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From: metabase:user:30dda8bc-2aae-11df-837a-5e0a49663a4f
Subject: PASS BioPerl-run-1.6.1 v5.12.2 GNU/Linux
Date: 2011-02-07T16:58:48Z
This distribution has been tested as part of the CPAN Testers
project, supporting the Perl programming language. See
http://wiki.cpantesters.org/ for more information or email
questions to cpan-testers-discuss@perl.org
--
Dear Christopher Fields,
This is a computer-generated report for BioPerl-run-1.6.1
on perl 5.12.2, created by CPAN-Reporter-1.1902.
Thank you for uploading your work to CPAN. Congratulations!
All tests were successful.
Sections of this report:
* Tester comments
* Program output
* Prerequisites
* Environment and other context
------------------------------
TESTER COMMENTS
------------------------------
Additional comments from tester:
none provided
------------------------------
PROGRAM OUTPUT
------------------------------
Output from './Build test':
blib/script/papplmaker.PLS -> blib/script/bp_papplmaker.pl
blib/script/run_neighbor.PLS -> blib/script/bp_run_neighbor.pl
blib/script/multi_hmmsearch.PLS -> blib/script/bp_multi_hmmsearch.pl
blib/script/panalysis.PLS -> blib/script/bp_panalysis.pl
blib/script/bioperl_application_installer.PLS -> blib/script/bp_bioperl_application_installer.pl
blib/script/run_protdist.PLS -> blib/script/bp_run_protdist.pl
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Alignment::Amap is not present
t/Amap.t ...................... ok
t/AnalysisFactory_soap.t ...... skipped: Network tests have not been requested
t/Analysis_soap.t ............. skipped: Network tests have not been requested
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Alignment::Blat is not present
t/Blat.t ...................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Tree/TreeFunctionsI.pm line 94
# Required executable for Bio::Tools::Run::Alignment::Clustalw is not present
t/Clustalw.t .................. ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required environment variable $COILSDIR is not set
t/Coil.t ...................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Tree/TreeFunctionsI.pm line 94
# Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present
t/Consense.t .................. ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
Find start end points: 1000 Cells done [ 2%] 2000 Cells done [ 4%] 3000 Cells done [ 6%] 4000 Cells done [ 8%] 5000 Cells done [10%] 6000 Cells done [12%] 7000 Cells done [14%] 8000 Cells done [17%] 9000 Cells done [19%] 10000 Cells done [21%] 11000 Cells done [23%] 12000 Cells done [25%] 13000 Cells done [27%] 14000 Cells done [29%] 15000 Cells done [32%] 16000 Cells done [34%] 17000 Cells done [36%] 18000 Cells done [38%] 19000 Cells done [40%] 20000 Cells done [42%] 21000 Cells done [44%] 22000 Cells done [46%] 23000 Cells done [49%] 24000 Cells done [51%] 25000 Cells done [53%] 26000 Cells done [55%] 27000 Cells done [57%] 28000 Cells done [59%] 29000 Cells done [61%] 30000 Cells done [64%] 31000 Cells done [66%] 32000 Cells done [68%] 33000 Cells done [70%] 34000 Cells done [72%] 35000 Cells done [74%] 36000 Cells done [76%] 37000 Cells done [79%] 38000 Cells done [81%] 39000 Cells done [83%] 40000 Cells done [85%] 41000 Cells done [87%] 42000 Cells done [89%] 43000 Cells done [91%] 44000 Cells done [93%] 45000 Cells done [96%] 46000 Cells done [98%][0,17][209,222] Score 109962
Recovering alignment: [0% done]Before mid-j 118 Cells done 4%[0% done]Before mid-j 118 Cells done 9%[0% done]Before mid-j 118 Cells done 14%[0% done]Before mid-j 118 Cells done 18%[0% done]Before mid-j 118 Cells done 23%[0% done]Before mid-j 118 Cells done 28%[0% done]Before mid-j 118 Cells done 32%[0% done]Before mid-j 118 Cells done 37%[0% done]Before mid-j 118 Cells done 42%[0% done]Before mid-j 118 Cells done 46%[0% done]Before mid-j 118 Cells done 51%[0% done]Before mid-j 118 Cells done 56%[0% done]Before mid-j 118 Cells done 60%[0% done]Before mid-j 118 Cells done 65%[0% done]Before mid-j 118 Cells done 70%[0% done]Before mid-j 118 Cells done 74%[0% done]Before mid-j 118 Cells done 79%[0% done]Before mid-j 118 Cells done 84%[0% done]Before mid-j 118 Cells done 88%[0% done]Before mid-j 118 Cells done 93%[0% done]Before mid-j 118 Cells done 98%[0% done]After mid-j 120 Cells done 4%[0% done]After mid-j 120 Cells done 9%[0% done]After mid-j 120 Cells done 13%[0% done]After mid-j 120 Cells done 18%[0% done]After mid-j 120 Cells done 23%[0% done]After mid-j 120 Cells done 27%[0% done]After mid-j 120 Cells done 32%[0% done]After mid-j 120 Cells done 36%[0% done]After mid-j 120 Cells done 41%[0% done]After mid-j 120 Cells done 46%[0% done]After mid-j 120 Cells done 50%[0% done]After mid-j 120 Cells done 55%[0% done]After mid-j 120 Cells done 60%[0% done]After mid-j 120 Cells done 64%[0% done]After mid-j 120 Cells done 69%[0% done]After mid-j 120 Cells done 73%[0% done]After mid-j 120 Cells done 78%[0% done]After mid-j 120 Cells done 83%[0% done]After mid-j 120 Cells done 87%[0% done]After mid-j 120 Cells done 92%[0% done]After mid-j 120 Cells done 97%[0% done]Before mid-j 169 Cells done 18%[0% done]Before mid-j 169 Cells done 36%[0% done]Before mid-j 169 Cells done 54%[0% done]Before mid-j 169 Cells done 73%[0% done]Before mid-j 169 Cells done 91%[0% done]After mid-j 171 Cells done 17%[0% done]After mid-j 171 Cells done 35%[0% done]After mid-j 171 Cells done 53%[0% done]After mid-j 171 Cells done 71%[0% done]After mid-j 171 Cells done 89%[0% done]Before mid-j 195 Cells done 72%[0% done]After mid-j 197 Cells done 72%[205,218][209,222] Explicit read off[202,215][204,217] Explicit read off[198,211][201,214] Explicit read off[196,209][197,210] Explicit read off[192,205][195,208] Explicit read off[189,202][191,204] Explicit read off[185,198][188,201] Explicit read off[183,196][184,197] Explicit read off[178,191][182,195] Explicit read off[175,188][177,190] Explicit read off[171,184][174,187] Explicit read off[169,182][170,183] Explicit read off[165,178][168,181] Explicit read off[162,175][164,177] Explicit read off[157,170][161,174] Explicit read off[18% done]Before mid-j 143 Cells done 74%[18% done]After mid-j 145 Cells done 74%[152,165][156,169] Explicit read off[149,162][151,164] Explicit read off[145,158][148,161] Explicit read off[143,156][144,157] Explicit read off[139,152][142,155] Explicit read off[136,149][138,151] Explicit read off[131,144][135,148] Explicit read off[127,140][130,143] Explicit read off[124,137][126,139] Explicit read off[120,133][123,136] Explicit read off[118,131][119,132] Explicit read off[114,127][117,130] Explicit read off[108,124][113,126] Explicit read off[103,119][107,123] Explicit read off[36% done]Before mid-j 66 Cells done 19%[36% done]Before mid-j 66 Cells done 38%[36% done]Before mid-j 66 Cells done 58%[36% done]Before mid-j 66 Cells done 77%[36% done]Before mid-j 66 Cells done 97%[36% done]After mid-j 68 Cells done 19%[36% done]After mid-j 68 Cells done 38%[36% done]After mid-j 68 Cells done 57%[36% done]After mid-j 68 Cells done 76%[36% done]After mid-j 68 Cells done 95%[36% done]Before mid-j 91 Cells done 76%[36% done]After mid-j 93 Cells done 73%[98,114][102,118] Explicit read off[95,111][97,113] Explicit read off[91,107][94,110] Explicit read off[89,105][90,106] Explicit read off[85,101][88,104] Explicit read off[82,98][84,100] Explicit read off[78,94][81,97] Explicit read off[76,92][77,93] Explicit read off[72,88][75,91] Explicit read off[69,85][71,87] Explicit read off[65,81][68,84] Explicit read off[63,79][64,80] Explicit read off[59,75][62,78] Explicit read off[56,72][58,74] Explicit read off[51,67][55,71] Explicit read off[54% done]Before mid-j 40 Cells done 81%[54% done]After mid-j 42 Cells done 78%[46,62][50,66] Explicit read off[43,59][45,61] Explicit read off[39,55][42,58] Explicit read off[37,53][38,54] Explicit read off[33,49][36,52] Explicit read off[30,46][32,48] Explicit read off[25,41][29,45] Explicit read off[21,37][24,40] Explicit read off[18,34][20,36] Explicit read off[14,30][17,33] Explicit read off[12,28][13,29] Explicit read off[8,24][11,27] Explicit read off[6,22][7,23] Explicit read off[0,17][5,21] Explicit read offAlignment recovered
Find start end points: 1000 Cells done [ 2%] 2000 Cells done [ 4%] 3000 Cells done [ 7%] 4000 Cells done [ 9%] 5000 Cells done [12%] 6000 Cells done [14%] 7000 Cells done [17%] 8000 Cells done [19%] 9000 Cells done [21%] 10000 Cells done [24%] 11000 Cells done [26%] 12000 Cells done [29%] 13000 Cells done [31%] 14000 Cells done [34%] 15000 Cells done [36%] 16000 Cells done [38%] 17000 Cells done [41%] 18000 Cells done [43%] 19000 Cells done [46%] 20000 Cells done [48%] 21000 Cells done [51%] 22000 Cells done [53%] 23000 Cells done [55%] 24000 Cells done [58%] 25000 Cells done [60%] 26000 Cells done [63%] 27000 Cells done [65%] 28000 Cells done [68%] 29000 Cells done [70%] 30000 Cells done [72%] 31000 Cells done [75%] 32000 Cells done [77%] 33000 Cells done [80%] 34000 Cells done [82%] 35000 Cells done [85%] 36000 Cells done [87%] 37000 Cells done [89%] 38000 Cells done [92%] 39000 Cells done [94%] 40000 Cells done [97%] 41000 Cells done [99%][0,0][209,195] Score 99400
Recovering alignment: [0% done]Before mid-j 96 Cells done 4%[0% done]Before mid-j 96 Cells done 9%[0% done]Before mid-j 96 Cells done 14%[0% done]Before mid-j 96 Cells done 19%[0% done]Before mid-j 96 Cells done 24%[0% done]Before mid-j 96 Cells done 29%[0% done]Before mid-j 96 Cells done 34%[0% done]Before mid-j 96 Cells done 39%[0% done]Before mid-j 96 Cells done 44%[0% done]Before mid-j 96 Cells done 49%[0% done]Before mid-j 96 Cells done 54%[0% done]Before mid-j 96 Cells done 58%[0% done]Before mid-j 96 Cells done 63%[0% done]Before mid-j 96 Cells done 68%[0% done]Before mid-j 96 Cells done 73%[0% done]Before mid-j 96 Cells done 78%[0% done]Before mid-j 96 Cells done 83%[0% done]Before mid-j 96 Cells done 88%[0% done]Before mid-j 96 Cells done 93%[0% done]Before mid-j 96 Cells done 98%[0% done]After mid-j 98 Cells done 4%[0% done]After mid-j 98 Cells done 9%[0% done]After mid-j 98 Cells done 14%[0% done]After mid-j 98 Cells done 19%[0% done]After mid-j 98 Cells done 24%[0% done]After mid-j 98 Cells done 29%[0% done]After mid-j 98 Cells done 34%[0% done]After mid-j 98 Cells done 38%[0% done]After mid-j 98 Cells done 43%[0% done]After mid-j 98 Cells done 48%[0% done]After mid-j 98 Cells done 53%[0% done]After mid-j 98 Cells done 58%[0% done]After mid-j 98 Cells done 63%[0% done]After mid-j 98 Cells done 68%[0% done]After mid-j 98 Cells done 72%[0% done]After mid-j 98 Cells done 77%[0% done]After mid-j 98 Cells done 82%[0% done]After mid-j 98 Cells done 87%[0% done]After mid-j 98 Cells done 92%[0% done]After mid-j 98 Cells done 97%[0% done]Before mid-j 145 Cells done 20%[0% done]Before mid-j 145 Cells done 41%[0% done]Before mid-j 145 Cells done 61%[0% done]Before mid-j 145 Cells done 82%[0% done]After mid-j 147 Cells done 20%[0% done]After mid-j 147 Cells done 41%[0% done]After mid-j 147 Cells done 61%[0% done]After mid-j 147 Cells done 82%[0% done]Before mid-j 169 Cells done 83%[0% done]After mid-j 171 Cells done 80%[205,191][209,195] Explicit read off[202,188][204,190] Explicit read off[198,184][201,187] Explicit read off[196,182][197,183] Explicit read off[192,178][195,181] Explicit read off[189,175][191,177] Explicit read off[184,170][188,174] Explicit read off[180,166][183,169] Explicit read off[177,163][179,165] Explicit read off[173,159][176,162] Explicit read off[171,157][172,158] Explicit read off[167,153][170,156] Explicit read off[165,151][166,152] Explicit read off[160,146][164,150] Explicit read off[18% done]Before mid-j 120 Cells done 85%[18% done]After mid-j 122 Cells done 85%[156,142][159,145] Explicit read off[153,139][155,141] Explicit read off[149,135][152,138] Explicit read off[147,133][148,134] Explicit read off[143,129][146,132] Explicit read off[140,126][142,128] Explicit read off[135,121][139,125] Explicit read off[131,117][134,120] Explicit read off[128,114][130,116] Explicit read off[124,110][127,113] Explicit read off[122,108][123,109] Explicit read off[118,104][121,107] Explicit read off[116,102][117,103] Explicit read off[111,97][115,101] Explicit read off[36% done]Before mid-j 47 Cells done 18%[36% done]Before mid-j 47 Cells done 37%[36% done]Before mid-j 47 Cells done 56%[36% done]Before mid-j 47 Cells done 75%[36% done]Before mid-j 47 Cells done 93%[36% done]After mid-j 49 Cells done 18%[36% done]After mid-j 49 Cells done 37%[36% done]After mid-j 49 Cells done 56%[36% done]After mid-j 49 Cells done 75%[36% done]After mid-j 49 Cells done 93%[36% done]Before mid-j 71 Cells done 66%[36% done]After mid-j 73 Cells done 66%[107,93][110,96] Explicit read off[104,90][106,92] Explicit read off[86,86][103,89] Explicit read off[84,84][85,85] Explicit read off[80,80][83,83] Explicit read off[77,77][79,79] Explicit read off[72,72][76,76] Explicit read off[68,68][71,71] Explicit read off[65,65][67,67] Explicit read off[61,61][64,64] Explicit read off[59,59][60,60] Explicit read off[55,55][58,58] Explicit read off[53,53][54,54] Explicit read off[48,48][52,52] Explicit read off[54% done]Before mid-j 22 Cells done 90%[54% done]After mid-j 24 Cells done 86%[44,44][47,47] Explicit read off[41,41][43,43] Explicit read off[37,37][40,40] Explicit read off[35,35][36,36] Explicit read off[31,31][34,34] Explicit read off[28,28][30,30] Explicit read off[23,23][27,27] Explicit read off[19,19][22,22] Explicit read off[16,16][18,18] Explicit read off[11,11][15,15] Explicit read off[7,7][10,10] Explicit read off[5,5][6,6] Explicit read off[0,0][4,4] Explicit read offAlignment recovered
Find start end points: 1000 Cells done [ 2%] 2000 Cells done [ 4%] 3000 Cells done [ 6%] 4000 Cells done [ 8%] 5000 Cells done [10%] 6000 Cells done [12%] 7000 Cells done [14%] 8000 Cells done [17%] 9000 Cells done [19%] 10000 Cells done [21%] 11000 Cells done [23%] 12000 Cells done [25%] 13000 Cells done [27%] 14000 Cells done [29%] 15000 Cells done [32%] 16000 Cells done [34%] 17000 Cells done [36%] 18000 Cells done [38%] 19000 Cells done [40%] 20000 Cells done [42%] 21000 Cells done [44%] 22000 Cells done [46%] 23000 Cells done [49%] 24000 Cells done [51%] 25000 Cells done [53%] 26000 Cells done [55%] 27000 Cells done [57%] 28000 Cells done [59%] 29000 Cells done [61%] 30000 Cells done [64%] 31000 Cells done [66%] 32000 Cells done [68%] 33000 Cells done [70%] 34000 Cells done [72%] 35000 Cells done [74%] 36000 Cells done [76%] 37000 Cells done [79%] 38000 Cells done [81%] 39000 Cells done [83%] 40000 Cells done [85%] 41000 Cells done [87%] 42000 Cells done [89%] 43000 Cells done [91%] 44000 Cells done [93%] 45000 Cells done [96%] 46000 Cells done [98%][0,17][209,222] Score 109962
Recovering alignment: [0% done]Before mid-j 118 Cells done 4%[0% done]Before mid-j 118 Cells done 9%[0% done]Before mid-j 118 Cells done 14%[0% done]Before mid-j 118 Cells done 18%[0% done]Before mid-j 118 Cells done 23%[0% done]Before mid-j 118 Cells done 28%[0% done]Before mid-j 118 Cells done 32%[0% done]Before mid-j 118 Cells done 37%[0% done]Before mid-j 118 Cells done 42%[0% done]Before mid-j 118 Cells done 46%[0% done]Before mid-j 118 Cells done 51%[0% done]Before mid-j 118 Cells done 56%[0% done]Before mid-j 118 Cells done 60%[0% done]Before mid-j 118 Cells done 65%[0% done]Before mid-j 118 Cells done 70%[0% done]Before mid-j 118 Cells done 74%[0% done]Before mid-j 118 Cells done 79%[0% done]Before mid-j 118 Cells done 84%[0% done]Before mid-j 118 Cells done 88%[0% done]Before mid-j 118 Cells done 93%[0% done]Before mid-j 118 Cells done 98%[0% done]After mid-j 120 Cells done 4%[0% done]After mid-j 120 Cells done 9%[0% done]After mid-j 120 Cells done 13%[0% done]After mid-j 120 Cells done 18%[0% done]After mid-j 120 Cells done 23%[0% done]After mid-j 120 Cells done 27%[0% done]After mid-j 120 Cells done 32%[0% done]After mid-j 120 Cells done 36%[0% done]After mid-j 120 Cells done 41%[0% done]After mid-j 120 Cells done 46%[0% done]After mid-j 120 Cells done 50%[0% done]After mid-j 120 Cells done 55%[0% done]After mid-j 120 Cells done 60%[0% done]After mid-j 120 Cells done 64%[0% done]After mid-j 120 Cells done 69%[0% done]After mid-j 120 Cells done 73%[0% done]After mid-j 120 Cells done 78%[0% done]After mid-j 120 Cells done 83%[0% done]After mid-j 120 Cells done 87%[0% done]After mid-j 120 Cells done 92%[0% done]After mid-j 120 Cells done 97%[0% done]Before mid-j 169 Cells done 18%[0% done]Before mid-j 169 Cells done 36%[0% done]Before mid-j 169 Cells done 54%[0% done]Before mid-j 169 Cells done 73%[0% done]Before mid-j 169 Cells done 91%[0% done]After mid-j 171 Cells done 17%[0% done]After mid-j 171 Cells done 35%[0% done]After mid-j 171 Cells done 53%[0% done]After mid-j 171 Cells done 71%[0% done]After mid-j 171 Cells done 89%[0% done]Before mid-j 195 Cells done 72%[0% done]After mid-j 197 Cells done 72%[205,218][209,222] Explicit read off[202,215][204,217] Explicit read off[198,211][201,214] Explicit read off[196,209][197,210] Explicit read off[192,205][195,208] Explicit read off[189,202][191,204] Explicit read off[185,198][188,201] Explicit read off[183,196][184,197] Explicit read off[178,191][182,195] Explicit read off[175,188][177,190] Explicit read off[171,184][174,187] Explicit read off[169,182][170,183] Explicit read off[165,178][168,181] Explicit read off[162,175][164,177] Explicit read off[157,170][161,174] Explicit read off[18% done]Before mid-j 143 Cells done 74%[18% done]After mid-j 145 Cells done 74%[152,165][156,169] Explicit read off[149,162][151,164] Explicit read off[145,158][148,161] Explicit read off[143,156][144,157] Explicit read off[139,152][142,155] Explicit read off[136,149][138,151] Explicit read off[131,144][135,148] Explicit read off[127,140][130,143] Explicit read off[124,137][126,139] Explicit read off[120,133][123,136] Explicit read off[118,131][119,132] Explicit read off[114,127][117,130] Explicit read off[108,124][113,126] Explicit read off[103,119][107,123] Explicit read off[36% done]Before mid-j 66 Cells done 19%[36% done]Before mid-j 66 Cells done 38%[36% done]Before mid-j 66 Cells done 58%[36% done]Before mid-j 66 Cells done 77%[36% done]Before mid-j 66 Cells done 97%[36% done]After mid-j 68 Cells done 19%[36% done]After mid-j 68 Cells done 38%[36% done]After mid-j 68 Cells done 57%[36% done]After mid-j 68 Cells done 76%[36% done]After mid-j 68 Cells done 95%[36% done]Before mid-j 91 Cells done 76%[36% done]After mid-j 93 Cells done 73%[98,114][102,118] Explicit read off[95,111][97,113] Explicit read off[91,107][94,110] Explicit read off[89,105][90,106] Explicit read off[85,101][88,104] Explicit read off[82,98][84,100] Explicit read off[78,94][81,97] Explicit read off[76,92][77,93] Explicit read off[72,88][75,91] Explicit read off[69,85][71,87] Explicit read off[65,81][68,84] Explicit read off[63,79][64,80] Explicit read off[59,75][62,78] Explicit read off[56,72][58,74] Explicit read off[51,67][55,71] Explicit read off[54% done]Before mid-j 40 Cells done 81%[54% done]After mid-j 42 Cells done 78%[46,62][50,66] Explicit read off[43,59][45,61] Explicit read off[39,55][42,58] Explicit read off[37,53][38,54] Explicit read off[33,49][36,52] Explicit read off[30,46][32,48] Explicit read off[25,41][29,45] Explicit read off[21,37][24,40] Explicit read off[18,34][20,36] Explicit read off[14,30][17,33] Explicit read off[12,28][13,29] Explicit read off[8,24][11,27] Explicit read off[6,22][7,23] Explicit read off[0,17][5,21] Explicit read offAlignment recovered
t/DBA.t ....................... ok
UNIVERSAL->import is deprecated and will be removed in a future perl at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Tree/TreeFunctionsI.pm line 94
# Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present
t/DrawGram.t .................. ok
UNIVERSAL->import is deprecated and will be removed in a future perl at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Tree/TreeFunctionsI.pm line 94
# Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present
t/DrawTree.t .................. ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
t/EMBOSS.t .................... ok
t/Ensembl.t ................... skipped: Network tests have not been requested
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required environment variable $EPONINEDIR is not set
t/Eponine.t ................... ok
# Required executable for Bio::Tools::Run::Alignment::Exonerate is not present
t/Exonerate.t ................. ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::FootPrinter is not present
t/FootPrinter.t ............... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required environment variable $GENEMARK_MODELS is not set
t/Genemark.hmm.prokaryotic.t .. ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Genewise is not present
t/Genewise.t .................. ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required environment variable $GENSCANDIR is not set
t/Genscan.t ................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Tree/TreeFunctionsI.pm line 94
# Required executable for Bio::Tools::Run::Phylo::Gerp is not present
t/Gerp.t ...................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Glimmer is not present
t/Glimmer2.t .................. ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Glimmer is not present
t/Glimmer3.t .................. ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Tree/TreeFunctionsI.pm line 94
# Required executable for Bio::Tools::Run::Phylo::Gumby is not present
t/Gumby.t ..................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Hmmer is not present
t/Hmmer.t ..................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Tree/TreeFunctionsI.pm line 94
# Required executable for Bio::Tools::Run::Phylo::Hyphy::SLAC is not present
t/Hyphy.t ..................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Alignment::Kalign is not present
t/Kalign.t .................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Tree/TreeFunctionsI.pm line 94
# Required executable for Bio::Tools::Run::Phylo::LVB is not present
t/LVB.t ....................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Alignment::Lagan is not present
t/Lagan.t ..................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Alignment::MAFFT is not present
t/MAFFT.t ..................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Tree/TreeFunctionsI.pm line 94
# Required executable for Bio::Tools::Run::MCS is not present
t/MCS.t ....................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Match is not present
t/Match.t ..................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Tree/TreeFunctionsI.pm line 94
# Required executable for Bio::Tools::Run::Mdust is not present
t/Mdust.t ..................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Meme is not present
t/Meme.t ...................... ok
UNIVERSAL->import is deprecated and will be removed in a future perl at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Tree/TreeFunctionsI.pm line 94
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present
t/Molphy.t .................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Alignment::Muscle is not present
t/Muscle.t .................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Tree/TreeFunctionsI.pm line 94
# Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present
t/Neighbor.t .................. ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Tree/TreeFunctionsI.pm line 94
# Required executable for Bio::Tools::Run::Phylo::Njtree::Best is not present
t/Njtree.t .................... ok
UNIVERSAL->import is deprecated and will be removed in a future perl at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Tree/TreeFunctionsI.pm line 94
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present
t/PAML.t ...................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Tree/TreeFunctionsI.pm line 94
# Required executable for Bio::Tools::Run::Alignment::Pal2Nal is not present
t/Pal2Nal.t ................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Tree/TreeFunctionsI.pm line 94
# Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
t/PhastCons.t ................. ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Phrap is not present
t/Phrap.t ..................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Tree/TreeFunctionsI.pm line 94
# Required executable for Bio::Tools::Run::Phylo::Phyml is not present
t/Phyml.t ..................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Primate is not present
t/Primate.t ................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Primer3 is not present
t/Primer3.t ................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Prints is not present
t/Prints.t .................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Alignment::Probalign is not present
t/Probalign.t ................. ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Alignment::Probcons is not present
t/Probcons.t .................. ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Profile is not present
t/Profile.t ................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Promoterwise is not present
t/Promoterwise.t .............. ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Tree/TreeFunctionsI.pm line 94
# Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present
t/ProtDist.t .................. ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Tree/TreeFunctionsI.pm line 94
# Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present
t/ProtPars.t .................. ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Pseudowise is not present
t/Pseudowise.t ................ ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Tree/TreeFunctionsI.pm line 94
# Required executable for Bio::Tools::Run::Phylo::QuickTree is not present
t/QuickTree.t ................. ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
RepeatMasker program not found as or not executable.
# Required executable for Bio::Tools::Run::RepeatMasker is not present
t/RepeatMasker.t .............. ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Tree/TreeFunctionsI.pm line 94
# Required executable for Bio::Tools::Run::Phylo::SLR is not present
t/SLR.t ....................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Seg is not present
t/Seg.t ....................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Tree/TreeFunctionsI.pm line 94
# Required executable for Bio::Tools::Run::Phylo::Semphy is not present
t/Semphy.t .................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Tree/TreeFunctionsI.pm line 94
# Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present
t/SeqBoot.t ................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Signalp is not present
t/Signalp.t ................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Alignment::Sim4 is not present
t/Sim4.t ...................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Tree/TreeFunctionsI.pm line 94
# Required executable for Bio::Tools::Run::Simprot is not present
t/Simprot.t ................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present
t/StandAloneFasta.t ........... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Alignment::TCoffee is not present
t/TCoffee.t ................... ok
# Required executable for Bio::Tools::Run::TigrAssembler is not present
t/TigrAssembler.t ............. ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::Tmhmm is not present
t/Tmhmm.t ..................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Tree/TreeFunctionsI.pm line 94
t/TribeMCL.t .................. ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Vista.jar is not in your class path:Exception in thread "main" java.lang.NoClassDefFoundError: Vista
t/Vista.t ..................... ok
Replacement list is longer than search list at /net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/Bio/Range.pm line 251.
# Required executable for Bio::Tools::Run::tRNAscanSE is not present
t/tRNAscanSE.t ................ ok
All tests successful.
Files=67, Tests=1705, 24 wallclock secs ( 0.41 usr 0.17 sys + 13.96 cusr 3.48 csys = 18.02 CPU)
Result: PASS
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
------ ------ --------
perl v5.6.1 5.012002
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
LANG = en_GB.utf8
LD_LIBRARY_PATH = :/usr/lib/jni:/usr/lib/mysql:/net/netfile2/ag-russell/install/Fedora-14-i686/lib:/net/netfile2/ag-russell/install/Fedora-14-i686/lib64:/usr/lib/mysql:/usr/lib/jni:/usr/lib/mysql:/net/netfile2/ag-russell/install/Fedora-14-i686/lib:/net/netfile2/ag-russell/install/Fedora-14-i686/lib64:/usr/lib/mysql
PATH = /home/bq_cdavis/Documents/src/sbglib/trunk/script:/home/bq_cdavis/Documents/src/acaweb/trunk/script:/usr/java/jdk1.6.0_22/bin:/usr/java/jdk1.6.0_21/bin:/net/netfile2/ag-russell/perl/Fedora-14-i686/bin:/usr/java/jdk1.6.0_16/bin:/home/bq_cdavis/scripts:/home/bq_cdavis/admin:/home/bq_cdavis/usr/bin:/home/bq_cdavis/bin:/usr/local/bin:/usr/local/sbin:/bin:/sbin:/usr/bin:/usr/sbin:/usr/X11R6/bin:/home/bq_cdavis/Documents/src/sbglib/trunk/script:/home/bq_cdavis/Documents/src/acaweb/trunk/script:/usr/java/jdk1.6.0_22/bin:/usr/java/jdk1.6.0_21/bin:/net/netfile2/ag-russell/perl/Fedora-14-i686/bin:/usr/java/jdk1.6.0_16/bin:/home/bq_cdavis/scripts:/home/bq_cdavis/admin:/home/bq_cdavis/usr/bin:/home/bq_cdavis/bin:/usr/local/bin:/usr/local/sbin:/bin:/sbin:/usr/bin:/usr/sbin:/usr/X11R6/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/bq_cdavis/.eclipse/org.eclipse.platform_3.4.0_155965261/plugins/com.google.appengine.eclipse.sdkbundle.1.3.8_1.3.8.v201010161036/appengine-java-sdk-1.3.8/bin:/sbin:/net/netfile2/ag-russell/admin:/net/netfile2/ag-russell/admin/data:/net/netfile2/ag-russell/install/Fedora-14-i686/bin:/net/netfile2/ag-russell/code/misc/bin:/opt/pbs/bin:/usr/pbs/bin:/net/netfile2/ag-russell/lbin:/home/bq_cdavis/.eclipse/org.eclipse.platform_3.4.0_155965261/plugins/com.google.appengine.eclipse.sdkbundle.1.3.8_1.3.8.v201010161036/appengine-java-sdk-1.3.8/bin:/sbin:/net/netfile2/ag-russell/admin:/net/netfile2/ag-russell/admin/data:/net/netfile2/ag-russell/install/Fedora-14-i686/bin:/net/netfile2/ag-russell/code/misc/bin:/opt/pbs/bin:/usr/pbs/bin:/net/netfile2/ag-russell/lbin
PERL5LIB = /home/bq_cdavis/Documents/src/sbglib/trunk/lib:/home/bq_cdavis/Documents/src/sbglib/trunk/t:/home/bq_cdavis/Documents/src/acaweb/trunk/lib:/home/bq_cdavis/Documents/src/acaweb/trunk/t:/net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/i386-linux-thread-multi:/net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5:/home/bq_cdavis/scripts:/home/bq_cdavis/scrap/perl:/home/bq_cdavis/Documents/src/sbglib/trunk/lib:/home/bq_cdavis/Documents/src/sbglib/trunk/t:/home/bq_cdavis/Documents/src/acaweb/trunk/lib:/home/bq_cdavis/Documents/src/acaweb/trunk/t:/net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/i386-linux-thread-multi:/net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5:/home/bq_cdavis/scripts:/home/bq_cdavis/scrap/perl::/net/netfile2/ag-russell/install/Fedora-14-i686/lib/perl5:/net/netfile2/ag-russell/code/misc/lib:/net/netfile2/ag-russell/install/Fedora-14-i686/lib/perl5:/net/netfile2/ag-russell/code/misc/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 10105
PERL5_CPAN_IS_RUNNING = 10105
PERL_LOCAL_LIB_ROOT = /net/netfile2/ag-russell/perl/Fedora-14-i686
PERL_MB_OPT = --install_base /net/netfile2/ag-russell/perl/Fedora-14-i686
PERL_MM_OPT = INSTALL_BASE=/net/netfile2/ag-russell/perl/Fedora-14-i686
SHELL = /bin/bash
TERM = xterm
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /usr/bin/perl
$UID/$EUID = 2699 / 2699
$GID = 2048 2048 10000 10003 10004 10099
$EGID = 2048 2048 10000 10003 10004 10099
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 1.94_56
Cwd 3.33
ExtUtils::CBuilder 0.280202
ExtUtils::Command 1.16
ExtUtils::Install 1.55
ExtUtils::MakeMaker 6.56
ExtUtils::Manifest 1.57
ExtUtils::ParseXS 2.2206
File::Spec 3.33
Module::Build 0.3624
Module::Signature 0.66
Test::Harness 3.22
Test::More 0.96
YAML 0.72
YAML::Syck n/a
version 0.88
--
Summary of my perl5 (revision 5 version 12 subversion 2) configuration:
Platform:
osname=linux, osvers=2.6.32-72.el6.bz634452.x86_64, archname=i386-linux-thread-multi
uname='linux x86-07.phx2.fedoraproject.org 2.6.32-72.el6.bz634452.x86_64 #1 smp fri sep 17 06:52:25 edt 2010 i686 i686 i386 gnulinux '
config_args='-des -Doptimize=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -Dccdlflags=-Wl,--enable-new-dtags -DDEBUGGING=-g -Dversion=5.12.2 -Dmyhostname=localhost -Dperladmin=root@localhost -Dcc=gcc -Dcf_by=Red Hat, Inc. -Dprefix=/usr -Dvendorprefix=/usr -Dsiteprefix=/usr/local -Dsitelib=/usr/local/share/perl5 -Dsitearch=/usr/local/lib/perl5 -Dprivlib=/usr/share/perl5 -Dvendorlib=/usr/share/perl5 -Darchlib=/usr/lib/perl5 -Dvendorarch=/usr/lib/perl5 -Darchname=i386-linux-thread-multi -Duseshrplib -Dusethreads -Duseithreads -Dusedtrace=/usr/bin/dtrace -Duselargefiles -Dd_semctl_semun -Di_db -Ui_ndbm -Di_gdbm -Di_shadow -Di_syslog -Dman3ext=3pm -Duseperlio -Dinstallusrbinperl=n -Ubincompat5005 -Uversiononly -Dpager=/usr/bin/less -isr -Dd_gethostent_r_proto -Ud_endhostent_r_proto -Ud_sethostent_r_proto -Ud_endprotoent_r_proto -Ud_setprotoent_r_proto -Ud_endservent_r_proto -Ud_setservent_r_proto -Dscriptdir=/usr/bin -Dotherlibdirs=/usr/local/lib/perl5/site_perl/5.10.0/i386-linux-thread-multi:/usr/local/lib/perl5/site_perl/5.10.0:/usr/lib/perl5/vendor_perl/5.10.0/i386-linux-thread-multi:/usr/lib/perl5/vendor_perl:/usr/lib/perl5/site_perl'
hint=recommended, useposix=true, d_sigaction=define
useithreads=define, usemultiplicity=define
useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
use64bitint=undef, use64bitall=undef, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='gcc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
optimize='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables',
cppflags='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include'
ccversion='', gccversion='4.5.1 20100924 (Red Hat 4.5.1-4)', gccosandvers=''
intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=1234
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=12
ivtype='long', ivsize=4, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
alignbytes=4, prototype=define
Linker and Libraries:
ld='gcc', ldflags =' -fstack-protector -L/usr/local/lib'
libpth=/usr/local/lib /lib /usr/lib
libs=-lresolv -lnsl -lgdbm -ldb -ldl -lm -lcrypt -lutil -lpthread -lc -lgdbm_compat
perllibs=-lresolv -lnsl -ldl -lm -lcrypt -lutil -lpthread -lc
libc=/lib/libc-2.12.90.so, so=so, useshrplib=true, libperl=libperl.so
gnulibc_version='2.12.90'
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib/perl5/CORE'
cccdlflags='-fPIC', lddlflags='-shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -L/usr/local/lib'
Characteristics of this binary (from libperl):
Compile-time options: MULTIPLICITY PERL_DONT_CREATE_GVSV
PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP USE_ITHREADS
USE_LARGE_FILES USE_PERLIO USE_PERL_ATOF
USE_REENTRANT_API
Built under linux
Compiled at Dec 1 2010 13:05:08
%ENV:
PERL5LIB="/home/bq_cdavis/Documents/src/sbglib/trunk/lib:/home/bq_cdavis/Documents/src/sbglib/trunk/t:/home/bq_cdavis/Documents/src/acaweb/trunk/lib:/home/bq_cdavis/Documents/src/acaweb/trunk/t:/net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/i386-linux-thread-multi:/net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5:/home/bq_cdavis/scripts:/home/bq_cdavis/scrap/perl:/home/bq_cdavis/Documents/src/sbglib/trunk/lib:/home/bq_cdavis/Documents/src/sbglib/trunk/t:/home/bq_cdavis/Documents/src/acaweb/trunk/lib:/home/bq_cdavis/Documents/src/acaweb/trunk/t:/net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/i386-linux-thread-multi:/net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5:/home/bq_cdavis/scripts:/home/bq_cdavis/scrap/perl::/net/netfile2/ag-russell/install/Fedora-14-i686/lib/perl5:/net/netfile2/ag-russell/code/misc/lib:/net/netfile2/ag-russell/install/Fedora-14-i686/lib/perl5:/net/netfile2/ag-russell/code/misc/lib"
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="10105"
PERL5_CPAN_IS_RUNNING="10105"
PERL_LOCAL_LIB_ROOT="/net/netfile2/ag-russell/perl/Fedora-14-i686"
PERL_MB_OPT="--install_base /net/netfile2/ag-russell/perl/Fedora-14-i686"
PERL_MM_OPT="INSTALL_BASE=/net/netfile2/ag-russell/perl/Fedora-14-i686"
@INC:
/home/bq_cdavis/Documents/src/sbglib/trunk/lib
/home/bq_cdavis/Documents/src/sbglib/trunk/t
/home/bq_cdavis/Documents/src/acaweb/trunk/lib
/home/bq_cdavis/Documents/src/acaweb/trunk/t
/net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/i386-linux-thread-multi
/net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/i386-linux-thread-multi
/net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5
/home/bq_cdavis/scripts
/home/bq_cdavis/scrap/perl
/home/bq_cdavis/Documents/src/sbglib/trunk/lib
/home/bq_cdavis/Documents/src/sbglib/trunk/t
/home/bq_cdavis/Documents/src/acaweb/trunk/lib
/home/bq_cdavis/Documents/src/acaweb/trunk/t
/net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/i386-linux-thread-multi
/net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5/i386-linux-thread-multi
/net/netfile2/ag-russell/perl/Fedora-14-i686/lib/perl5
/home/bq_cdavis/scripts
/home/bq_cdavis/scrap/perl
/net/netfile2/ag-russell/install/Fedora-14-i686/lib/perl5
/net/netfile2/ag-russell/code/misc/lib
/net/netfile2/ag-russell/install/Fedora-14-i686/lib/perl5
/net/netfile2/ag-russell/code/misc/lib
/usr/local/lib/perl5
/usr/local/share/perl5
/usr/lib/perl5
/usr/share/perl5
/usr/lib/perl5
/usr/share/perl5
/usr/local/lib/perl5/site_perl/5.10.0/i386-linux-thread-multi
/usr/local/lib/perl5/site_perl/5.10.0
/usr/lib/perl5/vendor_perl/5.10.0/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl
/usr/lib/perl5/site_perl
.