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Sync with trunk
2009-01-06
cjfields
Sync with t
r
un
k
commit
|
commitdiff
|
tree
2009-01-05
cjfi
e
ld
s
Bum
p
RC to 2; will tag
,
ba
g
,
and shi
p
tomor
r
ow
afte
r
.
.
.
commit
|
commitdiff
|
tree
2009-01-05
cjfield
s
Sync
w
i
t
h
trunk
commit
|
commitdiff
|
tree
2009-01-04
c
jf
i
elds
sync with
trunk
commit
|
commitdiff
|
tree
2009-01-02
cjfields
sync fr
o
m trunk
commit
|
commitdiff
|
tree
2009-01-02
cjfield
s
sync last
commit
commit
|
commitdiff
|
tree
2009-01-02
cjfield
s
sync with HEAD
commit
|
commitdiff
|
tree
2009-01-02
cjfields
Remove t/Graphics
commit
|
commitdiff
|
tree
2009-01-02
cjfields
Remov
e
Bio::
G
raphic
s
examples and scrip
t
s
commit
|
commitdiff
|
tree
2008-12-26
cjfi
e
l
d
s
e
mpty directo
r
y
commit
|
commitdiff
|
tree
2008-12-26
c
jfiel
d
s
E
mpt
y
direc
t
ory
commit
|
commitdiff
|
tree
2008-12-26
cjfiel
d
s
em
p
t
y
directory
commit
|
commitdiff
|
tree
2008-12-26
cj
f
ields
sync wit
h
trunk
commit
|
commitdiff
|
tree
2008-12-24
cjfields
small clarification
commit
|
commitdiff
|
tree
2008-12-24
cjfields
Add list of bugs slated
for the 1
.
6
.
x series
commit
|
commitdiff
|
tree
2008-12-24
cjfields
Update
s
for RC1
commit
|
commitdiff
|
tree
2008-12-24
c
j
f
ields
remove Microar
r
a
y
deps
commit
|
commitdiff
|
tree
2008-12-24
c
j
fie
l
ds
S
m
a
l
l f
i
x for tests JIC there is a network er
r
o
r
commit
|
commitdiff
|
tree
2008-12-24
cjfields
Sync br
a
nch with
t
runk
commit
|
commitdiff
|
tree
2008-12-24
cjfields
Remove Bio::Mi
c
roarray
f
rom
b
ranch (
s
til
l
in d
e
ve
l
opment
.
.
.
commit
|
commitdiff
|
tree
2008-12-24
c
j
fields
Remove (merge di
d
n't remove th
i
s for some reason)
commit
|
commitdiff
|
tree
2008-12-24
cj
f
iel
d
s
Remove (merge didn't remove th
i
s
for so
m
e rea
s
on)
commit
|
commitdiff
|
tree
2008-12-22
cjf
i
e
l
ds
s
ync trunk
with branch
commit
|
commitdiff
|
tree
2008-12-20
cjfi
e
lds
5
.
6
.
1
is min perl versi
o
n r
e
quired for all core mo
d
ules
now
commit
|
commitdiff
|
tree
2008-12-19
cjfields
update NAMES
commit
|
commitdiff
|
tree
2008-12-19
cjfields
sm
a
l
l
typo
commit
|
commitdiff
|
tree
2008-12-18
cjfields
typo
commit
|
commitdiff
|
tree
2008-12-18
cjfi
e
lds
[bug 2714]
commit
|
commitdiff
|
tree
2008-12-17
cjfields
fix test
n
umber
commit
|
commitdiff
|
tree
2008-12-17
cjfields
update Test::Warn (fixes Qual
.
t test problems
w
i
t
h
.
.
.
commit
|
commitdiff
|
tree
2008-12-16
cjf
i
el
d
s
mis
s
e
d
one
commit
|
commitdiff
|
tree
2008-12-16
cjfi
e
lds
EU
t
ilities
r
emote
tes
t
s ba
c
k o
n
line (
s
imple tests only)
commit
|
commitdiff
|
tree
2008-12-16
cjfields
EUtilities
remote t
e
sts b
a
c
k
on
l
ine (simp
l
e
t
ests only)
commit
|
commitdiff
|
tree
2008-12-16
cjfields
You must
actually test d
a
ta if you wan
t
this
module
.
.
.
commit
|
commitdiff
|
tree
2008-12-16
cjf
i
elds
D
on't use print! Chan
g
in
g
to
$
self->debug or comme
n
ting
o
ut
commit
|
commitdiff
|
tree
2008-12-16
cj
f
i
elds
B
i
o
::Gr
a
p
h
deprecated in
1
.
6
commit
|
commitdiff
|
tree
2008-12-16
cjf
i
elds
stifle warnings
w
hen passing
s
tring instead of integer
commit
|
commitdiff
|
tree
2008-12-16
c
j
fields
ha
s
h r
e
f,
n
o
t
a
rray ref
commit
|
commitdiff
|
tree
2008-12-16
cjfields
[bug
2
637]
commit
|
commitdiff
|
tree
2008-12-16
cjfiel
d
s
[bug
2637]
commit
|
commitdiff
|
tree
2008-12-16
cj
f
ields
[b
u
g 2637]
commit
|
commitdiff
|
tree
2008-12-16
c
jfields
[bu
g
2637]
commit
|
commitdiff
|
tree
2008-12-15
cjfields
[bug 2637]
commit
|
commitdiff
|
tree
2008-12-15
c
j
f
i
elds
[bug
2
712]
commit
|
commitdiff
|
tree
2008-12-15
cjfi
e
ld
s
score
s
commit
|
commitdiff
|
tree
2008-12-15
cjfield
s
remaining te
s
ts
for Bio::Tool::EUti
l
i
ties
commit
|
commitdiff
|
tree
2008-12-15
cjfields
mor
e
t
e
st data
commit
|
commitdiff
|
tree
2008-12-15
cj
f
ields
Upd
a
tes:
commit
|
commitdiff
|
tree
2008-12-13
cjfields
initial batch
o
f
E
U
til
P
arameters tests
commit
|
commitdiff
|
tree
2008-12-13
cjfields
einfo tests
commit
|
commitdiff
|
tree
2008-12-12
cjfi
e
l
ds
s
ome EUti
l
ities t
e
sts (par
s
ing from files)
commit
|
commitdiff
|
tree
2008-12-12
c
jfi
e
lds
some test data for Bio::Tools::EUti
l
ities
commit
|
commitdiff
|
tree
2008-12-12
cjfields
updates to EUt
i
lities (ge
t
t
i
ng
r
eady for docs,
t
e
sts
.
.
.
commit
|
commitdiff
|
tree
2008-12-12
cjfields
Move
EUtilPar
a
meters to Too
l
s (seems more appropria
t
e)
commit
|
commitdiff
|
tree
2008-12-11
c
jfields
f
ix for bug when getting
cached response wi
t
h fi
l
e
name
.
.
.
commit
|
commitdiff
|
tree
2008-12-11
cjfiel
d
s
small pointer to wi
k
i page
(
w
i
ll u
p
date alon
g
with
.
.
.
commit
|
commitdiff
|
tree
2008-12-11
cjf
i
elds
sma
l
l
update
commit
|
commitdiff
|
tree
2008-12-11
cjfields
u
p
dates
commit
|
commitdiff
|
tree
2008-12-11
cjfields
return, not 'return
undef'
commit
|
commitdiff
|
tree
2008-12-11
cjfield
s
return, not 're
t
u
r
n undef'
commit
|
commitdiff
|
tree
2008-12-11
cjfields
[bug
2699]
commit
|
commitdiff
|
tree
2008-12-11
cjfields
[
b
u
g 2699]
commit
|
commitdiff
|
tree
2008-12-11
cjfie
l
ds
[bug 2707]
commit
|
commitdiff
|
tree
2008-12-10
cjfields
Removing from
HEAD
(
deprecate
d
f
o
r 1
.
6)
commit
|
commitdiff
|
tree
2008-12-10
c
j
f
i
elds
mini pod f
i
x
commit
|
commitdiff
|
tree
2008-12-10
cjfield
s
update d
e
p
recation
l
ist
commit
|
commitdiff
|
tree
2008-12-10
cjfields
remove Bio::Graphics (s
e
parate package n
o
w)
commit
|
commitdiff
|
tree
2008-12-10
c
jfields
[
b
ug 2637]
commit
|
commitdiff
|
tree
2008-12-10
cj
f
i
e
l
ds
Remove de
p
endencies for B
i
o::Gr
a
phics and deprecated
.
.
.
commit
|
commitdiff
|
tree
2008-12-09
cj
f
ields
Squash warning
commit
|
commitdiff
|
tree
2008-12-09
cjfiel
d
s
diag()
o
nly
on ve
r
bos
e
commit
|
commitdiff
|
tree
2008-12-09
cjfields
F
i
x last
loop tests, move
s
ome to can_ok
commit
|
commitdiff
|
tree
2008-12-09
cjfi
e
lds
Mo
d
i
f
y
to
t
est new tem
p
classes and en
s
ure
t
hat ad
d
ed
.
.
.
commit
|
commitdiff
|
tree
2008-12-09
cjfields
update Mauric
i
o's
email
commit
|
commitdiff
|
tree
2008-12-08
cj
f
ields
Up
d
ate Roy's
e
m
ail
commit
|
commitdiff
|
tree
2008-12-08
cjfi
e
lds
Roy's email
(and
biope
r
l
.
o
r
g not b
i
operl
.
e
d
u)
commit
|
commitdiff
|
tree
2008-12-08
cjfields
Updated emails
commit
|
commitdiff
|
tree
2008-12-07
cjfields
[
b
u
g 269
9
]
commit
|
commitdiff
|
tree
2008-12-05
cjfields
Need t
o
r
etrieve the tree for output
commit
|
commitdiff
|
tree
2008-12-05
c
j
f
i
e
lds
[bug 2
4
50]
commit
|
commitdiff
|
tree
2008-12-04
cjfields
Make
Target a true DBLi
n
k
commit
|
commitdiff
|
tree
2008-12-04
cjfields
D
i
rectory is
n
o
l
on
g
er needed
(
He
i
kki
s
plit
t
his up
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
cjfield
s
a
dd forc
e
_nse
t
e
s
ts
commit
|
commitdiff
|
tree
2008-12-03
cjfields
leave ID unde
f
ined if it isn't presen
t
, but allow
the
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Remove files accidently added
from last commit
commit
|
commitdiff
|
tree
2008-12-03
c
j
fi
e
l
ds
R
e
organize
T
ools tests (ne
e
ds some mor
e
splitting
)
commit
|
commitdiff
|
tree
2008-12-03
c
j
field
s
Remo
v
e (tests are redundan
t
, in Consed
.
t)
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Merge tests and
rem
o
ve red
u
ndant file
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Upd
a
t
e
te
s
t count
commit
|
commitdiff
|
tree
2008-12-03
cjfi
e
lds
Mer
g
e
tests
commit
|
commitdiff
|
tree
2008-12-03
cjf
i
elds
Remo
v
e redundant f
i
le
commit
|
commitdiff
|
tree
2008-12-03
cjfi
e
lds
Remo
v
e old
f
iles
commit
|
commitdiff
|
tree
2008-12-03
c
j
f
ields
Start Tools mo
v
e
commit
|
commitdiff
|
tree
2008-12-03
cj
f
i
e
lds
s
m
all
u
pdates:
commit
|
commitdiff
|
tree
2008-12-03
cj
f
i
elds
forgot to increment test cou
n
t
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Add a couple of tests for seq_id (
s
mall bu
t
signi
f
ican
t
.
.
.
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[
b
ug 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
cj
f
ields
[bug 2450
]
commit
|
commitdiff
|
tree
next