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Sync with trunk. This will appear in final release.
2009-01-06
cjfields
Syn
c
w
i
th trunk
.
T
his will appear in fin
a
l relea
s
e
.
commit
|
commitdiff
|
tree
2009-01-06
c
j
field
s
Resolve conflict (ca
n
't directly
merge
si
n
ce trunk
.
.
.
commit
|
commitdiff
|
tree
2009-01-06
cjfie
l
d
s
Sync that last
bit wi
t
h trunk
.
I'll
h
ave t
o
merg
e
.
.
.
commit
|
commitdiff
|
tree
2009-01-06
cjfie
l
d
s
Syn
c
with trunk
commit
|
commitdiff
|
tree
2009-01-05
cjfiel
d
s
B
um
p
RC
to 2; will tag,
b
ag,
and ship tomor
r
ow after
.
.
.
commit
|
commitdiff
|
tree
2009-01-05
cjfields
S
ync with tr
u
nk
commit
|
commitdiff
|
tree
2009-01-04
cjfie
l
d
s
s
y
n
c
with trun
k
commit
|
commitdiff
|
tree
2009-01-02
cjfield
s
sync from trunk
commit
|
commitdiff
|
tree
2009-01-02
cjfi
e
lds
sync last commi
t
commit
|
commitdiff
|
tree
2009-01-02
cjfields
sync w
i
t
h
HEAD
commit
|
commitdiff
|
tree
2009-01-02
cjfields
R
emove t/Graphics
commit
|
commitdiff
|
tree
2009-01-02
cj
f
iel
d
s
R
e
move Bio::Graphics ex
a
mple
s
a
nd scr
i
pts
commit
|
commitdiff
|
tree
2008-12-26
cjfie
l
ds
empty directory
commit
|
commitdiff
|
tree
2008-12-26
cjfiel
d
s
Empty d
i
r
e
ct
o
r
y
commit
|
commitdiff
|
tree
2008-12-26
c
j
fi
e
lds
empt
y
directory
commit
|
commitdiff
|
tree
2008-12-26
cjfi
e
lds
s
y
nc with trunk
commit
|
commitdiff
|
tree
2008-12-24
cjfi
e
lds
sma
l
l clarifi
c
a
tion
commit
|
commitdiff
|
tree
2008-12-24
cj
f
ields
Add list
o
f b
u
gs slated for
th
e
1
.
6
.
x series
commit
|
commitdiff
|
tree
2008-12-24
cjfi
e
lds
Upd
a
t
es for RC1
commit
|
commitdiff
|
tree
2008-12-24
cjfields
r
e
mo
v
e Microarr
a
y deps
commit
|
commitdiff
|
tree
2008-12-24
cjfields
Small fix for tests JIC there is a n
e
t
work error
commit
|
commitdiff
|
tree
2008-12-24
c
j
fields
Sy
n
c b
r
anch with trunk
commit
|
commitdiff
|
tree
2008-12-24
cj
f
ield
s
Remo
v
e Bio::Microarray from b
r
anch (sti
l
l
in devel
o
p
ment
.
.
.
commit
|
commitdiff
|
tree
2008-12-24
cj
f
ields
Remove (merge didn't remove thi
s
for
s
ome reason)
commit
|
commitdiff
|
tree
2008-12-24
cjfiel
d
s
R
emove (merge did
n
't remove th
i
s for s
o
me reason
)
commit
|
commitdiff
|
tree
2008-12-22
cjfields
sync
trunk w
i
th branch
commit
|
commitdiff
|
tree
2008-12-20
c
jf
i
elds
5
.
6
.
1 i
s
mi
n
perl ve
r
s
i
on r
e
quired
for
a
l
l cor
e
m
odules
n
ow
commit
|
commitdiff
|
tree
2008-12-19
cjfield
s
update NAMES
commit
|
commitdiff
|
tree
2008-12-19
cjf
i
el
d
s
sm
a
l
l
typo
commit
|
commitdiff
|
tree
2008-12-18
c
j
fi
e
lds
typo
commit
|
commitdiff
|
tree
2008-12-18
cjfie
l
ds
[
bug 2714]
commit
|
commitdiff
|
tree
2008-12-17
cjfields
fix test nu
m
ber
commit
|
commitdiff
|
tree
2008-12-17
cjf
i
e
ld
s
u
p
date T
e
st::Warn (f
i
xes Qual
.
t test probl
e
ms with
.
.
.
commit
|
commitdiff
|
tree
2008-12-16
cjfields
missed one
commit
|
commitdiff
|
tree
2008-12-16
cjfields
EUtilities remote tests back onlin
e
(s
i
mple tests only)
commit
|
commitdiff
|
tree
2008-12-16
cjfields
EUtilities rem
o
te tes
t
s ba
c
k online (
s
imp
l
e tests only)
commit
|
commitdiff
|
tree
2008-12-16
cjfields
Y
ou must actually test data
if you want t
h
is
module
.
.
.
commit
|
commitdiff
|
tree
2008-12-16
cj
f
ields
Don't
use print! Changing to $self->debug or commenting out
commit
|
commitdiff
|
tree
2008-12-16
cjfiel
d
s
Bio::Graph depre
c
ated in 1
.
6
commit
|
commitdiff
|
tree
2008-12-16
cj
f
ields
stifle war
n
ings when pa
s
sing string instead of integ
e
r
commit
|
commitdiff
|
tree
2008-12-16
cjfiel
d
s
h
a
s
h
ref, no
t
a
r
ra
y
re
f
commit
|
commitdiff
|
tree
2008-12-16
cjfields
[bug 2637]
commit
|
commitdiff
|
tree
2008-12-16
cjfields
[bu
g
2637]
commit
|
commitdiff
|
tree
2008-12-16
cjfield
s
[bug 2637]
commit
|
commitdiff
|
tree
2008-12-16
cjfields
[
bug 2637]
commit
|
commitdiff
|
tree
2008-12-15
cjfields
[bu
g
2637]
commit
|
commitdiff
|
tree
2008-12-15
cjfie
l
d
s
[bug 2712]
commit
|
commitdiff
|
tree
2008-12-15
cjfields
scores
commit
|
commitdiff
|
tree
2008-12-15
cjfields
remaining tes
t
s for Bio::To
o
l::EUtilities
commit
|
commitdiff
|
tree
2008-12-15
c
jfields
more
test
dat
a
commit
|
commitdiff
|
tree
2008-12-15
cjfields
Up
d
ates
:
commit
|
commitdiff
|
tree
2008-12-13
cjfields
i
nitial batch of
E
UtilParameters t
e
sts
commit
|
commitdiff
|
tree
2008-12-13
cjfields
einfo tests
commit
|
commitdiff
|
tree
2008-12-12
cjfields
some EUtilitie
s
tests (parsi
n
g from files)
commit
|
commitdiff
|
tree
2008-12-12
cjfields
some
test data for
B
io::Tools::EUtiliti
e
s
commit
|
commitdiff
|
tree
2008-12-12
cjfiel
d
s
up
d
ate
s
t
o EUtiliti
e
s
(
g
e
t
ting ready for
do
c
s, tests
.
.
.
commit
|
commitdiff
|
tree
2008-12-12
cjf
i
e
l
ds
M
o
ve EUtilPa
r
ameters to Tools (seems more appr
o
p
r
iate)
commit
|
commitdiff
|
tree
2008-12-11
cjfiel
d
s
fi
x
for
b
ug when gett
i
n
g
cached response wi
t
h fi
l
ename
.
.
.
commit
|
commitdiff
|
tree
2008-12-11
c
j
f
ields
smal
l
pointer to
w
i
k
i page
(
w
ill up
d
ate
a
long with
.
.
.
commit
|
commitdiff
|
tree
2008-12-11
cjfields
small
upd
a
te
commit
|
commitdiff
|
tree
2008-12-11
cjfields
upda
t
es
commit
|
commitdiff
|
tree
2008-12-11
c
jfield
s
re
t
urn,
n
ot 'return
u
n
def'
commit
|
commitdiff
|
tree
2008-12-11
cjfields
r
e
turn, not 'return undef
'
commit
|
commitdiff
|
tree
2008-12-11
cjfields
[bug 269
9
]
commit
|
commitdiff
|
tree
2008-12-11
cjfields
[bug
26
9
9]
commit
|
commitdiff
|
tree
2008-12-11
cjfields
[bug 2707]
commit
|
commitdiff
|
tree
2008-12-10
cjfields
Removing fr
o
m H
E
AD
(
d
eprec
a
ted
for 1
.
6)
commit
|
commitdiff
|
tree
2008-12-10
cjfiel
d
s
mini
pod fix
commit
|
commitdiff
|
tree
2008-12-10
cjfields
up
d
ate deprecation list
commit
|
commitdiff
|
tree
2008-12-10
cjfie
l
ds
remove Bio::
G
raphics (separate pa
c
kage
n
ow)
commit
|
commitdiff
|
tree
2008-12-10
cjfields
[bug 2637]
commit
|
commitdiff
|
tree
2008-12-10
cjfields
Re
m
ove dependencies f
o
r
B
io::Graphics
a
n
d d
e
precated
.
.
.
commit
|
commitdiff
|
tree
2008-12-09
cjfield
s
Squash warning
commit
|
commitdiff
|
tree
2008-12-09
cjfields
diag() o
n
ly on verbose
commit
|
commitdiff
|
tree
2008-12-09
c
j
fields
Fix l
a
s
t loop tests, move so
m
e to
can_ok
commit
|
commitdiff
|
tree
2008-12-09
c
jfields
M
odify to
test n
e
w temp classes and ensure that added
.
.
.
commit
|
commitdiff
|
tree
2008-12-09
c
j
fi
e
lds
update Mauricio's email
commit
|
commitdiff
|
tree
2008-12-08
cjfields
U
p
date Roy's e
m
ai
l
commit
|
commitdiff
|
tree
2008-12-08
c
j
fields
Roy's email (
a
nd bioperl
.
o
r
g not bioperl
.
edu)
commit
|
commitdiff
|
tree
2008-12-08
cj
f
ields
U
pdated emails
commit
|
commitdiff
|
tree
2008-12-07
cjfields
[bug 2699]
commit
|
commitdiff
|
tree
2008-12-05
cjfields
Need to retr
i
eve the
t
ree for output
commit
|
commitdiff
|
tree
2008-12-05
cjfields
[b
u
g
2
450]
commit
|
commitdiff
|
tree
2008-12-04
c
j
fields
Make Target a true DBL
i
n
k
commit
|
commitdiff
|
tree
2008-12-04
cjf
i
e
lds
D
irectory is no longer ne
e
de
d
(Heikki
split this up
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
cjfield
s
add forc
e
_
nse tests
commit
|
commitdiff
|
tree
2008-12-03
cjf
i
elds
leave ID undefined if i
t
isn't
pres
e
nt, but allow th
e
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
cj
f
ield
s
Remov
e
f
iles a
c
cidentl
y
a
d
d
ed
f
rom last comm
i
t
commit
|
commitdiff
|
tree
2008-12-03
cjfi
e
lds
R
eorganize Tools
t
e
sts (needs som
e
more sp
l
itti
n
g)
commit
|
commitdiff
|
tree
2008-12-03
c
jfield
s
R
e
m
o
ve (tests are redundant, in
C
onsed
.
t)
commit
|
commitdiff
|
tree
2008-12-03
c
j
fields
Merge te
s
t
s and
remov
e
redund
a
nt file
commit
|
commitdiff
|
tree
2008-12-03
cjfields
U
p
date t
e
st c
o
unt
commit
|
commitdiff
|
tree
2008-12-03
cjfiel
d
s
Merge tests
commit
|
commitdiff
|
tree
2008-12-03
c
jfields
Rem
o
ve r
e
dundant fi
l
e
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Remove old files
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Sta
r
t Tools move
commit
|
commitdiff
|
tree
2008-12-03
cjf
i
e
lds
small update
s
:
commit
|
commitdiff
|
tree
2008-12-03
c
jfields
forgot
to
i
n
crement tes
t
count
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Add a couple
o
f
tests for
s
eq_id (small but signific
a
nt
.
.
.
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[bug 245
0
]
commit
|
commitdiff
|
tree
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