bppsuite some crashes with Example data

Hello,

testing a fresh build of bppsuite (commit 4cad9e7)

built using not yet published bpplibs3 bpp-core (commit 6de759a) bpp-seq (commit db76604) bpp-seq-omics (commit 7f04fd7) bpp-phyl (commit da6bf9a2) bpp-phyl-omics (commit ad03d9d) bpp-popgen (commit 72de565)

I have crashes//problems with the Examples. problems range from missing files, misspeled parameters (eg optimization = Brent vs optimization = D-Brent) and I guess easy to fix

it would be nice to have for people that are not in the field (IT guy here trying to install stuff for our cluster useres), to be abble to test the program with valid data set // command line.

just as example,

Examples/ConsensusTree          missing//misspeled file
Examples/Distance               unknown parameter
Examples/SequenceManipulation   exit with error.
Examples/ReRooting              segfault

see:

Examples/ConsensusTree > bppconsense param=Consense.bpp
******************************************************************
*       Bio++ Consensus and Bootstrap Methods, version 3.0.0     *
* Authors: J. Dutheil                       Created     06/06/07 *
*          N. Galtier                       Last Modif. (prerelease) *
******************************************************************

Parsing options:
Parsing file Consense.bpp for options.
File does not exists: ../Data/tree.dnd
    from  bpp::PhylogeneticsApplicationTools::getTrees
    from  bppconsense() [0x409220]

Examples/Distance > bppdist param=Dist.bpp
******************************************************************
*              Bio++ Distance Methods, version 3.0.0             *
* Author: J. Dutheil                        Created     05/05/07 *
*                                           Last Modif. (prerelease) *
******************************************************************

Parsing options:
Parsing file Dist.bpp for options.
Alphabet type .........................: DNA
Sequence file .........................: ../Data/LSU.phy
Sequence format .......................: Phylip file, extended,sequential
Selected sites.........................: 1:50

Data 1
Sites to use...........................: complete
Complete sites.........................: 50
Number of sites........................: 50

Tree 1
Number of leaves.......................: 79
Branch lengths.........................: Input

Rate 1
Distribution...........................: Constant
Number of classes......................: 1
- Category 0 (Pr = 1) rate.............: 1

Model 1
Substitution model.....................: HKY85
External model frequencies init........: None
Parameter found........................: HKY85.kappa=1
Parameter found........................: HKY85.theta=0.5
Parameter found........................: HKY85.theta1=0.5
Parameter found........................: HKY85.theta2=0.5

Process 1
Process type...........................: Homogeneous
 Model number..........................: 1
 Tree number...........................: 1
 Rate number...........................: 1
 Stationarity assumed.

Phylolikelihood 1
 Data used ............................: 1
 Process ..............................: 1

Result Phylolikelihood
WARNING!!! Parameter result not specified. Default used instead: phylo1
 Result................................: phylo1
Tree reconstruction method.............: bionj
Model parameters estimation method.....: iterations
Unknown optimization method Brent
    from  bppdist() [0x42ed22]

Examples/SequenceManipulation > bppseqman param=SeqMan.bpp
******************************************************************
*           Bio++ Sequence Manipulator, version 3.0.0.           *
* Author: J. Dutheil                        Last Modif. (prerelease) *
******************************************************************

Parsing options:
Parsing file SeqMan.bpp for options.
Alphabet type .........................: DNA
Sequence file .........................: ../Data/LSU.phy
Sequence format .......................: Phylip file, extended,sequential
Number of sequences....................: 79
Performing action......................: Switch
Performing action......................: Transcript
Performing action......................: CoerceToAlignment
Performing action......................: KeepComplete
Performing action......................: GapToUnknown
Final sequences are aligned............: yes
Output alignment file .................: LSU.fas
Output alignment format ...............: FASTA file
VectorMappedContainer::getObjectPosition : Not found object with name Bradyrhizobium
    from  virtual thunk to bpp::TemplateVectorSiteContainer<bpp::Site, bpp::Sequence>::sequence
    from  bpp::Fasta::writeSequences
    from  bpp::AbstractOSequence::writeSequences
    from  bpp::SequenceApplicationTools::writeAlignmentFile
    from  bppseqman() [0x41e43b]

Examples/ReRooting > bppreroot param=ReRoot.bpp
******************************************************************
*                  Bio++ ReRoot, version 3.0.0                   *
* Author: C. Scornavacca                    Created     15/01/08 *
*                                           Last Modif. (prerelease) *
******************************************************************

Parsing options:
Parsing file ReRoot.bpp for options.
Input list file........................: ../Data/treeList2.dnd
Outgroups file.........................: ../Data/OutGroup.txt
Output file............................: treeList2_rooted.dnd
WARNING!!! Parameter tryAgain.option not specified. Default used instead: 1
- 12 nodes loaded.
Segmentation fault

BioPP / bppsuite

bppsuite some crashes with Example data #22