[Phylobase-devl] readNexus crashes R

Mon Oct 25 23:24:49 CEST 2010

The email below is from the R-sig-phylo list regarding a Nexus file that APE struggles with.  My attempts to read this with readNexus() result in a hard R crash on snow leopard, can someone confirm this on linux?  

The nexus file is probably malformed in some way, but it shouldn't crash R.  R immediately exits for me, without even the option for a core dump, so I have no idea what part of the code is causing the crash.

Peter

Begin forwarded message:

> From: Joey Pakes <joey.pakes at gmail.com>
> Date: October 25, 2010 2:13:33 PM PDT
> To: r-sig-phylo at r-project.org
> Subject: [R-sig-phylo] Error in if (tp[3] != "") obj$node.label <- tp[3] :
> 
> Hello,
> 
> I have made a tree with RAXML have viewed it in Mesquite and saved it as a
> nexus file. I would like to modify the tree in R, but cannot get R (2.11.1
> for Leopard) to read or plot the tree. I can however get the program to read
> the nexus file and spit out the node lavels, edge lengths, tip labels, etc
> (all using the APE package).
> 
> I have copied and pasted the error I get when trying read tree command:
> ----------------
> newtree<-read.tree("/Users/pakes/Desktop/ape/Use
> these/RAxML_bipartitions.16Sproteoplusphy_10_22noHf0.nex")
> 
> Error in if (tp[3] != "") obj$node.label <- tp[3] :
>  missing value where TRUE/FALSE needed
> --------------
> One issue is that I'm not sure what tp is?
> 
> Below is my nexus file:
> 
> #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;
> -----------------------------------
> Any help would be greatly appreciated!
> 
> Thank you!
> 
> 	[[alternative HTML version deleted]]
> 
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