[Bioperl-guts-l] [Bug 2312] New: './Build test' failures on linux with bioperl-live from cvs now()

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Thu Jun 7 09:57:06 EDT 2007


http://bugzilla.open-bio.org/show_bug.cgi?id=2312

           Summary: './Build test' failures on linux with bioperl-live from
                    cvs now()
           Product: BioPerl
           Version: main-trunk
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Unclassified
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: mmokrejs at ribosome.natur.cuni.cz


I did perl Build.PL and asked to install most of the optional stuff, except
the AceDB viewer and the GFF/mysql database stuff. Anyway, something got
installed and the testsuite should at least skip those test which have no
prerequisities installed. If the summary error message below would point me
where to look for the stacktraces from perl, I could post them. I am overhauled
with a number of other tasks, so I cannot spend much time on reading docs,
sorry. Just wanted to test current cvs and Genbank parser. ;-)


t/BioDBGFF...................ok 1/278# Looks like you planned 278 tests but
only ran 104.
t/BioDBGFF...................dubious                                         
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 105-278
        Failed 174/278 tests, 37.41% okay (less 1 skipped test: 103 okay,
37.05%)
t/BioDBSeqFeature............ok                                              
t/BioDBSeqFeature_BDB........ok                                              
t/BioFetch_DB................skipped
        all skipped: Must set BIOPERLDEBUG=1 for network tests
t/BioGraphics................NOK 3/38                                        
#   Failed test in t/BioGraphics.t at line 170.
t/BioGraphics................NOK 4/38                                        
#   Failed test in t/BioGraphics.t at line 170.
t/BioGraphics................NOK 5/38                                        
#   Failed test in t/BioGraphics.t at line 170.
t/BioGraphics................ok 6/38# Looks like you failed 3 tests of 38.   
t/BioGraphics................dubious                                         
        Test returned status 3 (wstat 768, 0x300)
DIED. FAILED tests 3-5
        Failed 3/38 tests, 92.11% okay
t/BlastIndex.................ok                                       



t/RemoteBlast................ok 18/21                                        
-------------------- WARNING ---------------------
MSG: Server failed to return any data
---------------------------------------------------

#   Failed test in t/RemoteBlast.t at line 164.
t/RemoteBlast................NOK 19/21# Looks like you planned 21 tests but
only ran 19.
# Looks like you failed 1 test of 19 run.
t/RemoteBlast................dubious                                         
        Test returned status 1 (wstat 256, 0x100)
DIED. FAILED tests 19-21
        Failed 3/21 tests, 85.71% okay (less 4 skipped tests: 14 okay, 66.67%)


t/Tree.......................FAILED tests 30-39                              
        Failed 10/29 tests, 65.52% okay


t/embl.......................ok                                              
t/entrezgene.................ok 545/1423Pseudo-hashes are deprecated at
/home/mmokrejs/proj/bioperl/bioperl-live/blib/lib/Bio/SeqIO/entrezgene.pm line
491.
t/entrezgene.................ok 981/1423Pseudo-hashes are deprecated at
/home/mmokrejs/proj/bioperl/bioperl-live/blib/lib/Bio/SeqIO/entrezgene.pm line
491.
Pseudo-hashes are deprecated at
/home/mmokrejs/proj/bioperl/bioperl-live/blib/lib/Bio/SeqIO/entrezgene.pm line
491.
t/entrezgene.................ok 1143/1423Pseudo-hashes are deprecated at
/home/mmokrejs/proj/bioperl/bioperl-live/blib/lib/Bio/SeqIO/entrezgene.pm line
491.


t/ztr........................ok                                              
Failed Test     Stat Wstat Total Fail  List of Failed
-------------------------------------------------------------------------------
t/BioDBGFF.t     255 65280   278  348  105-278
t/BioGraphics.t    3   768    38    3  3-5
t/RemoteBlast.t    1   256    21    5  19-21
t/Tree.t                      29   10  30-39
19 tests and 134 subtests skipped.
Failed 4/244 test scripts. 170/14656 subtests failed.
Files=244, Tests=14656, 256 wallclock secs (177.32 cusr +  7.50 csys = 184.82
CPU)
Failed 4/244 test programs. 170/14656 subtests failed.




$ perl -V
Summary of my perl5 (revision 5 version 8 subversion 8) configuration:
  Platform:
    osname=linux, osvers=2.6.18.1, archname=i686-linux-thread-multi
    uname='linux vrapenec 2.6.18.1 #5 tue oct 24 13:01:30 cest 2006 i686 mobile
intel(r) pentium(r) 4 - m cpu 1.80ghz genuineintel gnulinux '
    config_args='-des -Darchname=i686-linux-thread -Dcccdlflags=-fPIC
-Dccdlflags=-rdynamic -Dcc=i686-pc-linux-gnu-gcc -Dprefix=/usr
-Dvendorprefix=/usr -Dsiteprefix=/usr -Dlocincpth=  -Doptimize=-O2
-march=pentium4 -mmmx -msse 
sse2 -fomit-frame-pointer -pipe -Duselargefiles -Dd_semctl_semun
-Dscriptdir=/usr/bin -Dman1dir=/usr/share/man/man1
-Dman3dir=/usr/share/man/man3 -Dinstallman1dir=/usr/share/man/man1
-Dinstallman3dir=/usr/share/man/man3 -Dman1ex
1 -Dman3ext=3pm -Dinc_version_list=5.8.0 5.8.0/i686-linux-thread-multi 5.8.2
5.8.2/i686-linux-thread-multi 5.8.4 5.8.4/i686-linux-thread-multi 5.8.5
5.8.5/i686-linux-thread-multi 5.8.6 5.8.6/i686-linux-thread-multi 5.8.7 5.8.7/i
6-linux-thread-multi  -Dcf_by=Gentoo -Ud_csh -Dusenm -Dusethreads -Di_ndbm
-Di_gdbm -Di_db'
    hint=recommended, useposix=true, d_sigaction=define
    usethreads=define use5005threads=undef 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='i686-pc-linux-gnu-gcc', ccflags ='-D_REENTRANT -D_GNU_SOURCE
-DTHREADS_HAVE_PIDS -fno-strict-aliasing -pipe -Wdeclaration-after-statement
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
    optimize='-O2 -march=pentium4 -mmmx -msse -msse2 -fomit-frame-pointer
-pipe',
    cppflags='-D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS
-fno-strict-aliasing -pipe -Wdeclaration-after-statement'
    ccversion='', gccversion='4.1.1 (Gentoo 4.1.1-r1)', 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='i686-pc-linux-gnu-gcc', ldflags =' -L/usr/local/lib'
    libpth=/usr/local/lib /lib /usr/lib
    libs=-lpthread -lnsl -lndbm -lgdbm -ldb -ldl -lm -lcrypt -lutil -lc
    perllibs=-lpthread -lnsl -ldl -lm -lcrypt -lutil -lc
    libc=/lib/libc-2.5.so, so=so, useshrplib=false, libperl=libperl.a
    gnulibc_version='2.5'
  Dynamic Linking:
    dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-rdynamic'
    cccdlflags='-fPIC', lddlflags='-shared -L/usr/local/lib'


Characteristics of this binary (from libperl): 
  Compile-time options: MULTIPLICITY PERL_IMPLICIT_CONTEXT
                        PERL_MALLOC_WRAP THREADS_HAVE_PIDS USE_ITHREADS
                        USE_LARGE_FILES USE_PERLIO USE_REENTRANT_API
  Built under linux
  Compiled at Oct 27 2006 16:23:07
  @INC:
    /etc/perl
    /usr/lib/perl5/vendor_perl/5.8.8/i686-linux-thread-multi
    /usr/lib/perl5/vendor_perl/5.8.8
    /usr/lib/perl5/vendor_perl
    /usr/lib/perl5/site_perl/5.8.8/i686-linux-thread-multi
    /usr/lib/perl5/site_perl/5.8.8
    /usr/lib/perl5/site_perl
    /usr/lib/perl5/5.8.8/i686-linux-thread-multi
    /usr/lib/perl5/5.8.8
    /usr/local/lib/site_perl
    .
$


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