FAIL bioperl-run-1.4 sun4-solaris 2.8

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--
This is an error report generated automatically by CPANPLUS,
version 0.048.

Below is the error stack during 'make test':

PERL_DL_NONLAZY=1 /usr/local/perl-5.8.1/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/Analysis_soap...........ok
t/AnalysisFactory_soap....ok
t/Blat....................blat  program not found. Skipping tests 2 to 11.
FAILED tests 2-11
	Failed 10/11 tests, 9.09% okay
t/Clustalw................ok
        6/9 skipped: Clustalw program not found. Skipping. (Be sure you have clustalw > 1.4)
t/Coil....................Need to define env variable COILSDIR to run test at t/Coil.t line 27.
ok
        4/4 skipped: Unable to run Coil tests, exe may not be installed or configured properly
t/Consense................Using a hash as a reference is deprecated at /net/sunu991/disc1/.cpanplus/5.8.1/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm line 501.
Consense program not found. Skipping tests 2 to 7.
ok
        6/7 skipped: consense not found. Skipping.
t/DBA.....................DBA program not found. Skipping tests 2 to 15.
ok
        14/15 skipped: dba program not found. Skipping. (Be sure you have the wise package > 2.2.0)
t/DrawGram................drawgram program not found. Skipping tests 1 to 4.
ok
        4/4 skipped: drawgram not found. Skipping.
t/DrawTree................drawgram program not found. Skipping tests 1 to 4.
ok
        4/4 skipped: drawtree not found. Skipping.
t/EMBOSS..................ok
        28/30 skipped: EMBOSS not installed locally or XML::Twig not installed
t/Eponine.................ok
        5/5 skipped: You must have defined EPONINEDIR to run these tests
t/FootPrinter.............FootPrinter program not found. Skipping tests 1 to 18.
ok
        18/18 skipped: FootPrinter program not found. Skipping.
t/Genewise................Genewise program not found. Skipping tests 3 to 13.
ok
        11/13 skipped: genewise program not found. Skipping. (Be sure you have the wise package > 2.2.0)
t/Genscan.................Need to define env variable GENSCAN_DIR to run test at t/Genscan.t line 28.
ok
        4/4 skipped: Unable to run Genscan tests, exe may not be installed
t/Hmmer..................."my" variable @params masks earlier declaration in same scope at t/Hmmer.t line 68.
"my" variable @params masks earlier declaration in same scope at t/Hmmer.t line 104.
Useless use of private array in void context at t/Hmmer.t line 87.
hmmpfam  program not found. Skipping tests 4 to 17.
ok
        14/17 skipped: Unable to run Prints tests, exe may not be installed
t/Hmmpfam.................hmmpfam  program not found. Skipping tests 4 to 8.
ok
        5/8 skipped: Unable to run Prints tests, exe may not be installed
t/Lagan...................lagan program not found. Skipping tests 3 to 5.
ok
        3/5 skipped: Unable to run Lagan tests, exe may not be installed
t/Mdust...................Mdust not installed Skipping tests 2 to 2.
ok
        1/2 skipped: Mdust not found. Skpping.
t/Molphy..................Molphy package not installed. Skipping tests 1 to 7.
ok
        7/7 skipped: Molphy not found. Skipping.
t/Neighbor................Using a hash as a reference is deprecated at /net/sunu991/disc1/.cpanplus/5.8.1/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm line 517.
ok
        14/14 skipped: Neighbor not found. Skipping.
t/PAML....................PAML not is installed. skipping tests 2 to 17
ok
        16/17 skipped: unable to run all of the PAML tests
t/Pise....................Need XML::Parser::PerlSA to run test, skipping test
ok
        10/10 skipped: unable to the Pise tests -- Need XML::Parser::PerlSAX
t/Primate.................Primate program not found. Skipping tests 1 to 6.
ok
        6/6 skipped: unable to run all of the primate tests
t/Primer3.................Primer3 program not found. Skipping tests 4 to NUMTESTS.
ok
        4/7 skipped: primer3 program not found. Skipping. You can get this from http://www-genome.wi.mit.edu/genome_software/other/primer3.html
t/Prints..................prints program not found. Skipping tests 3 to 5.
ok
        3/5 skipped: Unable to run Prints tests, exe may not be installed
t/Profile................. profile program not found. Skipping tests 3 to 5.
ok
        3/5 skipped: Unable to run Profile tests, exe may not be installed
t/Promoterwise............Promoterwise program not found. Skipping tests 3 to 8.
ok
        6/8 skipped: promoterwise program not found. Skipping. (Be sure you have the wise package > 2.2.0)
t/ProtDist................Using a hash as a reference is deprecated at /net/sunu991/disc1/.cpanplus/5.8.1/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm line 517.
Protdist program not found. Skipping tests 2 to 11.
ok
        10/11 skipped: ProtDist not found. Skipping.
t/ProtPars................Using a hash as a reference is deprecated at /net/sunu991/disc1/.cpanplus/5.8.1/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm line 421.
Protpars program not found. Skipping tests 3 to 7.
ok
        5/7 skipped: Protpars not found. Skipping.
t/Pseudowise..............Pseudowise program not found. Skipping tests 2 to 13.
ok
        12/13 skipped: pseudowise program not found. Skipping. (Be sure you have the wise package > 2.2.0)
t/RepeatMasker............Use of uninitialized value in concatenation (.) or string at /net/sunu991/disc1/.cpanplus/5.8.1/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/RepeatMasker.pm line 174.
RepeatMasker program not found as  or not executable. 
RepeatMasker program not found. Skipping tests 1 to 8.
ok
        8/8 skipped: RepeatMasker program not found. Skipping. (Be sure you have the phrap package )
t/Seg.....................seg  program not found. Skipping tests 3 to 6.
ok
        4/6 skipped: Unable to run Seg tests, exe may not be installed
t/SeqBoot.................Using a hash as a reference is deprecated at /net/sunu991/disc1/.cpanplus/5.8.1/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm line 441.
SeqBoot program not found. Skipping tests 2 to 6.
ok
        5/6 skipped: SeqBoot not found. Skipping.
t/Signalp.................signalp program not found. Skipping tests 3 to 5.
ok
        3/5 skipped: Unable to run SignalP tests, exe may not be installed
t/Sim4....................Sim4 program not found. Skipping tests 2 to 20.
ok
        19/20 skipped: sim4 program not found. Skipping. (Be sure you have installed Sim4)
t/StandAloneFasta.........ok
        13/15 skipped: various reasons
t/TCoffee.................tcoffee program not found. Skipping tests 5 to 22.
ok
        18/22 skipped: TCoffee program not found. Skipping.
t/Tmhmm...................Use of uninitialized value in substitution (s///) at /usr/local/perl-5.8.1/lib/5.8.1/File/Spec/Unix.pm line 52.
Use of uninitialized value in substitution (s///) at /usr/local/perl-5.8.1/lib/5.8.1/File/Spec/Unix.pm line 53.
Use of uninitialized value in string eq at /usr/local/perl-5.8.1/lib/5.8.1/File/Spec/Unix.pm line 54.
Use of uninitialized value in substitution (s///) at /usr/local/perl-5.8.1/lib/5.8.1/File/Spec/Unix.pm line 54.
Use of uninitialized value in substitution (s///) at /usr/local/perl-5.8.1/lib/5.8.1/File/Spec/Unix.pm line 55.
Use of uninitialized value in string eq at /usr/local/perl-5.8.1/lib/5.8.1/File/Spec/Unix.pm line 56.
Use of uninitialized value in substitution (s///) at /usr/local/perl-5.8.1/lib/5.8.1/File/Spec/Unix.pm line 56.
Use of uninitialized value in concatenation (.) or string at /usr/local/perl-5.8.1/lib/5.8.1/File/Spec/Unix.pm line 57.
ok
        3/5 skipped: Unable to run Tmhmm tests, exe may not be installed
t/TribeMCL................Tribe Matrix program not found. Skipping tests 2 to 22.
ok
        21/22 skipped: TribeMCL program not found. Skipping. (Be sure you have the TribeMCL package
t/Vista...................Vista.jar is not your class path 
ok
        5/5 skipped: Unable to run Vista , java may not be installed
Failed Test Stat Wstat Total Fail  Failed  List of Failed
-------------------------------------------------------------------------------
t/Blat.t                  11   10  90.91%  2-11
322 subtests skipped.
Failed 1/40 test scripts, 97.50% okay. 10/405 subtests failed, 97.53% okay.
make: *** [test_dynamic] Error 29


Additional comments:
--

Summary of my perl5 (revision 5.0 version 8 subversion 1) configuration:
  Platform:
    osname=solaris, osvers=2.8, archname=sun4-solaris
    uname='sunos sunu991 5.8 generic_108528-14 sun4u sparc sunw,ultra-5_10 solaris '
    config_args=''
    hint=recommended, useposix=true, d_sigaction=define
    usethreads=undef use5005threads=undef useithreads=undef usemultiplicity=undef
    useperlio=define d_sfio=undef uselargefiles=define usesocks=undef
    use64bitint=undef use64bitall=undef uselongdouble=undef
    usemymalloc=n, bincompat5005=undef
  Compiler:
    cc='gcc', ccflags ='-fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
    optimize='-O',
    cppflags='-fno-strict-aliasing -I/usr/local/include'
    ccversion='', gccversion='3.0.3', gccosandvers='solaris2.8'
    intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=4321
    d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16
    ivtype='long', ivsize=4, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
    alignbytes=8, prototype=define
  Linker and Libraries:
    ld='gcc', ldflags =' -L/usr/local/lib '
    libpth=/usr/local/lib /usr/lib /usr/ccs/lib
    libs=-lsocket -lnsl -lgdbm -ldb -ldl -lm -lc
    perllibs=-lsocket -lnsl -ldl -lm -lc
    libc=/lib/libc.so, so=so, useshrplib=false, libperl=libperl.a
    gnulibc_version=''
  Dynamic Linking:
    dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='  -z ignore -z lazyload -z combreloc'
    cccdlflags='-fPIC', lddlflags=' -G  -z ignore -z lazyload -z combreloc -L/usr/local/lib'

• FAIL bioperl-run-1.4 sun4-solaris 2.8 by Jost.Krieger+smokeback