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Sync that last bit with trunk. I'll have to merge that over to the tag for the next RC.
2009-01-06
cjfields
Sync that last bit with trunk
.
I'll ha
v
e
t
o merge
.
.
.
commit
|
commitdiff
|
tree
2009-01-06
c
j
f
ields
S
y
n
c
w
i
th trunk
commit
|
commitdiff
|
tree
2009-01-05
cjfields
Bum
p
RC to 2; wi
l
l tag, ba
g
,
and ship tomo
r
row after
.
.
.
commit
|
commitdiff
|
tree
2009-01-05
cjfields
Sync with
t
runk
commit
|
commitdiff
|
tree
2009-01-04
c
j
fields
s
y
nc wi
t
h
trunk
commit
|
commitdiff
|
tree
2009-01-02
cj
f
ields
sync fr
o
m
trunk
commit
|
commitdiff
|
tree
2009-01-02
cjf
i
elds
sync last c
o
m
m
it
commit
|
commitdiff
|
tree
2009-01-02
cjfiel
d
s
sync with HEAD
commit
|
commitdiff
|
tree
2009-01-02
cjfie
l
ds
Remo
v
e t/Graphic
s
commit
|
commitdiff
|
tree
2009-01-02
c
jfi
e
l
ds
Remove Bio
:
:Graph
i
cs
examples
and scripts
commit
|
commitdiff
|
tree
2008-12-26
cjfields
empty directory
commit
|
commitdiff
|
tree
2008-12-26
c
j
fie
l
ds
E
mpty d
i
recto
r
y
commit
|
commitdiff
|
tree
2008-12-26
cjfields
empty
directory
commit
|
commitdiff
|
tree
2008-12-26
cjfields
s
ync
with
t
r
unk
commit
|
commitdiff
|
tree
2008-12-24
cj
f
ie
l
ds
s
m
all clarific
a
tion
commit
|
commitdiff
|
tree
2008-12-24
cjfiel
d
s
Add list of bu
g
s slated f
o
r the 1
.
6
.
x s
e
ries
commit
|
commitdiff
|
tree
2008-12-24
cjfields
Updates for
R
C
1
commit
|
commitdiff
|
tree
2008-12-24
cjfields
r
e
m
ove Microa
r
ray deps
commit
|
commitdiff
|
tree
2008-12-24
cjfields
S
m
a
l
l fix for test
s
JIC there is a network erro
r
commit
|
commitdiff
|
tree
2008-12-24
c
jf
i
el
d
s
Sync branch with trunk
commit
|
commitdiff
|
tree
2008-12-24
c
jfields
Remove Bio::Microarray from branch (s
t
ill in d
e
velopment
.
.
.
commit
|
commitdiff
|
tree
2008-12-24
cjf
i
eld
s
Remove (merge didn't re
m
ove this for som
e
reas
o
n)
commit
|
commitdiff
|
tree
2008-12-24
cjfiel
d
s
Re
m
ove
(me
r
ge didn't remove
this
f
or s
o
me
r
easo
n
)
commit
|
commitdiff
|
tree
2008-12-22
cjfields
sync tr
u
n
k with b
r
a
n
c
h
commit
|
commitdiff
|
tree
2008-12-20
cjfields
5
.
6
.
1 is min p
e
r
l
versio
n
r
eq
u
ir
e
d for all
c
ore modules now
commit
|
commitdiff
|
tree
2008-12-19
cjfields
update N
A
MES
commit
|
commitdiff
|
tree
2008-12-19
cjfie
l
ds
s
mall typo
commit
|
commitdiff
|
tree
2008-12-18
cjfields
typo
commit
|
commitdiff
|
tree
2008-12-18
cjfields
[bug
2714]
commit
|
commitdiff
|
tree
2008-12-17
cjfields
f
ix
test number
commit
|
commitdiff
|
tree
2008-12-17
cjfields
update Te
s
t::Wa
r
n (
f
ixes Qual
.
t test pr
o
blems wit
h
.
.
.
commit
|
commitdiff
|
tree
2008-12-16
cj
f
ields
missed one
commit
|
commitdiff
|
tree
2008-12-16
cjfields
EU
t
ilities r
e
mote
t
ests
b
a
ck online (simple te
s
ts only)
commit
|
commitdiff
|
tree
2008-12-16
cjfields
E
Utilities remote tests back
o
nlin
e
(sim
p
le
tests only)
commit
|
commitdiff
|
tree
2008-12-16
cjfie
l
d
s
Y
ou must actu
a
lly
test da
t
a if you want
this module
.
.
.
commit
|
commitdiff
|
tree
2008-12-16
cjfields
Don't use pr
i
n
t
! Changing t
o
$sel
f
->debug
o
r
c
ommenting
out
commit
|
commitdiff
|
tree
2008-12-16
cjfi
e
lds
Bio::Graph deprecated
in 1
.
6
commit
|
commitdiff
|
tree
2008-12-16
cjfields
s
ti
f
le warnings when passing str
i
ng instead of
i
nteger
commit
|
commitdiff
|
tree
2008-12-16
cjf
i
elds
h
a
sh re
f
, not
a
rray r
e
f
commit
|
commitdiff
|
tree
2008-12-16
cjfields
[bug 26
3
7
]
commit
|
commitdiff
|
tree
2008-12-16
cjfields
[
bug 2637]
commit
|
commitdiff
|
tree
2008-12-16
cjfield
s
[bug 2
6
37]
commit
|
commitdiff
|
tree
2008-12-16
c
j
fields
[bug
2
637]
commit
|
commitdiff
|
tree
2008-12-15
cjfie
l
ds
[bu
g
2637]
commit
|
commitdiff
|
tree
2008-12-15
cj
f
ields
[bug 271
2
]
commit
|
commitdiff
|
tree
2008-12-15
cjfield
s
s
cores
commit
|
commitdiff
|
tree
2008-12-15
c
j
fields
remaining tests f
o
r
Bio::Tool::EU
t
ilities
commit
|
commitdiff
|
tree
2008-12-15
cj
f
ie
l
d
s
more test data
commit
|
commitdiff
|
tree
2008-12-15
cjfields
U
pdat
e
s:
commit
|
commitdiff
|
tree
2008-12-13
c
j
f
ields
i
n
itial b
a
tch of EUtilPar
a
meters
t
es
t
s
commit
|
commitdiff
|
tree
2008-12-13
cjfi
e
lds
einfo tests
commit
|
commitdiff
|
tree
2008-12-12
cjfi
e
lds
some EU
t
ili
t
ies tests (parsing from files)
commit
|
commitdiff
|
tree
2008-12-12
c
jfields
s
o
me test
data for Bio::To
o
ls::EUtilities
commit
|
commitdiff
|
tree
2008-12-12
c
jfiel
d
s
updates
t
o EUtilities (
g
ett
i
ng ready f
o
r docs, te
s
t
s
.
.
.
commit
|
commitdiff
|
tree
2008-12-12
c
j
fields
Mov
e
EUtilParame
t
ers
to
T
ools (se
e
ms
m
ore
a
p
p
ropriat
e
)
commit
|
commitdiff
|
tree
2008-12-11
c
j
fields
fix for
bug when gett
i
ng cache
d
re
s
p
onse w
i
t
h
filename
.
.
.
commit
|
commitdiff
|
tree
2008-12-11
c
jfields
small p
o
inter to wiki page (will update along with
.
.
.
commit
|
commitdiff
|
tree
2008-12-11
cjfields
small upda
t
e
commit
|
commitdiff
|
tree
2008-12-11
cjfi
e
ld
s
up
d
ates
commit
|
commitdiff
|
tree
2008-12-11
cjfields
retur
n
, not '
r
eturn unde
f
'
commit
|
commitdiff
|
tree
2008-12-11
cjfields
r
e
turn
,
not 'r
e
turn
u
ndef'
commit
|
commitdiff
|
tree
2008-12-11
cjfields
[bug 2699]
commit
|
commitdiff
|
tree
2008-12-11
cjfields
[bug 2699]
commit
|
commitdiff
|
tree
2008-12-11
cjfields
[bug
2
707]
commit
|
commitdiff
|
tree
2008-12-10
cjfie
l
d
s
Removing from H
E
AD (deprecated f
o
r 1
.
6)
commit
|
commitdiff
|
tree
2008-12-10
c
j
fields
min
i
po
d
fix
commit
|
commitdiff
|
tree
2008-12-10
cjfields
update deprecation
l
ist
commit
|
commitdiff
|
tree
2008-12-10
cjfiel
d
s
remove Bio::Graphics (separate pa
c
kage now
)
commit
|
commitdiff
|
tree
2008-12-10
cjfield
s
[bu
g
2637]
commit
|
commitdiff
|
tree
2008-12-10
cjfields
Remove depe
n
dencies
f
or Bio::Graphics and deprecated
.
.
.
commit
|
commitdiff
|
tree
2008-12-09
c
j
fiel
d
s
Squash warning
commit
|
commitdiff
|
tree
2008-12-09
cjfiel
d
s
diag() only on v
e
rbos
e
commit
|
commitdiff
|
tree
2008-12-09
cjfields
Fix
last
lo
o
p tests
,
move some to can_ok
commit
|
commitdiff
|
tree
2008-12-09
c
jfields
Mod
i
fy to t
e
st new temp
classes and en
s
ure that added
.
.
.
commit
|
commitdiff
|
tree
2008-12-09
cjfields
update Mauricio's e
m
ail
commit
|
commitdiff
|
tree
2008-12-08
cjfields
Update
R
oy
'
s email
commit
|
commitdiff
|
tree
2008-12-08
cjfiel
d
s
Roy's email (and bioperl
.
org n
o
t
b
i
operl
.
e
du)
commit
|
commitdiff
|
tree
2008-12-08
cj
f
i
elds
Updated emails
commit
|
commitdiff
|
tree
2008-12-07
cjfields
[bug 2
6
99]
commit
|
commitdiff
|
tree
2008-12-05
c
jfields
Need t
o
retr
i
eve th
e
tree fo
r
o
u
t
put
commit
|
commitdiff
|
tree
2008-12-05
c
jfields
[bug 2450]
commit
|
commitdiff
|
tree
2008-12-04
cjfields
Make Target a true D
B
Link
commit
|
commitdiff
|
tree
2008-12-04
cjfiel
d
s
D
i
r
e
c
tory
is no longer needed (Heikki split this u
p
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
c
j
fie
l
ds
add
f
orce
_
nse
tests
commit
|
commitdiff
|
tree
2008-12-03
c
jfields
leave
I
D u
n
d
efine
d
i
f
it isn't present, but
allow the
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Remove files accident
l
y
a
dded from last
c
ommit
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Reorganize
Tool
s
tests (needs some mo
r
e splitting)
commit
|
commitdiff
|
tree
2008-12-03
cj
f
i
e
lds
Remove (tests are redu
n
dant,
in Consed
.
t)
commit
|
commitdiff
|
tree
2008-12-03
cjfields
M
e
r
ge te
s
ts and remove redundant file
commit
|
commitdiff
|
tree
2008-12-03
cjfi
e
l
d
s
Update test co
u
n
t
commit
|
commitdiff
|
tree
2008-12-03
cjfields
M
e
rge te
s
ts
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Remove
r
e
d
undant fil
e
commit
|
commitdiff
|
tree
2008-12-03
cj
f
ields
Re
m
o
v
e o
l
d fil
e
s
commit
|
commitdiff
|
tree
2008-12-03
cjf
i
elds
S
t
art Tools
move
commit
|
commitdiff
|
tree
2008-12-03
c
jfields
s
m
al
l
updates:
commit
|
commitdiff
|
tree
2008-12-03
cjfi
e
l
d
s
forgot to increment
t
e
st count
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Add a c
o
u
ple of tests f
o
r seq_i
d
(smal
l
but significant
.
.
.
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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