[Bioperl-l] bioperl - must it have mysql to work?
Sciencelife@aol.com
Sciencelife@aol.com
Mon, 04 Mar 2002 19:47:54 EST
Is there an installation method which
is not reliant on mysql? Is there
still no way to interface Oracle? Make test
failed although "make" ran error free (see below).
Does absence of mysql render bioperl install
useless & is this why all 16 make tests
failed?
Is there way to use bioperl without mysql?
make tests failed starting with absence
of "Root" directory creation under Bio.
Other installations of perl & modules (e.g. CGI,
DBI, & DBD compiled with gcc) work fine.
perl is: ActiveState v5.6.1 built for
sun4-solaris-thread-multi
with gcc.
gcc is: 3.0.3 for sparc-sun-solaris2.8
Thanks I.A.
---------------- make test output ----------------
PERL_DL_NONLAZY=1 /usr/local/ActivePerl-5.6/bin/perl -Iblib/arch -Iblib/lib -I/usr/local/ActivePerl-5.6/lib/5.6.1/sun4-solaris-thread-multi -I/usr/local/ActivePerl-5.6/lib/5.6.1 -e 'use Test::Harness qw(&runtests $verbose); $verbose=0; runtests @ARGV;' t/*.t
t/comment...........Can't locate Bio/Root/RootI.pm in @INC (@INC contains: t blib/arch blib/lib /usr/local/ActivePerl-5.6/lib/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/5.6.1 /md14/installables/ /md14/installables/DBI-1.21/ /md14/installables/DBI-1.21/lib/ /md14/installables/DBI-1.21/lib/Bundle /md14/installables/DBI-1.21/lib/DBD /md14/installables/DBI-1.21/lib/DBI /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1 /usr/local/ActivePerl-5.6/lib/site_perl .) at
blib/lib/Bio/DB/SQL/DBAdaptor.pm line 46.
BEGIN failed--compilation aborted at blib/lib/Bio/DB/SQL/DBAdaptor.pm line 46.
Compilation failed in require at t/comment.t line 16.
BEGIN failed--compilation aborted at t/comment.t line 16.
dubious
Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-6
Failed 6/6 tests, 0.00% okay
t/dbadaptor.........Can't locate Bio/Root/RootI.pm in @INC (@INC contains: t blib/arch blib/lib /usr/local/ActivePerl-5.6/lib/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/5.6.1 /md14/installables/ /md14/installables/DBI-1.21/ /md14/installables/DBI-1.21/lib/ /md14/installables/DBI-1.21/lib/Bundle /md14/installables/DBI-1.21/lib/DBD /md14/installables/DBI-1.21/lib/DBI /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1 /usr/local/ActivePerl-5.6/lib/site_perl .) at blib/lib/Bio/DB/SQL/DBAdaptor.pm line 46.
BEGIN failed--compilation aborted at blib/lib/Bio/DB/SQL/DBAdaptor.pm line 46.
Compilation failed in require at t/dbadaptor.t line 15.
BEGIN failed--compilation aborted at t/dbadaptor.t line 15.
dubious
Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-3
Failed 3/3 tests, 0.00% okay
t/dblink............Can't locate Bio/Root/RootI.pm in @INC (@INC contains: t blib/arch blib/lib /usr/local/ActivePerl-5.6/lib/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/5.6.1 /md14/installables/ /md14/installables/DBI-1.21/ /md14/installables/DBI-1.21/lib/ /md14/installables/DBI-1.21/lib/Bundle /md14/installables/DBI-1.21/lib/DBD /md14/installables/DBI-1.21/lib/DBI /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1 /usr/local/ActivePerl-5.6/lib/site_perl .) at blib/lib/Bio/DB/SQL/DBAdaptor.pm line 46.
BEGIN failed--compilation aborted at blib/lib/Bio/DB/SQL/DBAdaptor.pm line 46.
Compilation failed in require at t/dblink.t line 16.
BEGIN failed--compilation aborted at t/dblink.t line 16.
dubious
Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-7
Failed 7/7 tests, 0.00% okay
t/ePCRdb............Can't locate Bio/Root/RootI.pm in @INC (@INC contains: t blib/arch blib/lib /usr/local/ActivePerl-5.6/lib/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/5.6.1 /md14/installables/ /md14/installables/DBI-1.21/ /md14/installables/DBI-1.21/lib/ /md14/installables/DBI-1.21/lib/Bundle /md14/installables/DBI-1.21/lib/DBD /md14/installables/DBI-1.21/lib/DBI /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1 /usr/local/ActivePerl-5.6/lib/site_perl .) at blib/lib/Bio/DB/Map/SQL/DBAdaptor.pm line 72.
BEGIN failed--compilation aborted at blib/lib/Bio/DB/Map/SQL/DBAdaptor.pm line 72.
Compilation failed in require at t/ePCRdb.t line 17.
BEGIN failed--compilation aborted at t/ePCRdb.t line 17.
dubious
Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-3
Failed 3/3 tests, 0.00% okay
t/ensembl...........Can't locate Bio/Root/RootI.pm in @INC (@INC contains: t blib/arch blib/lib /usr/local/ActivePerl-5.6/lib/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/5.6.1 /md14/installables/ /md14/installables/DBI-1.21/ /md14/installables/DBI-1.21/lib/ /md14/installables/DBI-1.21/lib/Bundle /md14/installables/DBI-1.21/lib/DBD /md14/installables/DBI-1.21/lib/DBI /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1 /usr/local/ActivePerl-5.6/lib/site_perl .) at blib/lib/Bio/DB/SQL/DBAdaptor.pm line 46.
BEGIN failed--compilation aborted at blib/lib/Bio/DB/SQL/DBAdaptor.pm line 46.
Compilation failed in require at t/ensembl.t line 14.
BEGIN failed--compilation aborted at t/ensembl.t line 14.
dubious
Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-14
Failed 14/14 tests, 0.00% okay
t/map...............Can't locate Bio/Root/RootI.pm in @INC (@INC contains: t blib/arch blib/lib /usr/local/ActivePerl-5.6/lib/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/5.6.1 /md14/installables/ /md14/installables/DBI-1.21/ /md14/installables/DBI-1.21/lib/ /md14/installables/DBI-1.21/lib/Bundle /md14/installables/DBI-1.21/lib/DBD /md14/installables/DBI-1.21/lib/DBI /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1 /usr/local/ActivePerl-5.6/lib/site_perl .) at blib/lib/Bio/DB/Map/SQL/DBAdaptor.pm line 72.
BEGIN failed--compilation aborted at blib/lib/Bio/DB/Map/SQL/DBAdaptor.pm line 72.
Compilation failed in require at t/map.t line 17.
BEGIN failed--compilation aborted at t/map.t line 17.
dubious
Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-6
Failed 6/6 tests, 0.00% okay
t/marker............Can't locate Bio/Root/RootI.pm in @INC (@INC contains: t blib/arch blib/lib /usr/local/ActivePerl-5.6/lib/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/5.6.1 /md14/installables/ /md14/installables/DBI-1.21/ /md14/installables/DBI-1.21/lib/ /md14/installables/DBI-1.21/lib/Bundle /md14/installables/DBI-1.21/lib/DBD /md14/installables/DBI-1.21/lib/DBI /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1 /usr/local/ActivePerl-5.6/lib/site_perl .) at blib/lib/Bio/DB/Map/SQL/DBAdaptor.pm line 72.
BEGIN failed--compilation aborted at blib/lib/Bio/DB/Map/SQL/DBAdaptor.pm line 72.
Compilation failed in require at t/marker.t line 17.
BEGIN failed--compilation aborted at t/marker.t line 17.
dubious
Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-19
Failed 19/19 tests, 0.00% okay
t/remove............Can't locate Bio/Root/RootI.pm in @INC (@INC contains: t blib/arch blib/lib /usr/local/ActivePerl-5.6/lib/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/5.6.1 /md14/installables/ /md14/installables/DBI-1.21/ /md14/installables/DBI-1.21/lib/ /md14/installables/DBI-1.21/lib/Bundle /md14/installables/DBI-1.21/lib/DBD /md14/installables/DBI-1.21/lib/DBI /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1 /usr/local/ActivePerl-5.6/lib/site_perl .) at blib/lib/Bio/DB/SQL/DBAdaptor.pm line 46.
BEGIN failed--compilation aborted at blib/lib/Bio/DB/SQL/DBAdaptor.pm line 46.
Compilation failed in require at t/remove.t line 13.
BEGIN failed--compilation aborted at t/remove.t line 13.
dubious
Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-22
Failed 22/22 tests, 0.00% okay
t/seqfeature........Can't locate Bio/Root/RootI.pm in @INC (@INC contains: t blib/arch blib/lib /usr/local/ActivePerl-5.6/lib/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/5.6.1 /md14/installables/ /md14/installables/DBI-1.21/ /md14/installables/DBI-1.21/lib/ /md14/installables/DBI-1.21/lib/Bundle /md14/installables/DBI-1.21/lib/DBD /md14/installables/DBI-1.21/lib/DBI /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1 /usr/local/ActivePerl-5.6/lib/site_perl .) at blib/lib/Bio/DB/SQL/DBAdaptor.pm line 46.
BEGIN failed--compilation aborted at blib/lib/Bio/DB/SQL/DBAdaptor.pm line 46.
Compilation failed in require at t/seqfeature.t line 15.
BEGIN failed--compilation aborted at t/seqfeature.t line 15.
dubious
Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-9
Failed 9/9 tests, 0.00% okay
t/seqfeaturekey.....Can't locate Bio/Root/RootI.pm in @INC (@INC contains: t blib/arch blib/lib /usr/local/ActivePerl-5.6/lib/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/5.6.1 /md14/installables/ /md14/installables/DBI-1.21/ /md14/installables/DBI-1.21/lib/ /md14/installables/DBI-1.21/lib/Bundle /md14/installables/DBI-1.21/lib/DBD /md14/installables/DBI-1.21/lib/DBI /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1 /usr/local/ActivePerl-5.6/lib/site_perl .) at blib/lib/Bio/DB/SQL/DBAdaptor.pm line 46.
BEGIN failed--compilation aborted at blib/lib/Bio/DB/SQL/DBAdaptor.pm line 46.
Compilation failed in require at t/seqfeaturekey.t line 15.
BEGIN failed--compilation aborted at t/seqfeaturekey.t line 15.
dubious
Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-11
Failed 11/11 tests, 0.00% okay
t/seqlocation.......Can't locate Bio/Root/RootI.pm in @INC (@INC contains: t blib/arch blib/lib /usr/local/ActivePerl-5.6/lib/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/5.6.1 /md14/installables/ /md14/installables/DBI-1.21/ /md14/installables/DBI-1.21/lib/ /md14/installables/DBI-1.21/lib/Bundle /md14/installables/DBI-1.21/lib/DBD /md14/installables/DBI-1.21/lib/DBI /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1 /usr/local/ActivePerl-5.6/lib/site_perl .) at blib/lib/Bio/DB/SQL/DBAdaptor.pm line 46.
BEGIN failed--compilation aborted at blib/lib/Bio/DB/SQL/DBAdaptor.pm line 46.
Compilation failed in require at t/seqlocation.t line 16.
BEGIN failed--compilation aborted at t/seqlocation.t line 16.
dubious
Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-10
Failed 10/10 tests, 0.00% okay
t/simpleseq.........Can't locate Bio/Root/RootI.pm in @INC (@INC contains: t blib/arch blib/lib /usr/local/ActivePerl-5.6/lib/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/5.6.1 /md14/installables/ /md14/installables/DBI-1.21/ /md14/installables/DBI-1.21/lib/ /md14/installables/DBI-1.21/lib/Bundle /md14/installables/DBI-1.21/lib/DBD /md14/installables/DBI-1.21/lib/DBI /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1 /usr/local/ActivePerl-5.6/lib/site_perl .) at blib/lib/Bio/DB/SQL/DBAdaptor.pm line 46.
BEGIN failed--compilation aborted at blib/lib/Bio/DB/SQL/DBAdaptor.pm line 46.
Compilation failed in require at t/simpleseq.t line 15.
BEGIN failed--compilation aborted at t/simpleseq.t line 15.
dubious
Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-20
Failed 20/20 tests, 0.00% okay
t/species...........Can't locate Bio/Root/RootI.pm in @INC (@INC contains: t blib/arch blib/lib /usr/local/ActivePerl-5.6/lib/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/5.6.1 /md14/installables/ /md14/installables/DBI-1.21/ /md14/installables/DBI-1.21/lib/ /md14/installables/DBI-1.21/lib/Bundle /md14/installables/DBI-1.21/lib/DBD /md14/installables/DBI-1.21/lib/DBI /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1 /usr/local/ActivePerl-5.6/lib/site_perl .) at blib/lib/Bio/DB/SQL/DBAdaptor.pm line 46.
BEGIN failed--compilation aborted at blib/lib/Bio/DB/SQL/DBAdaptor.pm line 46.
Compilation failed in require at t/species.t line 15.
BEGIN failed--compilation aborted at t/species.t line 15.
dubious
Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-6
Failed 6/6 tests, 0.00% okay
t/swiss.............Can't locate Bio/Root/RootI.pm in @INC (@INC contains: t blib/arch blib/lib /usr/local/ActivePerl-5.6/lib/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/5.6.1 /md14/installables/ /md14/installables/DBI-1.21/ /md14/installables/DBI-1.21/lib/ /md14/installables/DBI-1.21/lib/Bundle /md14/installables/DBI-1.21/lib/DBD /md14/installables/DBI-1.21/lib/DBI /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1/sun4-solaris-thread-multi /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1 /usr/local/ActivePerl-5.6/lib/site_perl .) at blib/lib/Bio/DB/SQL/DBAdaptor.pm line 46.
BEGIN failed--compilation aborted at blib/lib/Bio/DB/SQL/DBAdaptor.pm line 46.
Compilation failed in require at t/swiss.t line 13.
BEGIN failed--compilation aborted at t/swiss.t line 13.
dubious
Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-16
Failed 16/16 tests, 0.00% okay
Failed Test Status Wstat Total Fail Failed List of Failed
--------------------------------------------------------------------------------
t/comment.t 2 512 6 6 100.00% 1-6
t/dbadaptor.t 2 512 3 3 100.00% 1-3
t/dblink.t 2 512 7 7 100.00% 1-7
t/ePCRdb.t 2 512 3 3 100.00% 1-3
t/ensembl.t 2 512 14 14 100.00% 1-14
t/map.t 2 512 6 6 100.00% 1-6
t/marker.t 2 512 19 19 100.00% 1-19
t/remove.t 2 512 22 22 100.00% 1-22
t/seqfeature.t 2 512 9 9 100.00% 1-9
t/seqfeaturekey.t 2 512 11 11 100.00% 1-11
t/seqlocation.t 2 512 10 10 100.00% 1-10
t/simpleseq.t 2 512 20 20 100.00% 1-20
t/species.t 2 512 6 6 100.00% 1-6
t/swiss.t 2 512 16 16 100.00% 1-16
Failed 14/14 test scripts, 0.00% okay. 152/152 subtests failed, 0.00% okay.
*** Error code 2
make: Fatal error: Command failed for target `test_dynamic'