From gabrielle_doan at gmx.net Tue Jul 1 04:29:37 2008 From: gabrielle_doan at gmx.net (Gabrielle Doan) Date: Tue, 01 Jul 2008 10:29:37 +0200 Subject: [Bioperl-l] Problems when trying to persist a sequence in my BioSQL database using BioPerl Message-ID: <4869EAF1.7010807@gmx.net> Hi Hilmar and Sendu, thanks a lot for your help! After installing the latest version of Scalar::Util I didn't get the error anymore. Unfortunately, I'm facing an other problem. I tried to insert the Genbank file of the human Chromosome 1 - downloaded from the NCBI (ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_01/hs_ref_chr1.gbk.gz) - into my BioSQL database with a perl script (load_seqdatabase.pl from the BioPerl db package), but after about one hour I received the message 'Out of memory'. After the abort I have only 13 entries in my database. I can't image that four GB RAM are not sufficient. Does anybody have the same problem? I am greateful for any hint! Cheers, Gabrielle From captainrave at hotmail.com Tue Jul 1 04:19:41 2008 From: captainrave at hotmail.com (Captainrave) Date: Tue, 1 Jul 2008 01:19:41 -0700 (PDT) Subject: [Bioperl-l] re ading in cds, outputting products Message-ID: <18211537.post@talk.nabble.com> How would I use bioperl to read in CDS positions (maybe in csv format in a list), find the releated products and/or genes for each and output these into a new csv file or similar file? -- View this message in context: http://www.nabble.com/reading-in-cds%2C-outputting-products-tp18211537p18211537.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From pallavi.sarmah at igib.res.in Wed Jul 2 03:36:24 2008 From: pallavi.sarmah at igib.res.in (Pallavi Sarmah) Date: Wed, 2 Jul 2008 13:06:24 +0530 Subject: [Bioperl-l] not being able to install Bio-ext-1.4 Message-ID: <4C33FA201D55F743B5DE794497FCA8971F0C9C@n1ex> 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 From nsh9351 at rit.edu Wed Jul 2 10:34:51 2008 From: nsh9351 at rit.edu (Nathan Haseley (RIT Student)) Date: Wed, 2 Jul 2008 10:34:51 -0400 Subject: [Bioperl-l] Clustalw module Message-ID: <7D75703BC8E1C149BF78A1E79AAAB169035BC544@svits28.main.ad.rit.edu> Hello, I am working with the Bioperl module Bio::Tools::Run::Alignment::Clustalw. I try to include the package in my script as follows: #!/usr/bin/perl use Bio::Seq; use Bio::SearchIO; use Bio::Tools::Run::StandAloneBlast; use Bio::DB::GenBank; use Bio::Tools::Run::Alignment::Clustalw; use Bio::Root::Exception; use Error qw(:try); but I keep getting the following error message: Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains: /etc/perl /usr/local/lib/perl/5.8.8 /usr/local/share/perl/5.8.8 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.8 /usr/share/perl/5.8 /usr/local/lib/site_perl .) at ./BlastTwoCompare.pl line 6. BEGIN failed--compilation aborted at ./BlastTwoCompare.pl line 6. The Clustalw program is configured correctly to work in my directory. Am I missing something obvious or is there something wrong with my BioPerl configuration? Any advice on how to fix this? Thank you for your time. Nathan From jason at bioperl.org Wed Jul 2 11:02:24 2008 From: jason at bioperl.org (Jason Stajich) Date: Wed, 2 Jul 2008 11:02:24 -0400 Subject: [Bioperl-l] Clustalw module In-Reply-To: <7D75703BC8E1C149BF78A1E79AAAB169035BC544@svits28.main.ad.rit.edu> References: <7D75703BC8E1C149BF78A1E79AAAB169035BC544@svits28.main.ad.rit.edu> Message-ID: did you install bioperl-run package as well as bioperl core? -jason On Jul 2, 2008, at 10:34 AM, Nathan Haseley (RIT Student) wrote: > Hello, > I am working with the Bioperl module > Bio::Tools::Run::Alignment::Clustalw. I try to include the package > in my script as follows: > > #!/usr/bin/perl > use Bio::Seq; > use Bio::SearchIO; > use Bio::Tools::Run::StandAloneBlast; > use Bio::DB::GenBank; > use Bio::Tools::Run::Alignment::Clustalw; > use Bio::Root::Exception; > use Error qw(:try); > > but I keep getting the following error message: > Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC > contains: /etc/perl /usr/local/lib/perl/5.8.8 /usr/local/share/perl/ > 5.8.8 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.8 /usr/share/ > perl/5.8 /usr/local/lib/site_perl .) at ./BlastTwoCompare.pl line 6. > BEGIN failed--compilation aborted at ./BlastTwoCompare.pl line 6. > > The Clustalw program is configured correctly to work in my > directory. Am I missing something obvious or is there something > wrong with my BioPerl configuration? Any advice on how to fix > this? Thank you for your time. > > Nathan > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From Kevin.M.Brown at asu.edu Wed Jul 2 11:10:43 2008 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Wed, 2 Jul 2008 08:10:43 -0700 Subject: [Bioperl-l] not being able to install Bio-ext-1.4 In-Reply-To: <4C33FA201D55F743B5DE794497FCA8971F0C9C@n1ex> References: <4C33FA201D55F743B5DE794497FCA8971F0C9C@n1ex> Message-ID: <1A4207F8295607498283FE9E93B775B405072F29@EX02.asurite.ad.asu.edu> Bioperl 1.4 is more than 5 years old. Try following the install instructions on the bioperl website for a more up2date version (v1.5.2): http://www.bioperl.org/wiki/Installing_BioPerl_on_Ubuntu_Server Or http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Pallavi Sarmah > Sent: Wednesday, July 02, 2008 12:36 AM > To: ymc at paxil.stanford.edu; birney at sanger.ac.uk; bioperl-l at bioperl.org > Subject: [Bioperl-l] not being able to install Bio-ext-1.4 > > > 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 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From jason at bioperl.org Wed Jul 2 11:25:09 2008 From: jason at bioperl.org (Jason Stajich) Date: Wed, 2 Jul 2008 11:25:09 -0400 Subject: [Bioperl-l] Clustalw module In-Reply-To: <7D75703BC8E1C149BF78A1E79AAAB169035BC545@svits28.main.ad.rit.edu> References: <7D75703BC8E1C149BF78A1E79AAAB169035BC544@svits28.main.ad.rit.edu> <7D75703BC8E1C149BF78A1E79AAAB169035BC545@svits28.main.ad.rit.edu> Message-ID: <47229074-D5EA-44C7-B820-6447BA8F19AA@bioperl.org> re: StandAloneBlast and RemoteBlast - due to their perceived widespread use was not moved from the core package to run so they come in with the basic Core modules install package. Given the error message I would again say that the bioperl-run was not installed. If you do perldoc ModuleName it will tell you if the module can be found. locate Clustalw.pm can also help you locate if it is installed but just not in PERL5LIB path. -jason On Jul 2, 2008, at 11:04 AM, Nathan Haseley (RIT Student) wrote: > I am running my script on a remote server, so I didn't do the > installation. I would assume so, however, since StandAloneBlast > works fine. > Nathan > > > -----Original Message----- > From: Jason Stajich on behalf of Jason Stajich > Sent: Wed 7/2/2008 11:02 AM > To: Nathan Haseley (RIT Student) > Cc: bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] Clustalw module > > did you install bioperl-run package as well as bioperl core? > -jason > On Jul 2, 2008, at 10:34 AM, Nathan Haseley (RIT Student) wrote: > >> Hello, >> I am working with the Bioperl module >> Bio::Tools::Run::Alignment::Clustalw. I try to include the package >> in my script as follows: >> >> #!/usr/bin/perl >> use Bio::Seq; >> use Bio::SearchIO; >> use Bio::Tools::Run::StandAloneBlast; >> use Bio::DB::GenBank; >> use Bio::Tools::Run::Alignment::Clustalw; >> use Bio::Root::Exception; >> use Error qw(:try); >> >> but I keep getting the following error message: >> Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC >> contains: /etc/perl /usr/local/lib/perl/5.8.8 /usr/local/share/perl/ >> 5.8.8 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.8 /usr/share/ >> perl/5.8 /usr/local/lib/site_perl .) at ./BlastTwoCompare.pl line 6. >> BEGIN failed--compilation aborted at ./BlastTwoCompare.pl line 6. >> >> The Clustalw program is configured correctly to work in my >> directory. Am I missing something obvious or is there something >> wrong with my BioPerl configuration? Any advice on how to fix >> this? Thank you for your time. >> >> Nathan >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From greener at u.washington.edu Wed Jul 2 14:10:20 2008 From: greener at u.washington.edu (RICHARD GREEN) Date: Wed, 2 Jul 2008 11:10:20 -0700 (PDT) Subject: [Bioperl-l] finding sequence 2000 bp upstream in bioperl? Message-ID: Howdy Bioperlers, Quick question, I have scripts that pull out a sequence from genbank, but I am looking for a command that would extract 2000 base pairs upstream of the sequence. Is there a way to extract just the Gene promoter region from genbank? Any advice that folks can give me a is muchly appreciated. Thanks again -Rich Green From Kevin.M.Brown at asu.edu Wed Jul 2 15:36:43 2008 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Wed, 2 Jul 2008 12:36:43 -0700 Subject: [Bioperl-l] finding sequence 2000 bp upstream in bioperl? In-Reply-To: References: Message-ID: <1A4207F8295607498283FE9E93B775B405073020@EX02.asurite.ad.asu.edu> Get the start point for a Sequence Feature and request a subseq of the main object that starts 2000 above that. my $gb = new Bio::DB::GenBank; $entry = $gb->get_Seq_by_id($id); foreach my $f ($entry->all_SeqFeatures()) { if ($f->primary_tag eq 'CDS') { my $seq = $entry->subseq($f->start - 2000,$f->start - 1); $out->write_seq($seq); } } > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > RICHARD GREEN > Sent: Wednesday, July 02, 2008 11:10 AM > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] finding sequence 2000 bp upstream in bioperl? > > Howdy Bioperlers, > > Quick question, I have scripts that pull out a sequence from > genbank, but I am looking for a command that would extract > 2000 base pairs upstream of the sequence. Is there a way to > extract just the Gene promoter region from genbank? Any > advice that folks can give me a is muchly appreciated. > > Thanks again > > -Rich Green > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From snoze.pa at gmail.com Wed Jul 2 15:56:18 2008 From: snoze.pa at gmail.com (snoze pa) Date: Wed, 2 Jul 2008 14:56:18 -0500 Subject: [Bioperl-l] Install help errors Message-ID: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> Dear Users, I am trying to install bioperl in fedora machine. I am using precompiled rpm from fedora repo. it is installed. Next I download the biosql and put in a dir /usr/local/biosql create a database bioseqdb and load the scema. However the bioperl-db is not working.. it is giving lots of error. I used CPAN and also the perl Build.PL. following are the results Please help me. thank you. Test Summary Report ------------------- t/04swiss (Wstat: 65280 Tests: 5 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 52 tests but ran 5. t/05seqfeature (Wstat: 65280 Tests: 3 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 48 tests but ran 3. t/06comment (Wstat: 65280 Tests: 2 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 11 tests but ran 2. t/07dblink (Wstat: 65280 Tests: 2 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 18 tests but ran 2. t/08genbank (Wstat: 65280 Tests: 2 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 18 tests but ran 2. t/09fuzzy2 (Wstat: 65280 Tests: 2 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 21 tests but ran 2. t/10ensembl (Wstat: 65280 Tests: 2 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 15 tests but ran 2. t/11locuslink (Wstat: 65280 Tests: 4 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 110 tests but ran 4. t/12ontology (Wstat: 65280 Tests: 4 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 738 tests but ran 4. t/13remove (Wstat: 0 Tests: 4 Failed: 1) Failed test: 4 Parse errors: Bad plan. You planned 59 tests but ran 4. t/15cluster (Wstat: 65280 Tests: 5 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 160 tests but ran 5. t/16obda (Wstat: 65280 Tests: 2 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 12 tests but ran 2. Files=16, Tests=198, 26 wallclock secs ( 0.21 usr 0.07 sys + 22.81 cusr 1.25 csys = 24.34 CPU) Result: FAIL Failed 12/16 test programs. 1/198 subtests failed. From jason at bioperl.org Wed Jul 2 15:57:15 2008 From: jason at bioperl.org (Jason Stajich) Date: Wed, 2 Jul 2008 15:57:15 -0400 Subject: [Bioperl-l] finding sequence 2000 bp upstream in bioperl? In-Reply-To: <1A4207F8295607498283FE9E93B775B405073020@EX02.asurite.ad.asu.edu> References: <1A4207F8295607498283FE9E93B775B405073020@EX02.asurite.ad.asu.edu> Message-ID: <3B11F357-E8FD-4027-B2D9-DB83634753E7@bioperl.org> Right on Kevin - except that you have to call trunc() not subseq() if you want to get back a sequence object that can be written out with Bio::SeqIO and you'll have to do it slightly differently if the gene is on the opposite strand operating on the $f->end, $f->end + 2000 and then doing a revcom. I *think* this will get you what you want: my $promotor; if( $f->strand < 0 ) { $promotor = $entry->trunc($f->end+1, $f->end + 2000)->revcom; } else { $promotor = $entry->trunc($f->start - 2000, $f->start -1); } -jason On Jul 2, 2008, at 3:36 PM, Kevin Brown wrote: > Get the start point for a Sequence Feature and request a subseq of the > main object that starts 2000 above that. > > my $gb = new Bio::DB::GenBank; > $entry = $gb->get_Seq_by_id($id); > foreach my $f ($entry->all_SeqFeatures()) > { > if ($f->primary_tag eq 'CDS') > { > my $seq = $entry->subseq($f->start - 2000,$f->start - > 1); > $out->write_seq($seq); > } > } > >> -----Original Message----- >> From: bioperl-l-bounces at lists.open-bio.org >> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of >> RICHARD GREEN >> Sent: Wednesday, July 02, 2008 11:10 AM >> To: bioperl-l at lists.open-bio.org >> Subject: [Bioperl-l] finding sequence 2000 bp upstream in bioperl? >> >> Howdy Bioperlers, >> >> Quick question, I have scripts that pull out a sequence from >> genbank, but I am looking for a command that would extract >> 2000 base pairs upstream of the sequence. Is there a way to >> extract just the Gene promoter region from genbank? Any >> advice that folks can give me a is muchly appreciated. >> >> Thanks again >> >> -Rich Green >> >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From apapanicolaou at ice.mpg.de Wed Jul 2 16:11:31 2008 From: apapanicolaou at ice.mpg.de (Alexie Papanicolaou) Date: Wed, 02 Jul 2008 22:11:31 +0200 Subject: [Bioperl-l] IUPAC support for DNA alignment In-Reply-To: References: Message-ID: <486BE0F3.4060702@ice.mpg.de> Hello I agree if it is not too much trouble for you. I think X (if users put them in DNA sequences) they will be masking characters (I 'm foolish enough to do it) so perhaps X =0? Does anyone else use Xs? I dunno about Ns too. They could be unknown characters (in which case full score version could be 0 as well) or really mean all four nucleotides are equally likely. Is it too much trouble to allow users to set X and N manually (since it is the same whether they align with an A,T,C,G)? ta a Yee Man Chan wrote: > Hi guys > > What about providing two switches; one for full score and one for > probabilistic score? > > Assume match is +3 and mismatch -1 > > Full score version: > 1) T - U = +3 (I assume U is the same as T for alignment purpose, right?) > 2) A - W = +3 > 3) A - D = +3 > 4) A - N = +3 > 5) A - X = -1 (not so sure about this one) > > Probabilistic score version: > 1) T - U = +3 > 2) A - W = +3/2-1/2 = +1 > 3) A - D = +3/3-1*2/3 = +1/3 > 4) A - N = +3/4-1*3/4 = 0 > 5) A - X = -1 > > What do you think? > > Yee Man > > On Fri, 27 Jun 2008 aaron.j.mackey at gsk.com wrote: > > >> You could replicate what they do here with EST_GENOME (re-engineered to >> accept ambiguity codes): >> >> http://www.genome.org/cgi/content/short/17/2/212 >> >> But I think the answer is user-dependent -- some might want the "full >> score" (as in the above case), others might want the "(probabilistically) >> averaged score", etc. So, let the scoring matrix be subclass-able (or >> mix-able), so that users can specify the exact desired behavior via a >> handful of predefined (and useful) behaviors. >> >> -Aaron >> >> > > -- "You can't find a hermit to teach you herming, because of course that rather spoils the whole thing." -- (Terry Pratchett, Small Gods) Alexie Papanicolaou Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, D-07745 Jena, Germany. From cain.cshl at gmail.com Wed Jul 2 16:13:24 2008 From: cain.cshl at gmail.com (Scott Cain) Date: Wed, 2 Jul 2008 16:13:24 -0400 Subject: [Bioperl-l] Install help errors In-Reply-To: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> Message-ID: <536f21b00807021313l6cec00devfd452db661ec1449@mail.gmail.com> Hello, When you say you installed the BioPerl RPM, do you mean the one at biopackages.net? It is very old and the likely problem you are running into is that it is too old to work with the version of BioSQL you have. Scott On Wed, Jul 2, 2008 at 3:56 PM, snoze pa wrote: > Dear Users, > I am trying to install bioperl in fedora machine. I am using > precompiled rpm from fedora repo. it is installed. Next I download the > biosql and put in a dir /usr/local/biosql > create a database bioseqdb and load the scema. > > However the bioperl-db is not working.. it is giving lots of error. I > used CPAN and also the perl Build.PL. following are the results > > Please help me. > thank you. > > > Test Summary Report > ------------------- > t/04swiss (Wstat: 65280 Tests: 5 Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 52 tests but ran 5. > t/05seqfeature (Wstat: 65280 Tests: 3 Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 48 tests but ran 3. > t/06comment (Wstat: 65280 Tests: 2 Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 11 tests but ran 2. > t/07dblink (Wstat: 65280 Tests: 2 Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 18 tests but ran 2. > t/08genbank (Wstat: 65280 Tests: 2 Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 18 tests but ran 2. > t/09fuzzy2 (Wstat: 65280 Tests: 2 Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 21 tests but ran 2. > t/10ensembl (Wstat: 65280 Tests: 2 Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 15 tests but ran 2. > t/11locuslink (Wstat: 65280 Tests: 4 Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 110 tests but ran 4. > t/12ontology (Wstat: 65280 Tests: 4 Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 738 tests but ran 4. > t/13remove (Wstat: 0 Tests: 4 Failed: 1) > Failed test: 4 > Parse errors: Bad plan. You planned 59 tests but ran 4. > t/15cluster (Wstat: 65280 Tests: 5 Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 160 tests but ran 5. > t/16obda (Wstat: 65280 Tests: 2 Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 12 tests but ran 2. > Files=16, Tests=198, 26 wallclock secs ( 0.21 usr 0.07 sys + 22.81 > cusr 1.25 csys = 24.34 CPU) > Result: FAIL > Failed 12/16 test programs. 1/198 subtests failed. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain.cshl at gmail.com GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory From apapanicolaou at ice.mpg.de Wed Jul 2 16:20:51 2008 From: apapanicolaou at ice.mpg.de (Alexie Papanicolaou) Date: Wed, 02 Jul 2008 22:20:51 +0200 Subject: [Bioperl-l] IUPAC support for DNA alignment In-Reply-To: <134AD76F-E008-4288-91BB-CBFA6042F54A@gmx.net> References: <134AD76F-E008-4288-91BB-CBFA6042F54A@gmx.net> Message-ID: <486BE323.60109@ice.mpg.de> >> Full score version: >> 1) T - U = +3 (I assume U is the same as T for alignment purpose, >> right?) > Right. yea... unless you are aligning RNAs and thus have wobble pairing UG :-) let's start simple though... > Note that there are also M, R, V, and H, and their complements (which > by definition would not match your example of 'A'). oh, I assumed Yee Man was just giving us a trimmed down example. Hilmar is very right. > Note also that the above implicitly assumes 50% GC content or equal > likelihood of the code-constituent bases, which in reality for most > coding sequences is not true.Also, if you have a known polymorphism at > the site, for 3-letter ambiguities not all 3 may be equally likely. > For example, if you have letter D for a [A/G] SNP, one may not want to > give 1/3 of weight to possibility T. > I would at least allow for the possibility to assign expected base > frequencies and weight the ambiguous possibilities by those. > -hilmar Ehm, wouldn't we now be walking in the twilight of modeling it? That might be a bit harder work for Yee Man, which I was trying to avoid. Perhaps for starters Yee Man can just document how the user can provide their own substitution matrix? ((s)he may have done already, sorry dunno if Yee is a boy or girl; like alexie too :-)) right a -- "You can't find a hermit to teach you herming, because of course that rather spoils the whole thing." -- (Terry Pratchett, Small Gods) Alexie Papanicolaou Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, D-07745 Jena, Germany. From apapanicolaou at ice.mpg.de Wed Jul 2 16:21:05 2008 From: apapanicolaou at ice.mpg.de (Alexie Papanicolaou) Date: Wed, 02 Jul 2008 22:21:05 +0200 Subject: [Bioperl-l] IUPAC support for DNA alignment In-Reply-To: <134AD76F-E008-4288-91BB-CBFA6042F54A@gmx.net> References: <134AD76F-E008-4288-91BB-CBFA6042F54A@gmx.net> Message-ID: <486BE331.7000605@ice.mpg.de> >> >> Full score version: >> 1) T - U = +3 (I assume U is the same as T for alignment purpose, >> right?) > > Right. > yea... unless you have wobble pairing UG :-) let's keep it simple though... >> >> 2) A - W = +3 >> 3) A - D = +3 >> 4) A - N = +3 >> 5) A - X = -1 (not so sure about this one) >> >> Probabilistic score version: >> 1) T - U = +3 >> 2) A - W = +3/2-1/2 = +1 >> 3) A - D = +3/3-1*2/3 = +1/3 >> 4) A - N = +3/4-1*3/4 = 0 >> 5) A - X = -1 > > Note that there are also M, R, V, and H, and their complements (which > by definition would not match your example of 'A'). > oh, I assumed Yee Man was just giving us a trimmed down example. Hilmar is very right. > Note also that the above implicitly assumes 50% GC content or equal > likelihood of the code-constituent bases, which in reality for most > coding sequences is not true.Also, if you have a known polymorphism at > the site, for 3-letter ambiguities not all 3 may be equally likely. > For example, if you have letter D for a [A/G] SNP, one may not want to > give 1/3 of weight to possibility T. > I would at least allow for the possibility to assign expected base > frequencies and weight the ambiguous possibilities by those. > -hilmar Ehm, wouldn't we now be walking in the twilight of modeling it? That might be a bit harder work for Yee Man, perhaps Yee Man can document how the user can provide their own substitution matrix? -- "You can't find a hermit to teach you herming, because of course that rather spoils the whole thing." -- (Terry Pratchett, Small Gods) Alexie Papanicolaou Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, D-07745 Jena, Germany. From apapanicolaou at ice.mpg.de Wed Jul 2 16:24:50 2008 From: apapanicolaou at ice.mpg.de (Alexie Papanicolaou) Date: Wed, 02 Jul 2008 22:24:50 +0200 Subject: [Bioperl-l] IUPAC support for DNA alignment In-Reply-To: <486BE0F3.4060702@ice.mpg.de> References: <486BE0F3.4060702@ice.mpg.de> Message-ID: <486BE412.4020807@ice.mpg.de> clarifying (also sorry for the double post before). "equally likely" => "found in sample in which case it is match" right it's dark outside, time to go home. a > > > I dunno about Ns too. They could be unknown characters (in which case > full score version could be 0 as well) or really mean all four > nucleotides are equally likely. From snoze.pa at gmail.com Wed Jul 2 16:49:39 2008 From: snoze.pa at gmail.com (snoze pa) Date: Wed, 2 Jul 2008 15:49:39 -0500 Subject: [Bioperl-l] Install help errors In-Reply-To: <536f21b00807021313l6cec00devfd452db661ec1449@mail.gmail.com> References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <536f21b00807021313l6cec00devfd452db661ec1449@mail.gmail.com> Message-ID: <10f848910807021349h70ea876dj9436a7892a5ed6af@mail.gmail.com> I used the latest rpm shipped with fedora 9. Next I removed the bioperl from fedora 9 and try to installed it from the CPAN.. it worked fine but thr bioperl-db again give me following messages using cpan. Seems nothing working properly! thanks a lot for your help. Test Summary Report ------------------- t/01dbadaptor (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 19 tests but ran 0. t/02species (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 65 tests but ran 0. t/03simpleseq (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 59 tests but ran 0. t/04swiss (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 52 tests but ran 0. t/05seqfeature (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 48 tests but ran 0. t/06comment (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 11 tests but ran 0. t/07dblink (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 18 tests but ran 0. t/08genbank (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 18 tests but ran 0. t/09fuzzy2 (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 21 tests but ran 0. t/10ensembl (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 15 tests but ran 0. t/11locuslink (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 110 tests but ran 0. t/12ontology (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 738 tests but ran 0. t/13remove (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 59 tests but ran 0. t/14query (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 18 tests but ran 0. t/15cluster (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 160 tests but ran 0. t/16obda (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 12 tests but ran 0. Files=16, Tests=0, 2 wallclock secs ( 0.09 usr 0.06 sys + 1.19 cusr 0.20 csys = 1.54 CPU) Result: FAIL Failed 16/16 test programs. 0/0 subtests failed. SENDU/bioperl-db-1.5.2_100.tar.gz ./Build test -- NOT OK //hint// to see the cpan-testers results for installing this module, try: reports SENDU/bioperl-db-1.5.2_100.tar.gz Warning (usually harmless): 'YAML' not installed, will not store persistent state Running Build install make test had returned bad status, won't install without force Failed during this command: BIRNEY/bioperl-1.4.tar.gz : make_test NO SENDU/bioperl-db-1.5.2_100.tar.gz : make_test NO On Wed, Jul 2, 2008 at 3:13 PM, Scott Cain wrote: > Hello, > > When you say you installed the BioPerl RPM, do you mean the one at > biopackages.net? It is very old and the likely problem you are > running into is that it is too old to work with the version of BioSQL > you have. > > Scott > > > On Wed, Jul 2, 2008 at 3:56 PM, snoze pa wrote: >> Dear Users, >> I am trying to install bioperl in fedora machine. I am using >> precompiled rpm from fedora repo. it is installed. Next I download the >> biosql and put in a dir /usr/local/biosql >> create a database bioseqdb and load the scema. >> >> However the bioperl-db is not working.. it is giving lots of error. I >> used CPAN and also the perl Build.PL. following are the results >> >> Please help me. >> thank you. >> >> >> Test Summary Report >> ------------------- >> t/04swiss (Wstat: 65280 Tests: 5 Failed: 0) >> Non-zero exit status: 255 >> Parse errors: Bad plan. You planned 52 tests but ran 5. >> t/05seqfeature (Wstat: 65280 Tests: 3 Failed: 0) >> Non-zero exit status: 255 >> Parse errors: Bad plan. You planned 48 tests but ran 3. >> t/06comment (Wstat: 65280 Tests: 2 Failed: 0) >> Non-zero exit status: 255 >> Parse errors: Bad plan. You planned 11 tests but ran 2. >> t/07dblink (Wstat: 65280 Tests: 2 Failed: 0) >> Non-zero exit status: 255 >> Parse errors: Bad plan. You planned 18 tests but ran 2. >> t/08genbank (Wstat: 65280 Tests: 2 Failed: 0) >> Non-zero exit status: 255 >> Parse errors: Bad plan. You planned 18 tests but ran 2. >> t/09fuzzy2 (Wstat: 65280 Tests: 2 Failed: 0) >> Non-zero exit status: 255 >> Parse errors: Bad plan. You planned 21 tests but ran 2. >> t/10ensembl (Wstat: 65280 Tests: 2 Failed: 0) >> Non-zero exit status: 255 >> Parse errors: Bad plan. You planned 15 tests but ran 2. >> t/11locuslink (Wstat: 65280 Tests: 4 Failed: 0) >> Non-zero exit status: 255 >> Parse errors: Bad plan. You planned 110 tests but ran 4. >> t/12ontology (Wstat: 65280 Tests: 4 Failed: 0) >> Non-zero exit status: 255 >> Parse errors: Bad plan. You planned 738 tests but ran 4. >> t/13remove (Wstat: 0 Tests: 4 Failed: 1) >> Failed test: 4 >> Parse errors: Bad plan. You planned 59 tests but ran 4. >> t/15cluster (Wstat: 65280 Tests: 5 Failed: 0) >> Non-zero exit status: 255 >> Parse errors: Bad plan. You planned 160 tests but ran 5. >> t/16obda (Wstat: 65280 Tests: 2 Failed: 0) >> Non-zero exit status: 255 >> Parse errors: Bad plan. You planned 12 tests but ran 2. >> Files=16, Tests=198, 26 wallclock secs ( 0.21 usr 0.07 sys + 22.81 >> cusr 1.25 csys = 24.34 CPU) >> Result: FAIL >> Failed 12/16 test programs. 1/198 subtests failed. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. cain.cshl at gmail.com > GMOD Coordinator (http://www.gmod.org/) 216-392-3087 > Cold Spring Harbor Laboratory > From bosborne11 at verizon.net Wed Jul 2 15:56:03 2008 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 02 Jul 2008 15:56:03 -0400 Subject: [Bioperl-l] finding sequence 2000 bp upstream in bioperl? In-Reply-To: References: Message-ID: <59E17CD3-C61E-4C4C-BAD7-D535D1F1134F@verizon.net> Richard, Some approaches are discussed here: http://www.bioperl.org/wiki/HOWTO:Getting_Genomic_Sequences Brian O. On Jul 2, 2008, at 2:10 PM, RICHARD GREEN wrote: > Howdy Bioperlers, > > Quick question, I have scripts that pull out a sequence from > genbank, but I am looking for a command that would extract 2000 base > pairs upstream of the sequence. Is there a way to extract just the > Gene promoter region from genbank? Any advice that folks can give me > a is muchly appreciated. > > Thanks again > > -Rich Green > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From captainrave at hotmail.com Wed Jul 2 17:00:09 2008 From: captainrave at hotmail.com (Captainrave) Date: Wed, 2 Jul 2008 14:00:09 -0700 (PDT) Subject: [Bioperl-l] re ading in cds, outputting products In-Reply-To: <18211537.post@talk.nabble.com> References: <18211537.post@talk.nabble.com> Message-ID: <18246685.post@talk.nabble.com> Captainrave wrote: > > How would I use bioperl to read in CDS positions (maybe in csv format in a > list), find the releated products and/or genes for each and output these > into a new csv file or similar file? > Any ideas? I obviously have rough ideas, but nothing substantial! Any help would REALLY be appreciated!!! This place has been good to me before :) -- View this message in context: http://www.nabble.com/reading-in-cds%2C-outputting-products-tp18211537p18246685.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From bix at sendu.me.uk Wed Jul 2 17:54:54 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 02 Jul 2008 22:54:54 +0100 Subject: [Bioperl-l] re ading in cds, outputting products In-Reply-To: <18246685.post@talk.nabble.com> References: <18211537.post@talk.nabble.com> <18246685.post@talk.nabble.com> Message-ID: <486BF92E.2070308@sendu.me.uk> Captainrave wrote: > > Captainrave wrote: >> How would I use bioperl to read in CDS positions (maybe in csv format in a >> list), find the releated products and/or genes for each and output these >> into a new csv file or similar file? > > Any ideas? I obviously have rough ideas, but nothing substantial! Any help > would REALLY be appreciated!!! This place has been good to me before :) Your question might be too broad. Narrow your problem down, give some specifics (what data are you working with?), tell us what you've tried. Have you checked the obvious HOW-TOs on the wiki? From ymc at shgc.stanford.edu Wed Jul 2 19:48:07 2008 From: ymc at shgc.stanford.edu (Yee Man Chan) Date: Wed, 2 Jul 2008 16:48:07 -0700 (PDT) Subject: [Bioperl-l] IUPAC support for DNA alignment In-Reply-To: <486BE412.4020807@ice.mpg.de> References: <486BE0F3.4060702@ice.mpg.de> <486BE412.4020807@ice.mpg.de> Message-ID: How about I implement the full score version first? I am going to do it as specified in my previous email. I can also add comments to ask people to specify their own matrix. Yee Man On Wed, 2 Jul 2008, Alexie Papanicolaou wrote: > clarifying (also sorry for the double post before). > > "equally likely" => "found in sample in which case it is match" > > right it's dark outside, time to go home. > a > > > > > > > I dunno about Ns too. They could be unknown characters (in which case > > full score version could be 0 as well) or really mean all four > > nucleotides are equally likely. > From David.Messina at sbc.su.se Thu Jul 3 05:08:19 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Thu, 3 Jul 2008 11:08:19 +0200 Subject: [Bioperl-l] Install help errors In-Reply-To: <10f848910807021349h70ea876dj9436a7892a5ed6af@mail.gmail.com> References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <536f21b00807021313l6cec00devfd452db661ec1449@mail.gmail.com> <10f848910807021349h70ea876dj9436a7892a5ed6af@mail.gmail.com> Message-ID: <628aabb70807030208y183e7ca7rb3f37f491b5fb6e3@mail.gmail.com> Here's your problem -- bioperl 1.4 is waaaay out of date. Don't use that. > BIRNEY/bioperl-1.4.tar.gz : make_test NO > Instead, use the 1.5.2_100 version of bioperl-core that matches this: > SENDU/bioperl-db-1.5.2_100.tar.gz : make_test NO > Or even better, you might want to get the latest versions of each from the bioperl website. Look here: http://www.bioperl.org/wiki/Getting_BioPerl and here: http://www.bioperl.org/wiki/Installing_BioPerl Dave From andreas.draeger at uni-tuebingen.de Thu Jul 3 07:48:55 2008 From: andreas.draeger at uni-tuebingen.de (=?ISO-8859-1?Q?Andreas_Dr=E4ger?=) Date: Thu, 03 Jul 2008 13:48:55 +0200 Subject: [Bioperl-l] Memory not sufficient when storing human chromosom 1 in BioSQL Message-ID: <486CBCA7.8080201@uni-tuebingen.de> Hi all, Recently I have successfully installed the latest version of BioPerl and BioSQL on my computer, which has 2 GB RAM. Both works fine, but when trying to insert the genbank file of the human chromosome 1, which I have downloaded from the NCBI website (ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_01/hs_ref_chr1.gbk.gz) I receive the error message 'Out of memory'. This takes about one hour. My question is, how I can insert large genbank files in my BioSQL database using BioPerl. I do not know, what to do. Thank you for your help!!! Cheers, Andreas From pallavi.sarmah at igib.res.in Thu Jul 3 05:06:12 2008 From: pallavi.sarmah at igib.res.in (Pallavi Sarmah) Date: Thu, 3 Jul 2008 14:36:12 +0530 Subject: [Bioperl-l] not being able to install Bio-ext-1.4 References: <4C33FA201D55F743B5DE794497FCA8971F0C9C@n1ex> <1A4207F8295607498283FE9E93B775B405072F29@EX02.asurite.ad.asu.edu> Message-ID: <4C33FA201D55F743B5DE794497FCA8971F0CA1@n1ex> Hi While trying to install Bio-ext-1.5.1 I get the following error Writing Makefile for Bio::Ext::Align ERROR from evaluation of /home/pallavi/Pallavi/downloads/bioperl-ext-1.5.1/Bio/SeqIO/staden/Makefile.PL: Invalid version '' for Bio::SeqIO::staden::read. Must be of the form '#.##'. (For instance '1.23') at ./Makefile.PL line 4 pallavi -----Original Message----- From: Kevin Brown [mailto:Kevin.M.Brown at asu.edu] Sent: Wed 7/2/2008 8:40 PM To: Pallavi Sarmah; bioperl-l at bioperl.org Subject: RE: [Bioperl-l] not being able to install Bio-ext-1.4 Bioperl 1.4 is more than 5 years old. Try following the install instructions on the bioperl website for a more up2date version (v1.5.2): http://www.bioperl.org/wiki/Installing_BioPerl_on_Ubuntu_Server Or http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Pallavi Sarmah > Sent: Wednesday, July 02, 2008 12:36 AM > To: ymc at paxil.stanford.edu; birney at sanger.ac.uk; bioperl-l at bioperl.org > Subject: [Bioperl-l] not being able to install Bio-ext-1.4 > > > 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: err