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Sync with trunk
2009-01-06
cjfields
Sy
n
c
with
trunk
commit
|
commitdiff
|
tree
2009-01-05
c
j
field
s
Bump RC to
2
; will tag, bag, an
d
ship tomorrow a
f
t
er
.
.
.
commit
|
commitdiff
|
tree
2009-01-05
cjfields
Sync with trunk
commit
|
commitdiff
|
tree
2009-01-04
cjfields
sync with trunk
commit
|
commitdiff
|
tree
2009-01-02
cjfields
sync from trunk
commit
|
commitdiff
|
tree
2009-01-02
c
jfields
sync las
t
commit
commit
|
commitdiff
|
tree
2009-01-02
c
j
fields
sync with HEA
D
commit
|
commitdiff
|
tree
2009-01-02
cjfi
e
lds
Remove t/Graphi
c
s
commit
|
commitdiff
|
tree
2009-01-02
cjfiel
d
s
Re
m
ove Bio::G
r
aphics examp
l
es and scripts
commit
|
commitdiff
|
tree
2008-12-26
c
j
f
iel
d
s
empty di
r
ectory
commit
|
commitdiff
|
tree
2008-12-26
c
jfields
Em
p
ty directory
commit
|
commitdiff
|
tree
2008-12-26
c
j
fields
empty directory
commit
|
commitdiff
|
tree
2008-12-26
cjfields
sy
n
c wit
h
t
runk
commit
|
commitdiff
|
tree
2008-12-24
cjfields
small cl
a
rifi
c
ation
commit
|
commitdiff
|
tree
2008-12-24
cjfi
e
lds
A
d
d list of b
u
gs
s
lated for
t
h
e
1
.
6
.
x series
commit
|
commitdiff
|
tree
2008-12-24
cj
f
iel
d
s
U
p
dates
f
or RC1
commit
|
commitdiff
|
tree
2008-12-24
cjfields
remove Microarray deps
commit
|
commitdiff
|
tree
2008-12-24
cjfields
Small
f
i
x
for tests JI
C
there is a network error
commit
|
commitdiff
|
tree
2008-12-24
cjf
i
elds
S
y
nc branch with trunk
commit
|
commitdiff
|
tree
2008-12-24
cjfie
l
ds
Remov
e
Bio::Microarray from branch (still in deve
l
op
m
ent
.
.
.
commit
|
commitdiff
|
tree
2008-12-24
cjfields
Rem
o
v
e (merge
did
n
't remove this
for
s
om
e
reason)
commit
|
commitdiff
|
tree
2008-12-24
cjfields
Remove (mer
g
e didn
'
t
r
emove th
i
s
f
o
r so
m
e reas
o
n)
commit
|
commitdiff
|
tree
2008-12-22
cjfi
e
ld
s
s
y
nc trun
k
w
i
th branc
h
commit
|
commitdiff
|
tree
2008-12-20
cjf
i
elds
5
.
6
.
1 is min
perl version required f
o
r all core mo
d
ules now
commit
|
commitdiff
|
tree
2008-12-19
cj
f
ields
up
d
ate NAMES
commit
|
commitdiff
|
tree
2008-12-19
cjfields
smal
l
t
y
po
commit
|
commitdiff
|
tree
2008-12-18
cjfie
l
ds
t
y
p
o
commit
|
commitdiff
|
tree
2008-12-18
c
j
fields
[bu
g
2
7
14]
commit
|
commitdiff
|
tree
2008-12-17
cjfie
l
ds
fix test number
commit
|
commitdiff
|
tree
2008-12-17
c
jf
i
el
d
s
update
Test
:
:Warn (fix
e
s Qu
a
l
.
t tes
t
problems with
.
.
.
commit
|
commitdiff
|
tree
2008-12-16
cjfields
missed on
e
commit
|
commitdiff
|
tree
2008-12-16
cjfields
EUtilities remote
te
s
t
s
back onlin
e
(s
i
mple test
s
only)
commit
|
commitdiff
|
tree
2008-12-16
cjfields
EUtilities remo
t
e tests back on
l
ine (s
i
mp
l
e tests only)
commit
|
commitdiff
|
tree
2008-12-16
cj
f
ie
l
ds
You mus
t
actually test data
if you want this module
.
.
.
commit
|
commitdiff
|
tree
2008-12-16
cj
f
iel
d
s
D
on
'
t use print! Changing t
o
$s
e
lf->debug or c
o
mm
e
nt
i
ng out
commit
|
commitdiff
|
tree
2008-12-16
cjfields
B
io::Gr
a
ph deprecat
e
d in 1
.
6
commit
|
commitdiff
|
tree
2008-12-16
c
j
fields
stifle w
a
rnings when
p
assing
string inst
e
ad of i
n
teger
commit
|
commitdiff
|
tree
2008-12-16
cjfields
hash ref, not arr
a
y
ref
commit
|
commitdiff
|
tree
2008-12-16
cjfi
e
lds
[
bug 2637]
commit
|
commitdiff
|
tree
2008-12-16
c
jfi
e
lds
[bug 26
3
7]
commit
|
commitdiff
|
tree
2008-12-16
cjfiel
d
s
[bug 26
3
7]
commit
|
commitdiff
|
tree
2008-12-16
c
jf
i
elds
[
bug 2637
]
commit
|
commitdiff
|
tree
2008-12-15
cjfields
[
bug
2
6
37]
commit
|
commitdiff
|
tree
2008-12-15
cjfields
[bug 2712
]
commit
|
commitdiff
|
tree
2008-12-15
cjfields
scores
commit
|
commitdiff
|
tree
2008-12-15
c
jfields
remaini
n
g
tests for
B
i
o
::Tool:
:
EUtili
t
ies
commit
|
commitdiff
|
tree
2008-12-15
c
j
fiel
d
s
m
ore
t
e
st
d
a
ta
commit
|
commitdiff
|
tree
2008-12-15
cjfie
l
ds
Updates:
commit
|
commitdiff
|
tree
2008-12-13
cjfields
initial batch of EUtilParameters tests
commit
|
commitdiff
|
tree
2008-12-13
cjfields
einfo tests
commit
|
commitdiff
|
tree
2008-12-12
cjf
i
elds
s
ome E
U
t
i
liti
e
s tests
(pa
r
sing fro
m
files
)
commit
|
commitdiff
|
tree
2008-12-12
c
j
fie
l
ds
some test data for B
i
o::Tool
s
::EUtilities
commit
|
commitdiff
|
tree
2008-12-12
cjfields
updates
t
o EU
t
ilities (gettin
g
rea
d
y for
d
ocs,
tests
.
.
.
commit
|
commitdiff
|
tree
2008-12-12
cjfie
l
d
s
M
o
ve E
U
tilParameters to Tools (seems mor
e
app
r
o
pri
a
te)
commit
|
commitdiff
|
tree
2008-12-11
cjfields
f
i
x fo
r
bug
w
hen getting cached resp
o
nse with file
n
ame
.
.
.
commit
|
commitdiff
|
tree
2008-12-11
cjfie
l
ds
small p
o
int
e
r to wiki page (
w
ill update along with
.
.
.
commit
|
commitdiff
|
tree
2008-12-11
cjfields
small update
commit
|
commitdiff
|
tree
2008-12-11
cjfields
updates
commit
|
commitdiff
|
tree
2008-12-11
cjfiel
d
s
retu
r
n, not 're
t
urn
u
ndef
'
commit
|
commitdiff
|
tree
2008-12-11
cjfields
retu
r
n, not '
r
eturn undef'
commit
|
commitdiff
|
tree
2008-12-11
c
jfi
e
lds
[bug 2699]
commit
|
commitdiff
|
tree
2008-12-11
cjf
i
e
lds
[bug 2699]
commit
|
commitdiff
|
tree
2008-12-11
cjfi
e
lds
[bug
2
707]
commit
|
commitdiff
|
tree
2008-12-10
cj
f
i
e
lds
Removi
n
g from HEAD (deprecated for 1
.
6)
commit
|
commitdiff
|
tree
2008-12-10
cjf
i
elds
mini
p
o
d fix
commit
|
commitdiff
|
tree
2008-12-10
cjfields
update d
e
pr
e
ca
t
ion
l
ist
commit
|
commitdiff
|
tree
2008-12-10
cjfields
re
m
ove Bio::Graphics
(
separate packag
e
now)
commit
|
commitdiff
|
tree
2008-12-10
cjfi
e
lds
[
bug 2637]
commit
|
commitdiff
|
tree
2008-12-10
cjfields
Remove d
e
p
e
n
de
n
cies for Bio::
G
raphics
a
nd dep
r
e
c
ated
.
.
.
commit
|
commitdiff
|
tree
2008-12-09
c
jfields
Sq
u
ash warnin
g
commit
|
commitdiff
|
tree
2008-12-09
cjfields
diag() on
l
y on
v
e
rbos
e
commit
|
commitdiff
|
tree
2008-12-09
cjfields
Fix la
s
t loop tests, move some to ca
n
_ok
commit
|
commitdiff
|
tree
2008-12-09
cjfi
e
l
d
s
Mod
i
fy to test
new temp clas
s
e
s
and
ens
u
re tha
t
add
e
d
.
.
.
commit
|
commitdiff
|
tree
2008-12-09
cjfiel
d
s
u
p
d
a
t
e
M
a
ur
i
cio
'
s
e
m
a
il
commit
|
commitdiff
|
tree
2008-12-08
cj
f
ields
Update
R
o
y's email
commit
|
commitdiff
|
tree
2008-12-08
cjfield
s
R
o
y
'
s email (and b
i
o
p
erl
.
org not
biop
e
rl
.
edu)
commit
|
commitdiff
|
tree
2008-12-08
c
jfi
e
l
ds
Updated
emails
commit
|
commitdiff
|
tree
2008-12-07
cjfields
[bug 2699]
commit
|
commitdiff
|
tree
2008-12-05
cjfields
Need
t
o
r
etrieve
t
h
e tree for outp
u
t
commit
|
commitdiff
|
tree
2008-12-05
cjfields
[bug 2450
]
commit
|
commitdiff
|
tree
2008-12-04
cjfiel
d
s
Make
Target
a
t
rue DBLink
commit
|
commitdiff
|
tree
2008-12-04
c
j
fie
l
ds
D
i
r
ector
y
i
s no longer nee
d
e
d
(Heik
k
i split t
h
is up
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
cjfields
add
force_nse tests
commit
|
commitdiff
|
tree
2008-12-03
cjfields
le
a
ve ID u
n
def
i
ned if it isn't pre
s
ent,
b
ut allow the
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
cjfields
R
emove files accid
e
nt
l
y a
d
d
ed from last commi
t
commit
|
commitdiff
|
tree
2008-12-03
cjfiel
d
s
Re
o
rganiz
e
Tools
t
e
st
s
(need
s
some mo
r
e splitting)
commit
|
commitdiff
|
tree
2008-12-03
c
j
field
s
Remove (tests are r
e
dundant,
in Consed
.
t)
commit
|
commitdiff
|
tree
2008-12-03
c
jfields
Merge
test
s
and re
m
o
v
e redundant file
commit
|
commitdiff
|
tree
2008-12-03
cj
f
ields
U
p
d
a
te test count
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Merge tests
commit
|
commitdiff
|
tree
2008-12-03
cjfields
R
emo
v
e re
d
undant file
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Re
m
ove old files
commit
|
commitdiff
|
tree
2008-12-03
cjf
i
elds
S
t
art Tools move
commit
|
commitdiff
|
tree
2008-12-03
cjfie
l
ds
small updates:
commit
|
commitdiff
|
tree
2008-12-03
c
j
fi
e
lds
forgot to i
n
cr
e
ment test cou
n
t
commit
|
commitdiff
|
tree
2008-12-03
c
j
fields
Add a
co
u
ple of t
e
sts for
s
eq_id (small but significant
.
.
.
commit
|
commitdiff
|
tree
2008-12-02
cjf
i
e
lds
[
b
u
g 2450]
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[bug 2450]
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[bug 2450]
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[bug 24
5
0]
commit
|
commitdiff
|
tree
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