[Bioperl-l] bioperl-db install doing more than burping
Keith Allen
kallen@paragen.com
Wed, 13 Mar 2002 12:41:01 -0500
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Hey Guys,
Filled with a glowing sense of optimism, I tried to build the
bioperl-db package (latest distro, 0.1), on Redhat 7.2, perl 5.6.0,
and gcc 3.0.2. The patient did more than burp, I'm afraid, in
fact, I'm going to spray the output from make test (make
proceeded with nary a whimper). The summary from make
test looks like:
Failed Test Status Wstat Total Fail Failed List of failed
-------------------------------------------------------------------------------
t/ePCRdb.t 255 65280 3 2 66.67% 2-3
t/ensembl.t 255 65280 14 1 7.14% 14
t/map.t 255 65280 6 5 83.33% 2-6
t/marker.t 255 65280 19 18 94.74% 2-19
Failed 4/14 test scripts, 71.43% okay. 26/152 subtests failed, 82.89% okay.
make: *** [test_dynamic] Error 29
Though it may well be that some of the errors are just in the
test scripts (there is a lot of carrying on about Bio::Root::RootI being
deprecated).
Being a programmer of very little brain, I went ahead and did
the make install, and then tried to run load_seqdatabase.pl (after
using the supplied SQL code to build the basicseqdb). I ended up
hitting a number of snags, but I'm guessing that these are not
informative before I know how bad the state of my build is based on
the failed tests.
Any thoughts?
-Keith Allen
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PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib/perl5/5.6.0/i386-linux -I/usr/lib/perl5/5.6.0 -e 'use Test::Harness qw(&runtests $verbose); $verbose=0; runtests @ARGV;' t/*.t
t/comment...........Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/comment.t line 0
ok
t/dbadaptor.........ok
t/dblink............Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/dblink.t line 0
ok
t/ensembl...........-------------------- WARNING ---------------------
MSG: moltype: pre v1.0 method. Calling alphabet() instead...
---------------------------------------------------
-------------------- WARNING ---------------------
MSG: moltype: pre v1.0 method. Calling alphabet() instead...
---------------------------------------------------
each_Comment (old style Annotation) on new style Annotation::Collection
STACK Bio::Annotation::Collection::each_Comment /usr/lib/perl5/site_perl/5.6.0/Bio/Annotation/Collection.pm:390
STACK Bio::DB::SQL::SeqAdaptor::store blib/lib/Bio/DB/SQL/SeqAdaptor.pm:470
STACK toplevel t/ensembl.t:42
each_Reference (old style Annotation) on new style Annotation::Collection
STACK Bio::Annotation::Collection::each_Reference /usr/lib/perl5/site_perl/5.6.0/Bio/Annotation/Collection.pm:348
STACK Bio::DB::SQL::SeqAdaptor::store blib/lib/Bio/DB/SQL/SeqAdaptor.pm:477
STACK toplevel t/ensembl.t:42
each_DBLink (old style Annotation) on new style Annotation::Collection
STACK Bio::Annotation::Collection::each_DBLink /usr/lib/perl5/site_perl/5.6.0/Bio/Annotation/Collection.pm:433
STACK Bio::DB::SQL::SeqAdaptor::store blib/lib/Bio/DB/SQL/SeqAdaptor.pm:496
STACK toplevel t/ensembl.t:42
-------------------- EXCEPTION --------------------
MSG: -text
STACK Bio::Root::RootI::throw_not_implemented /usr/lib/perl5/site_perl/5.6.0/Bio/Root/RootI.pm:562
STACK Bio::PrimarySeqI::alphabet /usr/lib/perl5/site_perl/5.6.0/Bio/PrimarySeqI.pm:330
STACK Bio::SeqIO::genbank::write_seq /usr/lib/perl5/site_perl/5.6.0/Bio/SeqIO/genbank.pm:364
STACK toplevel t/ensembl.t:74
-------------------------------------------
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/ensembl.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/ensembl.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/ensembl.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/ensembl.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/ensembl.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/ensembl.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/ensembl.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/ensembl.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/ensembl.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/ensembl.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/ensembl.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/ensembl.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/ensembl.t line 0
dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED test 14
Failed 1/14 tests, 92.86% okay
t/ePCRdb............Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/DBTestHarness.pm line 225
Can't locate object method "_db_handle" via package "Bio::Root::Root" at blib/lib/Bio/DB/Map/SQL/DBAdaptor.pm line 131.
dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 2-3
Failed 2/3 tests, 33.33% okay
t/map...............Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/DBTestHarness.pm line 225
Can't locate object method "_db_handle" via package "Bio::Root::Root" at blib/lib/Bio/DB/Map/SQL/DBAdaptor.pm line 131.
dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 2-6
Failed 5/6 tests, 16.67% okay
t/marker............Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/DBTestHarness.pm line 225
Can't locate object method "_db_handle" via package "Bio::Root::Root" at blib/lib/Bio/DB/Map/SQL/DBAdaptor.pm line 131.
dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 2-19
Failed 18/19 tests, 5.26% okay
t/remove............-------------------- WARNING ---------------------
MSG: moltype: pre v1.0 method. Calling alphabet() instead...
---------------------------------------------------
-------------------- WARNING ---------------------
MSG: moltype: pre v1.0 method. Calling alphabet() instead...
---------------------------------------------------
each_Comment (old style Annotation) on new style Annotation::Collection
STACK Bio::Annotation::Collection::each_Comment /usr/lib/perl5/site_perl/5.6.0/Bio/Annotation/Collection.pm:390
STACK Bio::DB::SQL::SeqAdaptor::store blib/lib/Bio/DB/SQL/SeqAdaptor.pm:470
STACK toplevel t/remove.t:48
each_Reference (old style Annotation) on new style Annotation::Collection
STACK Bio::Annotation::Collection::each_Reference /usr/lib/perl5/site_perl/5.6.0/Bio/Annotation/Collection.pm:348
STACK Bio::DB::SQL::SeqAdaptor::store blib/lib/Bio/DB/SQL/SeqAdaptor.pm:477
STACK toplevel t/remove.t:48
each_DBLink (old style Annotation) on new style Annotation::Collection
STACK Bio::Annotation::Collection::each_DBLink /usr/lib/perl5/site_perl/5.6.0/Bio/Annotation/Collection.pm:433
STACK Bio::DB::SQL::SeqAdaptor::store blib/lib/Bio/DB/SQL/SeqAdaptor.pm:496
STACK toplevel t/remove.t:48
-------------------- WARNING ---------------------
MSG: moltype: pre v1.0 method. Calling alphabet() instead...
---------------------------------------------------
-------------------- WARNING ---------------------
MSG: moltype: pre v1.0 method. Calling alphabet() instead...
---------------------------------------------------
each_Comment (old style Annotation) on new style Annotation::Collection
STACK Bio::Annotation::Collection::each_Comment /usr/lib/perl5/site_perl/5.6.0/Bio/Annotation/Collection.pm:390
STACK Bio::DB::SQL::SeqAdaptor::store blib/lib/Bio/DB/SQL/SeqAdaptor.pm:470
STACK toplevel t/remove.t:53
each_Reference (old style Annotation) on new style Annotation::Collection
STACK Bio::Annotation::Collection::each_Reference /usr/lib/perl5/site_perl/5.6.0/Bio/Annotation/Collection.pm:348
STACK Bio::DB::SQL::SeqAdaptor::store blib/lib/Bio/DB/SQL/SeqAdaptor.pm:477
STACK toplevel t/remove.t:53
each_DBLink (old style Annotation) on new style Annotation::Collection
STACK Bio::Annotation::Collection::each_DBLink /usr/lib/perl5/site_perl/5.6.0/Bio/Annotation/Collection.pm:433
STACK Bio::DB::SQL::SeqAdaptor::store blib/lib/Bio/DB/SQL/SeqAdaptor.pm:496
STACK toplevel t/remove.t:53
-------------------- WARNING ---------------------
MSG: moltype: pre v1.0 method. Calling alphabet() instead...
---------------------------------------------------
-------------------- WARNING ---------------------
MSG: moltype: pre v1.0 method. Calling alphabet() instead...
---------------------------------------------------
each_Comment (old style Annotation) on new style Annotation::Collection
STACK Bio::Annotation::Collection::each_Comment /usr/lib/perl5/site_perl/5.6.0/Bio/Annotation/Collection.pm:390
STACK Bio::DB::SQL::SeqAdaptor::store blib/lib/Bio/DB/SQL/SeqAdaptor.pm:470
STACK toplevel t/remove.t:53
each_Reference (old style Annotation) on new style Annotation::Collection
STACK Bio::Annotation::Collection::each_Reference /usr/lib/perl5/site_perl/5.6.0/Bio/Annotation/Collection.pm:348
STACK Bio::DB::SQL::SeqAdaptor::store blib/lib/Bio/DB/SQL/SeqAdaptor.pm:477
STACK toplevel t/remove.t:53
each_DBLink (old style Annotation) on new style Annotation::Collection
STACK Bio::Annotation::Collection::each_DBLink /usr/lib/perl5/site_perl/5.6.0/Bio/Annotation/Collection.pm:433
STACK Bio::DB::SQL::SeqAdaptor::store blib/lib/Bio/DB/SQL/SeqAdaptor.pm:496
STACK toplevel t/remove.t:53
-------------------- WARNING ---------------------
MSG: moltype: pre v1.0 method. Calling alphabet() instead...
---------------------------------------------------
-------------------- WARNING ---------------------
MSG: moltype: pre v1.0 method. Calling alphabet() instead...
---------------------------------------------------
each_Comment (old style Annotation) on new style Annotation::Collection
STACK Bio::Annotation::Collection::each_Comment /usr/lib/perl5/site_perl/5.6.0/Bio/Annotation/Collection.pm:390
STACK Bio::DB::SQL::SeqAdaptor::store blib/lib/Bio/DB/SQL/SeqAdaptor.pm:470
STACK toplevel t/remove.t:53
each_Reference (old style Annotation) on new style Annotation::Collection
STACK Bio::Annotation::Collection::each_Reference /usr/lib/perl5/site_perl/5.6.0/Bio/Annotation/Collection.pm:348
STACK Bio::DB::SQL::SeqAdaptor::store blib/lib/Bio/DB/SQL/SeqAdaptor.pm:477
STACK toplevel t/remove.t:53
each_DBLink (old style Annotation) on new style Annotation::Collection
STACK Bio::Annotation::Collection::each_DBLink /usr/lib/perl5/site_perl/5.6.0/Bio/Annotation/Collection.pm:433
STACK Bio::DB::SQL::SeqAdaptor::store blib/lib/Bio/DB/SQL/SeqAdaptor.pm:496
STACK toplevel t/remove.t:53
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/remove.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/remove.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/remove.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/remove.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/remove.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/remove.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/remove.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/remove.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/remove.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/remove.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/remove.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/remove.t line 0
ok
t/seqfeaturekey.....Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/seqfeaturekey.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/seqfeaturekey.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/seqfeaturekey.t line 0
ok
t/seqfeature........Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/seqfeature.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/seqfeature.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/seqfeature.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/seqfeature.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/seqfeature.t line 0
ok
t/seqlocation.......Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/seqlocation.t line 0
ok
t/simpleseq.........-------------------- WARNING ---------------------
MSG: moltype: pre v1.0 method. Calling alphabet() instead...
---------------------------------------------------
-------------------- WARNING ---------------------
MSG: moltype: pre v1.0 method. Calling alphabet() instead...
---------------------------------------------------
each_Comment (old style Annotation) on new style Annotation::Collection
STACK Bio::Annotation::Collection::each_Comment /usr/lib/perl5/site_perl/5.6.0/Bio/Annotation/Collection.pm:390
STACK Bio::DB::SQL::SeqAdaptor::store blib/lib/Bio/DB/SQL/SeqAdaptor.pm:470
STACK toplevel t/simpleseq.t:42
each_Reference (old style Annotation) on new style Annotation::Collection
STACK Bio::Annotation::Collection::each_Reference /usr/lib/perl5/site_perl/5.6.0/Bio/Annotation/Collection.pm:348
STACK Bio::DB::SQL::SeqAdaptor::store blib/lib/Bio/DB/SQL/SeqAdaptor.pm:477
STACK toplevel t/simpleseq.t:42
each_DBLink (old style Annotation) on new style Annotation::Collection
STACK Bio::Annotation::Collection::each_DBLink /usr/lib/perl5/site_perl/5.6.0/Bio/Annotation/Collection.pm:433
STACK Bio::DB::SQL::SeqAdaptor::store blib/lib/Bio/DB/SQL/SeqAdaptor.pm:496
STACK toplevel t/simpleseq.t:42
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/simpleseq.t line 71
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/simpleseq.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/simpleseq.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/simpleseq.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/simpleseq.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/simpleseq.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/simpleseq.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/simpleseq.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/simpleseq.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/simpleseq.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/simpleseq.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/simpleseq.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/simpleseq.t line 0
ok
t/species...........Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/species.t line 0
ok
t/swiss.............-------------------- WARNING ---------------------
MSG: moltype: pre v1.0 method. Calling alphabet() instead...
---------------------------------------------------
-------------------- WARNING ---------------------
MSG: moltype: pre v1.0 method. Calling alphabet() instead...
---------------------------------------------------
each_Comment (old style Annotation) on new style Annotation::Collection
STACK Bio::Annotation::Collection::each_Comment /usr/lib/perl5/site_perl/5.6.0/Bio/Annotation/Collection.pm:390
STACK Bio::DB::SQL::SeqAdaptor::store blib/lib/Bio/DB/SQL/SeqAdaptor.pm:470
STACK toplevel t/swiss.t:40
each_Reference (old style Annotation) on new style Annotation::Collection
STACK Bio::Annotation::Collection::each_Reference /usr/lib/perl5/site_perl/5.6.0/Bio/Annotation/Collection.pm:348
STACK Bio::DB::SQL::SeqAdaptor::store blib/lib/Bio/DB/SQL/SeqAdaptor.pm:477
STACK toplevel t/swiss.t:40
each_DBLink (old style Annotation) on new style Annotation::Collection
STACK Bio::Annotation::Collection::each_DBLink /usr/lib/perl5/site_perl/5.6.0/Bio/Annotation/Collection.pm:433
STACK Bio::DB::SQL::SeqAdaptor::store blib/lib/Bio/DB/SQL/SeqAdaptor.pm:496
STACK toplevel t/swiss.t:40
each_DBLink (old style Annotation) on new style Annotation::Collection
STACK Bio::Annotation::Collection::each_DBLink /usr/lib/perl5/site_perl/5.6.0/Bio/Annotation/Collection.pm:433
STACK toplevel t/swiss.t:67
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/swiss.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/swiss.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/swiss.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/swiss.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/swiss.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/swiss.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/swiss.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/swiss.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/swiss.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/swiss.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/swiss.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/swiss.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/swiss.t line 0
Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead at t/swiss.t line 0
ok
Failed Test Status Wstat Total Fail Failed List of failed
-------------------------------------------------------------------------------
t/ePCRdb.t 255 65280 3 2 66.67% 2-3
t/ensembl.t 255 65280 14 1 7.14% 14
t/map.t 255 65280 6 5 83.33% 2-6
t/marker.t 255 65280 19 18 94.74% 2-19
Failed 4/14 test scripts, 71.43% okay. 26/152 subtests failed, 82.89% okay.
make: *** [test_dynamic] Error 29
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