[Biojava-l] help for installation
Matthew Pocock
matthew_pocock@yahoo.co.uk
Fri, 22 Mar 2002 12:30:24 -0000
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Hi Dr Chen,
You say that you have placed the jar files in a c:\biojava directory, =
but your classpath entries don't seem to be respecting this. Have you =
tried the classpath:
set =
CLASSPATH=3DCLASSPATH=3DC:\biojava\biojava.jar;C:\biojava\xerces.jar;C:\b=
iojava\bytecode.jar;.
A good check to make sure things are in the classpath is to use the =
javap program. Try:
javap java.lang.String
You should get a lot of text describing the methods on the String class. =
Now try:
javap org.biojava.bio.Annotation
You should get text describing the methods on Annotation in biojava. If =
not, your classpath is incorrectly set, or the .jar archive is =
corrupted. To check the jar, change into the c:\biojava directory and =
type:
jar -tf biojava.jar
You should get a long listing of all the files in the archive. If you =
get an error message about the .jar being corrupted, then that is your =
problem.
I hope some of this helps. If you are still having problems then post to =
the list again, or come onto chat at:
irc.openprojects.net
#biojava
Best,
Matthew
Dear Biojava friends
I have donwnloaded the three files biojava-1.21jar, bytecode-0.90.jar =
and xerces.ar on my windows2000 machine. I put them in the directory =
c:\biojava. I set up the class path =
CLASSPATH=3DC:\biojava.jar;C:\xerces.jar;C:\bytecode.jar;.using control =
panel , system, user variables.=20
when I compile a demo progra GCContent.java , I get compile err,=20
biojava/GCContent.java [3:1] package org.biojava.bio.seq does not =
exist
import org.biojava.bio.seq.*;
^
biojava/GCContent.java [4:1] package org.biojava.bio.seq.io does not =
exist
import org.biojava.bio.seq.io.*;
^
biojava/GCContent.java [18:1] cannot resolve symbol
symbol : class SequenceIterator =20
location: class GCContent
SequenceIterator stream =3D SeqIOTools.readFastaDNA(br);
^
biojava/GCContent.java [18:1] cannot resolve symbol
symbol : variable SeqIOTools =20
location: class GCContent
SequenceIterator stream =3D SeqIOTools.readFastaDNA(br);
^
biojava/GCContent.java [23:1] cannot resolve symbol
symbol : class Sequence =20
location: class GCContent
Sequence seq =3D stream.nextSequence();
^
biojava/GCContent.java [26:1] cannot resolve symbol
symbol : class Symbol =20
location: class GCContent
Symbol sym =3D seq.symbolAt(pos);
^
biojava/GCContent.java [27:1] cannot resolve symbol
symbol : variable DNATools =20
location: class GCContent
if (sym =3D=3D DNATools.g() || sym =3D=3D =
DNATools.c())
^
biojava/GCContent.java [27:1] cannot resolve symbol
symbol : variable DNATools =20
location: class GCContent
if (sym =3D=3D DNATools.g() || sym =3D=3D =
DNATools.c())
^
9 errors
Errors compiling GCContent.
I would like to get some help to solve the problem. I am newcomer in =
java
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<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial size=3D2>Hi Dr Chen,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>You say that you have placed the jar =
files in a=20
c:\biojava directory, but your classpath entries don't seem to be =
respecting=20
this. Have you tried the classpath:</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>set=20
CLASSPATH=3DCLASSPATH=3DC:\biojava\biojava.jar;C:\biojava\xerces.jar;C:\b=
iojava\bytecode.jar;.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>A good check to make sure things are in =
the=20
classpath is to use the javap program. Try:</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>javap java.lang.String</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>You should get a lot of text describing =
the methods=20
on the String class. Now try:</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>javap =
org.biojava.bio.Annotation</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>You should get text describing the =
methods on=20
Annotation in biojava. If not, your classpath is incorrectly set, or the =
.jar=20
archive is corrupted. To check the jar, change into the c:\biojava =
directory and=20
type:</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>jar -tf biojava.jar</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>You should get a long listing of all =
the files in=20
the archive. If you get an error message about the .jar being corrupted, =
then=20
that is your problem.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>I hope some of this helps. If you are =
still having=20
problems then post to the list again, or come onto chat at:</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>irc.openprojects.net</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>#biojava</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Best,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Matthew</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<BLOCKQUOTE dir=3Dltr=20
style=3D"PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; =
BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
<DIV style=3D"FONT: 10pt arial">Dear Biojava friends<BR><BR>I have =
donwnloaded=20
the three files biojava-1.21jar, bytecode-0.90.jar and xerces.ar on my =
windows2000 machine. I put them in the directory c:\biojava. I =
set up=20
the class path =
CLASSPATH=3DC:\biojava.jar;C:\xerces.jar;C:\bytecode.jar;.using=20
control panel , system, user variables. <BR>when I compile a demo =
progra=20
GCContent.java , I get compile err, <BR><BR>biojava/GCContent.java =
[3:1]=20
package org.biojava.bio.seq does not exist<BR>import=20
org.biojava.bio.seq.*;<BR>^<BR>biojava/GCContent.java [4:1] package=20
org.biojava.bio.seq.io does not exist<BR>import=20
org.biojava.bio.seq.io.*;<BR>^<BR>biojava/GCContent.java [18:1] cannot =
resolve=20
symbol<BR>symbol : class SequenceIterator <BR>location: =
class=20
GCContent<BR> =
SequenceIterator=20
stream =3D=20
=
SeqIOTools.readFastaDNA(br);<BR>  =
;=20
^<BR>biojava/GCContent.java [18:1] cannot resolve =
symbol<BR>symbol :=20
variable SeqIOTools <BR>location: class=20
GCContent<BR> =
SequenceIterator=20
stream =3D=20
=
SeqIOTools.readFastaDNA(br);<BR>  =
; =
&=
nbsp; =20
^<BR>biojava/GCContent.java [23:1] cannot resolve =
symbol<BR>symbol :=20
class Sequence <BR>location: class=20
=
GCContent<BR> =
=20
Sequence seq =3D=20
=
stream.nextSequence();<BR>  =
; =20
^<BR>biojava/GCContent.java [26:1] cannot resolve =
symbol<BR>symbol :=20
class Symbol <BR>location: class=20
=
GCContent<BR> =
=20
Symbol sym =3D=20
=
seq.symbolAt(pos);<BR> &nb=
sp; =20
^<BR>biojava/GCContent.java [27:1] cannot resolve =
symbol<BR>symbol :=20
variable DNATools <BR>location: class=20
=
GCContent<BR> =
=20
if (sym =3D=3D DNATools.g() || sym =3D=3D=20
=
DNATools.c())<BR> &n=
bsp; &nb=
sp; =20
^<BR>biojava/GCContent.java [27:1] cannot resolve =
symbol<BR>symbol :=20
variable DNATools <BR>location: class=20
=
GCContent<BR> =
=20
if (sym =3D=3D DNATools.g() || sym =3D=3D=20
=
DNATools.c())<BR> &n=
bsp; &nb=
sp; &nbs=
p;  =
; =20
^<BR>9 errors<BR>Errors compiling GCContent.<BR><BR><BR>I would like =
to get=20
some help to solve the problem. I am newcomer in=20
java<BR></DIV></BLOCKQUOTE></BODY></HTML>
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