[Phylobase-devl] readNexus crashes R
François Michonneau
francois.michonneau at gmail.com
Mon Oct 25 23:52:00 CEST 2010
Hi,
I'll look into it, but I won't have much time before the end of the
week.
Cheers,
-- François
On Mon, 2010-10-25 at 16:39 -0500, Mark Holder wrote:
> Hi,
> The file is not a valid NEXUS file.
>
>
> The C++ code in phylobase (an adaptation of the nexus class library) is probably throwing an exception. I base that guess on the fact that when I run the file on the NEXUSnormalizer program ( a testing program for NCL) I get an error message. The source of the error in the nexus file is the fact that the names in the TRANSLATE command of the TREES block do not match the TAXLABELS in the TAXA block.
>
> Errors in an input file should not cause a crash in R, so there is probably so hole in the phylobase wrapping of NCL exceptions.
>
>
> I'm not sure when I'll be able to look at that code, so if someone has the time and energy, then go for it (I'll certainly try to answer any NCL questions that come up).
>
>
> cheers,
> Mark
>
>
>
>
>
>
> On Oct 25, 2010, at 4:24 PM, Peter Cowan wrote:
>
> >> #NEXUS
> >> [written Sat Oct 23 12:11:18 PDT 2010 by Mesquite version 2.6 (build 486)
> >> at Macintosh-101.local/10.0.1.6]
> >>
> >> BEGIN TAXA;
> >> TITLE Taxa;
> >> DIMENSIONS NTAX=32;
> >> TAXLABELS
> >> S1FS3_S3FS1_&_S2LS4 Desulfodehalobacter_spongiphilus_strain_
> >> Desulfobacterium_indolicum_strain_DSM_33
> >> Desulfobacter_postgatei_strain_DSM_2034_ Geobacter_sulfurreducens_#U13928
> >> S2HS1_&_S3HS1 Geobacter_chapelleii_strain_172_#NR_0259 F2HS1b
> >> Shewanella_putrefaciens_strain_Hac334_#D Shewanella_aquimarina_#AY485225
> >> Pseudomonas_meridiana_strain_CMS_38T_AJ5 F2FS1_&_F3FS2 F2HS1_&_F2HS3
> >> Pseudomonas_stutzeri_strain_LS401_#U2641 F2FS2_&_F3HS2
> >> Marinobacter_hydrocarbonoclasticus_strai S3FS4_S3FS5_&_S3FS6
> >> Marinobacter_guineae_strain_LMG_24048_#A Marinobacter_lipolyticus_strain_SM
> >> S1HS1 Desulfopila_aestuarii_#AB110542 S3FS2
> >> S1HS2_S1HS3_S1HS4_S1HS5_S3HS4_&_F2HA2a F3FS1
> >> Desulfovibrio_putealis_#AY574979 Desulfovibrio_desulfuricans_subsp._desul
> >> S2LS1 Desulfovibrio_bizertensis_strain_MB3_#DQ S1FS1
> >> Desulfovibrio_marinisediminis_#AB353727 S2LS3_S3LS1_S3FS3_&_F2HA2b
> >> Acidobacterium_capsulatum_#D26171
> >> ;
> >>
> >> END;
> >>
> >>
> >> BEGIN TREES;
> >> Title Imported_trees;
> >> LINK Taxa = Taxa;
> >> TRANSLATE
> >> 1 S1FS3_S3FS1_&_S2LS4,
> >> 2 D_s_strain_,
> >> 3 D_i_strain_DSM_3,
> >> 4 D_p_strain_DSM_2_,
> >> 5 G_s_#,
> >> 6 S2HS1_&_S3HS1,
> >> 7 G_c_strain_1_#NR_0,
> >> 8 F2HS1b,
> >> 9 S_p_strain_H_#D,
> >> 10 S_a_#,
> >> 11 P_m_strain_C_3_A,
> >> 12 F2FS1_&_F3FS2,
> >> 13 F2HS1_&_F2HS3,
> >> 14 P_s_strain_L_#,
> >> 15 F2FS2_&_F3HS2,
> >> 16 M_h_s,
> >> 17 S3FS4_S3FS5_&_S3FS6,
> >> 18 M_g_s_L_2_#A,
> >> 19 M_l_s_S,
> >> 20 S1HS1,
> >> 21 D_a_#A,
> >> 22 S3FS2,
> >> 23 S1HS2_S1HS3_S1HS4_S1HS5_S3HS4_&_F2HA2a,
> >> 24 F3FS1,
> >> 25 D_p_#,
> >> 26 D_d_s._d,
> >> 27 S2LS1,
> >> 28 D_b_s_M_#D,
> >> 29 S1FS1,
> >> 30 D_m_#A,
> >> 31 S2LS3_S3LS1_S3FS3_&_F2HA2b,
> >> 32 A_c_#;
> >> TREE Imported_tree_0 =
> >> (((1:0.014294865658239897,2:0.016346131753724284)100:0.04531876862101268,(3:0.07787046050007705,(4:0.1575116382471088,((((5:0.04822215084893891,(6:0.0271216303442505,7:0.02007948214228989)100:0.03528659400373911)99:0.05981681725589428,(((8:1.12919178858362E-6,9:1.12919178858362E-6)100:0.057530109591399765,10:0.037691124354788864)100:0.08304244998885398,((11:0.030702696010829537,((12:8.544451267088965E-4,13:1.12919178858362E-6)100:0.020184245020285173,(14:1.12919178858362E-6,15:0.0034181003601162514)85:0.012235337246177081)93:0.01895791066948832)100:0.047681348350900744,(16:0.020642180955472003,(17:0.0033048657512852178,(18:0.005988936129628456,(19:0.005010797883775309,20:0.01691780810184798)67:0.007663605184147101)74:0.006198749083268308)74:0.014460306032529943)100:0.06150881986749245)96:0.03607879771546074)100:0.1898411550405616)61:0.05839829698184673,((21:0.03207541431435525,22:0.03529636469585623)86:0.014049212961742451,23:0.015891647611896632)100:0.12157794121374672)43
> :
> > 0!
> >> .025419418511636843,((24:0.008361788925720447,25:8.737200748323158E-4)100:0.12954900469798472,(26:0.12890159096837994,((27:1.12919178858362E-6,28:0.004140667057671182)100:0.07459471196756032,(29:1.12919178858362E-6,(30:1.12919178858362E-6,31:0.0033956963116614446)89:0.002536358334238893)100:0.14144374970927193)77:0.030026874274203138)83:0.03329468873634148)98:0.09177164340960056)45:0.034517167840112765)51:0.04130953485123759)27:0.02140636921130952)100:0.21688189318012785,32:0.21688189318012785)100:0.23;
> >>
> >> END;
> >>
> >>
> >> Begin MESQUITE;
> >> MESQUITESCRIPTVERSION 2;
> >> TITLE AUTO;
> >> tell ProjectCoordinator;
> >> getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
> >> tell It;
> >> setID 0 4448951287512167596;
> >> endTell;
> >> getWindow;
> >> tell It;
> >> suppress;
> >> setResourcesState true false 100;
> >> setPopoutState 400;
> >> setExplanationSize 0;
> >> setAnnotationSize 0;
> >> setFontIncAnnot 0;
> >> setFontIncExp 0;
> >> setSize 700 464;
> >> setLocation 8 8;
> >> setFont SanSerif;
> >> setFontSize 10;
> >> getToolPalette;
> >> tell It;
> >> endTell;
> >> desuppress;
> >> endTell;
> >> endTell;
> >> end;
>
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