘tmpXSoff’
Align.c:5972: error: invalid operands to binary +
Align.c:5972: error: ‘tmpXSoff’ undeclared (first use in this function)
Align.c: In function ‘XS_Bio__Ext__Align__FileSource_type’:
Align.c:5979: error: function ‘ax’ is initialized like a variable
Align.c:5979: error: invalid lvalue in increment
Align.c:5979: error: function ‘items’ is initialized like a variable
Align.c:5980: warning: comparison between pointer and integer
Align.c:5983: error: array subscript is not an integer
Align.c:5983: error: array subscript is not an integer
Align.c:5983: error: array subscript is not an integer
Align.c:5983: error: array subscript is not an integer
Align.c:5985: error: ‘OP’ has no member named ‘op_private’
Align.c:5985: error: ‘OP’ has no member named ‘op_targ’
Align.c:5989: error: invalid operands to binary +
Align.c:5989: error: ‘IV’ undeclared (first use in this function)
Align.c:5989: error: expected ‘)’ before ‘RETVAL’
Align.c:5989: error: too many arguments to function ‘Perl_sv_setiv’
Align.c:5989: error: ‘SV’ has no member named ‘sv_flags’
Align.c:5991: error: expected ‘;’ before ‘tmpXSoff’
Align.c:5991: error: invalid operands to binary +
Align.c:5991: error: ‘tmpXSoff’ undeclared (first use in this function)
Align.c: In function ‘XS_Bio__Ext__Align__FileSource_new’:
Align.c:5998: error: function ‘ax’ is initialized like a variable
Align.c:5998: error: invalid lvalue in increment
Align.c:5998: error: function ‘items’ is initialized like a variable
Align.c:5999: warning: comparison between pointer and integer
Align.c:6001: error: invalid operands to binary -
Align.c:6003: error: array subscript is not an integer
Align.c:6003: error: array subscript is not an integer
Align.c:6003: error: array subscript is not an integer
Align.c:6003: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.xs:3253: error: array subscript is not an integer
Align.xs:3254: error: array subscript is not an integer
Align.xs:3255: error: ‘IV’ undeclared (first use in this function)
Align.xs:3255: error: expected ‘;’ before ‘tmpXSoff’
Align.xs:3255: error: invalid operands to binary +
Align.xs:3255: error: ‘tmpXSoff’ undeclared (first use in this function)
Align.c: In function ‘XS_Bio__Ext__Align__FileSource_DESTROY’:
Align.c:6021: error: function ‘ax’ is initialized like a variable
Align.c:6021: error: invalid lvalue in increment
Align.c:6021: error: function ‘items’ is initialized like a variable
Align.c:6022: warning: comparison between pointer and integer
Align.c:6025: error: array subscript is not an integer
Align.c:6025: error: array subscript is not an integer
Align.c:6025: error: array subscript is not an integer
Align.c:6025: error: array subscript is not an integer
Align.c:6030: error: ‘IV’ undeclared (first use in this function)
Align.c:6030: error: expected ‘;’ before ‘tmpXSoff’
Align.c:6030: error: invalid operands to binary +
Align.c:6030: error: ‘tmpXSoff’ undeclared (first use in this function)
Align.c: In function ‘XS_Bio__Ext__Align_Align_strings_ProteinSmithWaterman’:
Align.c:6037: error: function ‘ax’ is initialized like a variable
Align.c:6037: error: invalid lvalue in increment
Align.c:6037: error: function ‘items’ is initialized like a variable
Align.c:6038: warning: comparison between pointer and integer
Align.c:6041: error: array subscript is not an integer
Align.c:6041: error: array subscript is not an integer
Align.c:6041: error: array subscript is not an integer
Align.c:6041: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6042: error: array subscript is not an integer
Align.c:6042: error: array subscript is not an integer
Align.c:6042: error: array subscript is not an integer
Align.c:6042: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6043: error: array subscript is not an integer
Align.c:6043: error: array subscript is not an integer
Align.c:6043: error: array subscript is not an integer
Align.c:6043: error: array subscript is not an integer
Align.c:6044: error: array subscript is not an integer
Align.c:6044: error: array subscript is not an integer
Align.c:6044: error: array subscript is not an integer
Align.c:6045: error: array subscript is not an integer
Align.c:6045: error: array subscript is not an integer
Align.c:6045: error: array subscript is not an integer
Align.c:6050: error: array subscript is not an integer
Align.c:6051: error: array subscript is not an integer
Align.c:6054: error: ‘IV’ undeclared (first use in this function)
Align.c:6054: error: expected ‘;’ before ‘tmpXSoff’
Align.c:6054: error: invalid operands to binary +
Align.c:6054: error: ‘tmpXSoff’ undeclared (first use in this function)
Align.c: In function ‘XS_Bio__Ext__Align_Align_Sequences_ProteinSmithWaterman’:
Align.c:6061: error: function ‘ax’ is initialized like a variable
Align.c:6061: error: invalid lvalue in increment
Align.c:6061: error: function ‘items’ is initialized like a variable
Align.c:6062: warning: comparison between pointer and integer
Align.c:6065: error: array subscript is not an integer
Align.c:6065: error: array subscript is not an integer
Align.c:6065: error: array subscript is not an integer
Align.c:6065: error: array subscript is not an integer
Align.c:6066: error: array subscript is not an integer
Align.c:6066: error: array subscript is not an integer
Align.c:6066: error: array subscript is not an integer
Align.c:6066: error: array subscript is not an integer
Align.c:6067: error: array subscript is not an integer
Align.c:6067: error: array subscript is not an integer
Align.c:6067: error: array subscript is not an integer
Align.c:6067: error: array subscript is not an integer
Align.c:6068: error: array subscript is not an integer
Align.c:6068: error: array subscript is not an integer
Align.c:6068: error: array subscript is not an integer
Align.c:6069: error: array subscript is not an integer
Align.c:6069: error: array subscript is not an integer
Align.c:6069: error: array subscript is not an integer
Align.c:6074: error: array subscript is not an integer
Align.c:6075: error: array subscript is not an integer
Align.c:6078: error: ‘IV’ undeclared (first use in this function)
Align.c:6078: error: expected ‘;’ before ‘tmpXSoff’
Align.c:6078: error: invalid operands to binary +
Align.c:6078: error: ‘tmpXSoff’ undeclared (first use in this function)
Align.c: In function ‘XS_Bio__Ext__Align_Align_Proteins_SmithWaterman’:
Align.c:6085: error: function ‘ax’ is initialized like a variable
Align.c:6085: error: invalid lvalue in increment
Align.c:6085: error: function ‘items’ is initialized like a variable
Align.c:6086: warning: comparison between pointer and integer
Align.c:6089: error: array subscript is not an integer
Align.c:6089: error: array subscript is not an integer
Align.c:6089: error: array subscript is not an integer
Align.c:6089: error: array subscript is not an integer
Align.c:6090: error: array subscript is not an integer
Align.c:6090: error: array subscript is not an integer
Align.c:6090: error: array subscript is not an integer
Align.c:6090: error: array subscript is not an integer
Align.c:6091: error: array subscript is not an integer
Align.c:6091: error: array subscript is not an integer
Align.c:6091: error: array subscript is not an integer
Align.c:6091: error: array subscript is not an integer
Align.c:6092: error: array subscript is not an integer
Align.c:6092: error: array subscript is not an integer
Align.c:6092: error: array subscript is not an integer
Align.c:6093: error: array subscript is not an integer
Align.c:6093: error: array subscript is not an integer
Align.c:6093: error: array subscript is not an integer
Align.c:6098: error: array subscript is not an integer
Align.c:6099: error: array subscript is not an integer
Align.c:6102: error: ‘IV’ undeclared (first use in this function)
Align.c:6102: error: expected ‘;’ before ‘tmpXSoff’
Align.c:6102: error: invalid operands to binary +
Align.c:6102: error: ‘tmpXSoff’ undeclared (first use in this function)
Align.c: In function ‘XS_Bio__Ext__Align_Align_DNA_Sequences’:
Align.c:6109: error: function ‘ax’ is initialized like a variable
Align.c:6109: error: invalid lvalue in increment
Align.c:6109: error: function ‘items’ is initialized like a variable
Align.c:6110: warning: comparison between pointer and integer
Align.c:6113: error: array subscript is not an integer
Align.c:6113: error: array subscript is not an integer
Align.c:6113: error: array subscript is not an integer
Align.c:6113: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6114: error: array subscript is not an integer
Align.c:6114: error: array subscript is not an integer
Align.c:6114: error: array subscript is not an integer
Align.c:6114: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6115: error: array subscript is not an integer
Align.c:6115: error: array subscript is not an integer
Align.c:6115: error: array subscript is not an integer
Align.c:6116: error: array subscript is not an integer
Align.c:6116: error: array subscript is not an integer
Align.c:6116: error: array subscript is not an integer
Align.c:6117: error: array subscript is not an integer
Align.c:6117: error: array subscript is not an integer
Align.c:6117: error: array subscript is not an integer
Align.c:6118: error: array subscript is not an integer
Align.c:6118: error: array subscript is not an integer
Align.c:6118: error: array subscript is not an integer
Align.c:6119: error: array subscript is not an integer
Align.c:6119: error: array subscript is not an integer
Align.c:6119: error: array subscript is not an integer
Align.c:6131: error: array subscript is not an integer
Align.c:6132: error: array subscript is not an integer
Align.c:6135: error: ‘IV’ undeclared (first use in this function)
Align.c:6135: error: expected ‘;’ before ‘tmpXSoff’
Align.c:6135: error: invalid operands to binary +
Align.c:6135: error: ‘tmpXSoff’ undeclared (first use in this function)
Align.c: In function ‘XS_Bio__Ext__Align_Align_Protein_Sequences’:
Align.c:6142: error: function ‘ax’ is initialized like a variable
Align.c:6142: error: invalid lvalue in increment
Align.c:6142: error: function ‘items’ is initialized like a variable
Align.c:6143: warning: comparison between pointer and integer
Align.c:6146: error: array subscript is not an integer
Align.c:6146: error: array subscript is not an integer
Align.c:6146: error: array subscript is not an integer
Align.c:6146: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6147: error: array subscript is not an integer
Align.c:6147: error: array subscript is not an integer
Align.c:6147: error: array subscript is not an integer
Align.c:6147: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6148: error: array subscript is not an integer
Align.c:6148: error: array subscript is not an integer
Align.c:6148: error: array subscript is not an integer
Align.c:6148: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6153: error: array subscript is not an integer
Align.c:6154: error: array subscript is not an integer
Align.c:6157: error: ‘IV’ undeclared (first use in this function)
Align.c:6157: error: expected ‘;’ before ‘tmpXSoff’
Align.c:6157: error: invalid operands to binary +
Align.c:6157: error: ‘tmpXSoff’ undeclared (first use in this function)
Align.c: In function ‘XS_Bio__Ext__Align__AlignOutput_aln1’:
Align.c:6164: error: function ‘ax’ is initialized like a variable
Align.c:6164: error: invalid lvalue in increment
Align.c:6164: error: function ‘items’ is initialized like a variable
Align.c:6165: warning: comparison between pointer and integer
Align.c:6168: error: array subscript is not an integer
Align.c:6168: error: array subscript is not an integer
Align.c:6168: error: array subscript is not an integer
Align.c:6168: error: array subscript is not an integer
Align.c:6170: error: ‘OP’ has no member named ‘op_private’
Align.c:6170: error: ‘OP’ has no member named ‘op_targ’
Align.c:6174: error: invalid operands to binary +
Align.c:6174: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6176: error: ‘IV’ undeclared (first use in this function)
Align.c:6176: error: expected ‘;’ before ‘tmpXSoff’
Align.c:6176: error: invalid operands to binary +
Align.c:6176: error: ‘tmpXSoff’ undeclared (first use in this function)
Align.c: In function ‘XS_Bio__Ext__Align__AlignOutput_aln2’:
Align.c:6183: error: function ‘ax’ is initialized like a variable
Align.c:6183: error: invalid lvalue in increment
Align.c:6183: error: function ‘items’ is initialized like a variable
Align.c:6184: warning: comparison between pointer and integer
Align.c:6187: error: array subscript is not an integer
Align.c:6187: error: array subscript is not an integer
Align.c:6187: error: array subscript is not an integer
Align.c:6187: error: array subscript is not an integer
Align.c:6189: error: ‘OP’ has no member named ‘op_private’
Align.c:6189: error: ‘OP’ has no member named ‘op_targ’
Align.c:6193: error: invalid operands to binary +
Align.c:6193: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6195: error: ‘IV’ undeclared (first use in this function)
Align.c:6195: error: expected ‘;’ before ‘tmpXSoff’
Align.c:6195: error: invalid operands to binary +
Align.c:6195: error: ‘tmpXSoff’ undeclared (first use in this function)
Align.c: In function ‘XS_Bio__Ext__Align__AlignOutput_start1’:
Align.c:6202: error: function ‘ax’ is initialized like a variable
Align.c:6202: error: invalid lvalue in increment
Align.c:6202: error: function ‘items’ is initialized like a variable
Align.c:6203: warning: comparison between pointer and integer
Align.c:6206: error: array subscript is not an integer
Align.c:6206: error: array subscript is not an integer
Align.c:6206: error: array subscript is not an integer
Align.c:6206: error: array subscript is not an integer
Align.c:6208: error: ‘OP’ has no member named ‘op_private’
Align.c:6208: error: ‘OP’ has no member named ‘op_targ’
Align.c:6212: error: invalid operands to binary +
Align.c:6212: error: ‘IV’ undeclared (first use in this function)
Align.c:6212: error: expected ‘)’ before ‘RETVAL’
Align.c:6212: error: too many arguments to function ‘Perl_sv_setiv’
Align.c:6212: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6214: error: expected ‘;’ before ‘tmpXSoff’
Align.c:6214: error: invalid operands to binary +
Align.c:6214: error: ‘tmpXSoff’ undeclared (first use in this function)
Align.c: In function ‘XS_Bio__Ext__Align__AlignOutput_end1’:
Align.c:6221: error: function ‘ax’ is initialized like a variable
Align.c:6221: error: invalid lvalue in increment
Align.c:6221: error: function ‘items’ is initialized like a variable
Align.c:6222: warning: comparison between pointer and integer
Align.c:6225: error: array subscript is not an integer
Align.c:6225: error: array subscript is not an integer
Align.c:6225: error: array subscript is not an integer
Align.c:6225: error: array subscript is not an integer
Align.c:6227: error: ‘OP’ has no member named ‘op_private’
Align.c:6227: error: ‘OP’ has no member named ‘op_targ’
Align.c:6231: error: invalid operands to binary +
Align.c:6231: error: ‘IV’ undeclared (first use in this function)
Align.c:6231: error: expected ‘)’ before ‘RETVAL’
Align.c:6231: error: too many arguments to function ‘Perl_sv_setiv’
Align.c:6231: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6233: error: expected ‘;’ before ‘tmpXSoff’
Align.c:6233: error: invalid operands to binary +
Align.c:6233: error: ‘tmpXSoff’ undeclared (first use in this function)
Align.c: In function ‘XS_Bio__Ext__Align__AlignOutput_start2’:
Align.c:6240: error: function ‘ax’ is initialized like a variable
Align.c:6240: error: invalid lvalue in increment
Align.c:6240: error: function ‘items’ is initialized like a variable
Align.c:6241: warning: comparison between pointer and integer
Align.c:6244: error: array subscript is not an integer
Align.c:6244: error: array subscript is not an integer
Align.c:6244: error: array subscript is not an integer
Align.c:6244: error: array subscript is not an integer
Align.c:6246: error: ‘OP’ has no member named ‘op_private’
Align.c:6246: error: ‘OP’ has no member named ‘op_targ’
Align.c:6250: error: invalid operands to binary +
Align.c:6250: error: ‘IV’ undeclared (first use in this function)
Align.c:6250: error: expected ‘)’ before ‘RETVAL’
Align.c:6250: error: too many arguments to function ‘Perl_sv_setiv’
Align.c:6250: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6252: error: expected ‘;’ before ‘tmpXSoff’
Align.c:6252: error: invalid operands to binary +
Align.c:6252: error: ‘tmpXSoff’ undeclared (first use in this function)
Align.c: In function ‘XS_Bio__Ext__Align__AlignOutput_end2’:
Align.c:6259: error: function ‘ax’ is initialized like a variable
Align.c:6259: error: invalid lvalue in increment
Align.c:6259: error: function ‘items’ is initialized like a variable
Align.c:6260: warning: comparison between pointer and integer
Align.c:6263: error: array subscript is not an integer
Align.c:6263: error: array subscript is not an integer
Align.c:6263: error: array subscript is not an integer
Align.c:6263: error: array subscript is not an integer
Align.c:6265: error: ‘OP’ has no member named ‘op_private’
Align.c:6265: error: ‘OP’ has no member named ‘op_targ’
Align.c:6269: error: invalid operands to binary +
Align.c:6269: error: ‘IV’ undeclared (first use in this function)
Align.c:6269: error: expected ‘)’ before ‘RETVAL’
Align.c:6269: error: too many arguments to function ‘Perl_sv_setiv’
Align.c:6269: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6271: error: expected ‘;’ before ‘tmpXSoff’
Align.c:6271: error: invalid operands to binary +
Align.c:6271: error: ‘tmpXSoff’ undeclared (first use in this function)
Align.c: In function ‘boot_Bio__Ext__Align’:
Align.c:6280: error: function ‘ax’ is initialized like a variable
Align.c:6280: error: invalid lvalue in increment
Align.c:6280: error: function ‘items’ is initialized like a variable
Align.c:6283: error: array subscript is not an integer
Align.c:6283: error: array subscript is not an integer
Align.c:6283: error: array subscript is not an integer
Align.c:6283: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6283: warning: comparison between pointer and integer
Align.c:6283: error: array subscript is not an integer
Align.c:6283: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6283: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6283: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6283: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6283: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6283: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6283: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6283: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6283: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6283: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6283: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6283: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6283: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6283: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6283: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6283: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6283: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6283: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6283: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6283: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6283: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6283: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6283: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6283: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6283: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6283: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6283: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6283: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6283: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6283: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6283: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6283: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6283: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6283: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6283: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6283: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6283: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6283: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6283: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6283: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6283: error: ‘SV’ has no member named ‘sv_flags’
Align.c:6283: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:6595: error: array subscript is not an integer
Align.c:6595: error: ‘IV’ undeclared (first use in this function)
Align.c:6595: error: expected ‘;’ before ‘tmpXSoff’
Align.c:6595: error: invalid operands to binary +
Align.c:6595: error: ‘tmpXSoff’ undeclared (first use in this function)
make[1]: *** [Align.o] Error 1
make[1]: Leaving directory `/home/pallavi/Pallavi/downloads/bioperl-ext-1.4/Bio/Ext/Align'
make: *** [subdirs] Error 2

thanks 
Pallavi