[Bioperl-l] Bioperl-ext test fails

a_arya2000 a_arya2000 at yahoo.com
Tue Nov 27 09:51:41 EST 2007


Hello,
I downloaded latest bioperl-ext from bioperl website,
and I have io_lib v1.8.11 installed, and I was trying
to install Bio::SeqIO::staden::read (of bioperl-ext).
It compiled fine without any error but when I run make
test I got following output. 


ERL_DL_NONLAZY=1 perl-5.8.8/bin/perl
"-MExtUtils::Command::MM" "-e" "test_harness(0,
'blib/lib', 'blib/arch')" t/*.t
t/staden_read....ok 3/94# Test 7 got: "0"
(t/staden_read.t at line 110 *TODO*)
#   Expected: <UNDEF> (We don't have the ability to
write files for abi format)
#  t/staden_read.t line 110 is:         ok(0, undef,
"We don't have the ability to write files for $format
format") for 1..7;
# Test 8 got: "0" (t/staden_read.t at line 110 fail #2
*TODO*)
#   Expected: <UNDEF> (We don't have the ability to
write files for abi format)
# Test 9 got: "0" (t/staden_read.t at line 110 fail #3
*TODO*)
#   Expected: <UNDEF> (We don't have the ability to
write files for abi format)
# Test 10 got: "0" (t/staden_read.t at line 110 fail
#4 *TODO*)
#    Expected: <UNDEF> (We don't have the ability to
write files for abi format)
# Test 11 got: "0" (t/staden_read.t at line 110 fail
#5 *TODO*)
#    Expected: <UNDEF> (We don't have the ability to
write files for abi format)
# Test 12 got: "0" (t/staden_read.t at line 110 fail
#6 *TODO*)
#    Expected: <UNDEF> (We don't have the ability to
write files for abi format)
# Test 13 got: "0" (t/staden_read.t at line 110 fail
#7 *TODO*)
#    Expected: <UNDEF> (We don't have the ability to
write files for abi format)
# Test 14 got: "0" (t/staden_read.t at line 62 *TODO*)
#    Expected: <UNDEF> (Still missing test files for
alf format)
#  t/staden_read.t line 62 is:  ok(0, undef, "Still
missing test files for $format format") for
(1..$formatlooptests);
# Test 15 got: "0" (t/staden_read.t at line 62 fail #2
*TODO*)
#    Expected: <UNDEF> (Still missing test files for
alf format)
# Test 16 got: "0" (t/staden_read.t at line 62 fail #3
*TODO*)
#    Expected: <UNDEF> (Still missing test files for
alf format)
# Test 17 got: "0" (t/staden_read.t at line 62 fail #4
*TODO*)
#    Expected: <UNDEF> (Still missing test files for
alf format)
# Test 18 got: "0" (t/staden_read.t at line 62 fail #5
*TODO*)
#    Expected: <UNDEF> (Still missing test files for
alf format)
# Test 19 got: "0" (t/staden_read.t at line 62 fail #6
*TODO*)
#    Expected: <UNDEF> (Still missing test files for
alf format)
# Test 20 got: "0" (t/staden_read.t at line 62 fail #7
*TODO*)
#    Expected: <UNDEF> (Still missing test files for
alf format)
# Test 21 got: "0" (t/staden_read.t at line 62 fail #8
*TODO*)
#    Expected: <UNDEF> (Still missing test files for
alf format)
# Test 22 got: "0" (t/staden_read.t at line 62 fail #9
*TODO*)
#    Expected: <UNDEF> (Still missing test files for
alf format)
# Test 23 got: "0" (t/staden_read.t at line 62 fail
#10 *TODO*)
#    Expected: <UNDEF> (Still missing test files for
alf format)
# Test 24 got: "0" (t/staden_read.t at line 62 fail
#11 *TODO*)
#    Expected: <UNDEF> (Still missing test files for
alf format)
# Test 25 got: "0" (t/staden_read.t at line 62 fail
#12 *TODO*)
#    Expected: <UNDEF> (Still missing test files for
alf format)
# Test 31 got: "0" (t/staden_read.t at line 107
*TODO*)
#    Expected: <UNDEF> (Can't write valid ctf files
until we have a trace object)
#  t/staden_read.t line 107 is:             ok(0,
undef, "Can't write valid ctf files until we have a
trace object") for 1..7;
# Test 32 got: "0" (t/staden_read.t at line 107 fail
#2 *TODO*)
#    Expected: <UNDEF> (Can't write valid ctf files
until we have a trace object)
# Test 33 got: "0" (t/staden_read.t at line 107 fail
#3 *TODO*)
#    Expected: <UNDEF> (Can't write valid ctf files
until we have a trace object)
# Test 34 got: "0" (t/staden_read.t at line 107 fail
#4 *TODO*)
#    Expected: <UNDEF> (Can't write valid ctf files
until we have a trace object)
# Test 35 got: "0" (t/staden_read.t at line 107 fail
#5 *TODO*)
#    Expected: <UNDEF> (Can't write valid ctf files
until we have a trace object)
# Test 36 got: "0" (t/staden_read.t at line 107 fail
#6 *TODO*)
#    Expected: <UNDEF> (Can't write valid ctf files
until we have a trace object)
# Test 37 got: "0" (t/staden_read.t at line 107 fail
#7 *TODO*)
#    Expected: <UNDEF> (Can't write valid ctf files
until we have a trace object)
t/staden_read....ok                                   
                      
All tests successful.
Files=1, Tests=94,  2 wallclock secs ( 1.56 cusr + 
0.15 csys =  1.71 CPU)


Anyone has any idea what might be going wrong here? By
the way, my OS is Linux. Thank you very much.

Arya




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