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sync from trunk
2009-01-02
cjfields
sy
n
c from
t
runk
commit
|
commitdiff
|
tree
2009-01-02
cjfields
syn
c
la
s
t commi
t
commit
|
commitdiff
|
tree
2009-01-02
cjfi
e
lds
sync with HEAD
commit
|
commitdiff
|
tree
2009-01-02
cjf
i
elds
Remove
t
/
Graphics
commit
|
commitdiff
|
tree
2009-01-02
cjfi
e
lds
R
emove
B
io
:
:
G
raphics
examples and script
s
commit
|
commitdiff
|
tree
2008-12-26
cjf
i
elds
e
mpty direc
t
o
r
y
commit
|
commitdiff
|
tree
2008-12-26
c
jfields
Empty directory
commit
|
commitdiff
|
tree
2008-12-26
cjfields
e
m
p
ty directo
r
y
commit
|
commitdiff
|
tree
2008-12-26
cjfields
sync wi
t
h
t
runk
commit
|
commitdiff
|
tree
2008-12-24
cjfields
small clarification
commit
|
commitdiff
|
tree
2008-12-24
cjfi
e
lds
Add list of bug
s
sl
a
ted fo
r
the
1
.
6
.
x serie
s
commit
|
commitdiff
|
tree
2008-12-24
cjf
i
e
l
ds
Updates for
R
C1
commit
|
commitdiff
|
tree
2008-12-24
cjfi
e
lds
remove Microa
r
ra
y
deps
commit
|
commitdiff
|
tree
2008-12-24
c
j
f
ields
Sma
l
l fi
x
for tes
t
s JIC there i
s
a netwo
r
k
e
rror
commit
|
commitdiff
|
tree
2008-12-24
cjfields
Sync
branch
with
trunk
commit
|
commitdiff
|
tree
2008-12-24
cjf
i
elds
Remove Bi
o
:
:
M
i
croa
r
r
ay
f
rom b
r
anch
(
stil
l
i
n deve
l
o
pment
.
.
.
commit
|
commitdiff
|
tree
2008-12-24
cjfields
Rem
o
v
e
(
merge d
i
dn't remove this for some r
e
ason
)
commit
|
commitdiff
|
tree
2008-12-24
cjf
i
elds
Remove (
m
e
r
ge
d
idn't remove this for some
r
eason)
commit
|
commitdiff
|
tree
2008-12-22
c
jfields
sync trunk
with bra
n
ch
commit
|
commitdiff
|
tree
2008-12-20
cjfi
e
lds
5
.
6
.
1
is min per
l
version
r
equired for all core modu
l
e
s
n
ow
commit
|
commitdiff
|
tree
2008-12-19
cjfields
update NAMES
commit
|
commitdiff
|
tree
2008-12-19
cjfields
s
mall typo
commit
|
commitdiff
|
tree
2008-12-18
cjfields
t
y
p
o
commit
|
commitdiff
|
tree
2008-12-18
cjfiel
d
s
[bu
g
2714]
commit
|
commitdiff
|
tree
2008-12-17
c
j
fi
e
lds
fix t
e
st num
b
er
commit
|
commitdiff
|
tree
2008-12-17
cj
f
ields
update Test::Warn (fixes Qual
.
t
test probl
e
ms with
.
.
.
commit
|
commitdiff
|
tree
2008-12-16
cjfiel
d
s
missed
o
ne
commit
|
commitdiff
|
tree
2008-12-16
c
jf
i
eld
s
EUtili
t
ie
s
remote tests bac
k
onlin
e
(simple
t
e
s
ts only)
commit
|
commitdiff
|
tree
2008-12-16
cjfields
EUt
i
lities r
e
mote tests back
o
nline (simp
l
e tests only)
commit
|
commitdiff
|
tree
2008-12-16
c
j
field
s
You must a
c
tually test d
a
t
a
if you want this module
.
.
.
commit
|
commitdiff
|
tree
2008-12-16
cjfield
s
D
on't use
p
r
int! Changing t
o
$se
l
f
->deb
u
g
o
r commenting out
commit
|
commitdiff
|
tree
2008-12-16
c
j
fields
Bio::G
r
aph
dep
r
ecated i
n
1
.
6
commit
|
commitdiff
|
tree
2008-12-16
cjfields
stifle warnings when passing stri
n
g
ins
t
ead of int
e
ger
commit
|
commitdiff
|
tree
2008-12-16
cjfields
hash r
e
f, not array ref
commit
|
commitdiff
|
tree
2008-12-16
cj
f
iel
d
s
[bug 2637
]
commit
|
commitdiff
|
tree
2008-12-16
cjfields
[bu
g
2637]
commit
|
commitdiff
|
tree
2008-12-16
cjf
i
el
d
s
[bug 2637]
commit
|
commitdiff
|
tree
2008-12-16
cjfields
[bug 2637]
commit
|
commitdiff
|
tree
2008-12-15
cj
f
ie
l
ds
[bug
2637]
commit
|
commitdiff
|
tree
2008-12-15
c
jfi
e
lds
[bug 2712]
commit
|
commitdiff
|
tree
2008-12-15
cjfields
scores
commit
|
commitdiff
|
tree
2008-12-15
cjfields
remaining
tests for
B
io:
:
T
o
ol::EUtilities
commit
|
commitdiff
|
tree
2008-12-15
c
jfields
mo
r
e te
s
t data
commit
|
commitdiff
|
tree
2008-12-15
c
j
fields
Up
d
ates:
commit
|
commitdiff
|
tree
2008-12-13
cjfiel
d
s
ini
t
ial b
a
tch o
f
EUtilP
a
r
am
e
ter
s
tests
commit
|
commitdiff
|
tree
2008-12-13
cjfields
einfo
t
es
t
s
commit
|
commitdiff
|
tree
2008-12-12
cjfields
some EUtilities tests (parsing from files)
commit
|
commitdiff
|
tree
2008-12-12
cjfie
l
ds
some test data
for Bio::Tools:
:
EU
t
iliti
e
s
commit
|
commitdiff
|
tree
2008-12-12
cjfiel
d
s
update
s
to EUtilities (getting re
a
dy for docs, test
s
.
.
.
commit
|
commitdiff
|
tree
2008-12-12
cj
f
ields
Move EUtilParameters to
Tools (seems
more appropria
t
e
)
commit
|
commitdiff
|
tree
2008-12-11
c
jfields
fix
for
b
u
g wh
e
n g
e
tting ca
c
he
d
response with filename
.
.
.
commit
|
commitdiff
|
tree
2008-12-11
cjfields
small poin
t
er to w
i
ki p
a
ge (will up
d
ate al
o
ng with
.
.
.
commit
|
commitdiff
|
tree
2008-12-11
cjfie
l
ds
small upd
a
te
commit
|
commitdiff
|
tree
2008-12-11
cjfie
l
ds
up
d
ates
commit
|
commitdiff
|
tree
2008-12-11
cjfields
return, no
t
'
r
eturn
undef
'
commit
|
commitdiff
|
tree
2008-12-11
c
j
f
ields
return
,
not 'return undef'
commit
|
commitdiff
|
tree
2008-12-11
c
jfields
[bug 2699]
commit
|
commitdiff
|
tree
2008-12-11
cjfields
[bug
2699]
commit
|
commitdiff
|
tree
2008-12-11
cjfi
e
lds
[
b
ug 2707]
commit
|
commitdiff
|
tree
2008-12-10
c
j
fields
Removing from HEAD (depre
c
ate
d
for
1
.
6)
commit
|
commitdiff
|
tree
2008-12-10
cjfields
mini
pod fix
commit
|
commitdiff
|
tree
2008-12-10
cjfields
update
d
epre
c
ation list
commit
|
commitdiff
|
tree
2008-12-10
cjfields
remove B
i
o::Graphi
c
s (sep
a
ra
t
e package now)
commit
|
commitdiff
|
tree
2008-12-10
cj
f
ields
[bug 2637]
commit
|
commitdiff
|
tree
2008-12-10
cjfields
Rem
o
ve de
p
endencies for Bio::Gra
p
hic
s
a
nd d
e
precated
.
.
.
commit
|
commitdiff
|
tree
2008-12-09
c
j
fields
Squ
a
s
h
warning
commit
|
commitdiff
|
tree
2008-12-09
c
j
fields
diag() onl
y
o
n verbose
commit
|
commitdiff
|
tree
2008-12-09
cjfields
Fix last loop tests, move
s
om
e
t
o
can_o
k
commit
|
commitdiff
|
tree
2008-12-09
cjfi
e
lds
Mod
i
f
y to
t
est new
t
emp classe
s
a
n
d ensure that added
.
.
.
commit
|
commitdiff
|
tree
2008-12-09
cjfields
up
d
ate Mauricio
'
s email
commit
|
commitdiff
|
tree
2008-12-08
cjfield
s
Update
Roy's
e
ma
i
l
commit
|
commitdiff
|
tree
2008-12-08
cjfields
R
oy's email (and bi
o
p
er
l
.
org not
b
ioperl
.
ed
u
)
commit
|
commitdiff
|
tree
2008-12-08
cjfields
Updated ema
i
ls
commit
|
commitdiff
|
tree
2008-12-07
c
j
fields
[bug
2699]
commit
|
commitdiff
|
tree
2008-12-05
cjfield
s
Need
t
o
r
etrieve the
tree for out
p
ut
commit
|
commitdiff
|
tree
2008-12-05
cjfiel
d
s
[bug 2450
]
commit
|
commitdiff
|
tree
2008-12-04
c
jfields
Make Targe
t
a true
D
BLi
n
k
commit
|
commitdiff
|
tree
2008-12-04
c
jfi
e
l
d
s
Directory is no longer needed
(
Heikk
i
split this up
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
cjfield
s
add f
o
rce_nse t
e
sts
commit
|
commitdiff
|
tree
2008-12-03
cjfields
leave ID u
n
defined if it isn't
present, b
u
t allow the
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Rem
o
ve
f
il
e
s
acc
i
dently a
d
d
ed from last c
o
mmit
commit
|
commitdiff
|
tree
2008-12-03
c
j
fie
l
ds
Reorganiz
e
Tools tests (
n
eeds
som
e
more sp
l
it
t
ing)
commit
|
commitdiff
|
tree
2008-12-03
c
j
f
ields
Remove (tests
a
re redundant
,
in Conse
d
.
t)
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Merge tests and remove redundant file
commit
|
commitdiff
|
tree
2008-12-03
cjf
i
elds
Update
t
e
st
c
ount
commit
|
commitdiff
|
tree
2008-12-03
cjfields
M
erge tests
commit
|
commitdiff
|
tree
2008-12-03
cjfie
l
d
s
Remove redundant file
commit
|
commitdiff
|
tree
2008-12-03
cjfiel
d
s
R
emove old files
commit
|
commitdiff
|
tree
2008-12-03
c
j
f
ield
s
S
tart Tools move
commit
|
commitdiff
|
tree
2008-12-03
cjfield
s
small updates:
commit
|
commitdiff
|
tree
2008-12-03
cjfields
fo
r
go
t
to i
n
crement test coun
t
commit
|
commitdiff
|
tree
2008-12-03
cjfield
s
Add a coupl
e
of tests for
seq_id (small but sig
n
if
i
cant
.
.
.
commit
|
commitdiff
|
tree
2008-12-02
cj
f
ields
[
bug 2450]
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[bug 2
4
5
0
]
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[bug 2450
]
commit
|
commitdiff
|
tree
2008-12-02
c
jfields
[bug
245
0
]
commit
|
commitdiff
|
tree
2008-12-02
cjfield
s
some pod updates
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[bug 2450
]
commit
|
commitdiff
|
tree
2008-12-02
cjfi
e
lds
fix erroneously
r
ename
d
stoc
k
holm t
e
s
t
s
commit
|
commitdiff
|
tree
2008-12-02
c
j
fields
small pod
f
ix
commit
|
commitdiff
|
tree
next