This is exactly why BioJava needs to be Mavenized!
On Sun, Jul 27, 2008 at 3:23 AM, Peter Robinson <[EMAIL PROTECTED]> wrote: > Hi, > Thanks. I think that squiggly braces are OK for the shell, but in any case, > I removed them from .bashrc, which now goes as follows: > > > export CLASSPATH=/home/peter/bin/biojava/biojava-live_1.6/biojava.jar > export > CLASSPATH=$CLASSPATH:/home/peter/bin/biojava/biojava-live_1.6/commons-dbcp-1.1.jar > export > CLASSPATH=$CLASSPATH:/home/peter/bin/biojava/biojava-live_1.6/commons-cli.jar > export > CLASSPATH=$CLASSPATH:/home/peter/bin/biojava/biojava-live_1.6/bytecode.jar > export > CLASSPATH=$CLASSPATH:/home/peter/bin/biojava/biojava-live_1.6/commons-collections-2.1.jar > export > CLASSPATH=$CLASSPATH:/home/peter/bin/biojava/biojava-live_1.6/commons-pool-1.1.jar > export CLASSPATH=$CLASSPATH:. > > **************The class path variable seems to be set OK > > [EMAIL PROTECTED]:~/bin/biojava/biojava-live_1.6/demos$ echo $CLASSPATH > /home/peter/bin/biojava/biojava-live_1.6/biojava.jar:/home/peter/bin/biojava/biojava-live_1.6/commons-dbcp-1.1.jar:/home/peter/bin/biojava/biojava-live_1.6/commons-cli.jar:/home/peter/bin/biojava/biojava-live_1.6/bytecode.jar:/home/peter/bin/biojava/biojava-live_1.6/commons-collections-2.1.jar:/home/peter/bin/biojava/biojava-live_1.6/commons-pool-1.1.jar:. > > ************ The paths appear to be correct: > [EMAIL PROTECTED]:~/bin/biojava/biojava-live_1.6/demos$ ls > /home/peter/bin/biojava/biojava-live_1.6/*.jar > /home/peter/bin/biojava/biojava-live_1.6/apps-live.jar > /home/peter/bin/biojava/biojava-live_1.6/commons-dbcp-1.1.jar > /home/peter/bin/biojava/biojava-live_1.6/biojava-live.jar > /home/peter/bin/biojava/biojava-live_1.6/commons-pool-1.1.jar > /home/peter/bin/biojava/biojava-live_1.6/bytecode.jar > /home/peter/bin/biojava/biojava-live_1.6/demos-live.jar > /home/peter/bin/biojava/biojava-live_1.6/commons-cli.jar > /home/peter/bin/biojava/biojava-live_1.6/jgrapht-jdk1.5.jar > /home/peter/bin/biojava/biojava-live_1.6/commons-collections-2.1.jar > /home/peter/bin/biojava/biojava-live_1.6/junit-4.4.jar > > ***********But again, I cannot compile any of the demo programs > > [EMAIL PROTECTED]:~/bin/biojava/biojava-live_1.6/demos$ javac > seq/TestEmbl.java > seq/TestEmbl.java:25: package org.biojavax does not exist > import org.biojavax.Namespace; > ^ > seq/TestEmbl.java:26: package org.biojavax does not exist > import org.biojavax.RichObjectFactory; > ^ > seq/TestEmbl.java:27: package org.biojavax.bio.seq does not exist > import org.biojavax.bio.seq.RichSequence; > ^ > seq/TestEmbl.java:28: package org.biojavax.bio.seq does not exist > import org.biojavax.bio.seq.RichSequenceIterator; > ^ > seq/TestEmbl.java:48: cannot find symbol > symbol : class Namespace > location: class seq.TestEmbl > Namespace ns = RichObjectFactory.getDefaultNamespace(); > ^ > seq/TestEmbl.java:48: cannot find symbol > symbol : variable RichObjectFactory > location: class seq.TestEmbl > Namespace ns = RichObjectFactory.getDefaultNamespace(); > ^ > seq/TestEmbl.java:50: cannot find symbol > symbol : class RichSequenceIterator > location: class seq.TestEmbl > RichSequenceIterator seqI = > ^ > seq/TestEmbl.java:51: package RichSequence does not exist > RichSequence.IOTools.readEMBLDNA(br, ns); > ^ > seq/TestEmbl.java:54: cannot find symbol > symbol : class RichSequence > location: class seq.TestEmbl > RichSequence seq = seqI.nextRichSequence(); > ^ > seq/TestEmbl.java:57: package RichSequence does not exist > RichSequence.IOTools.writeEMBL(System.out, seq, ns); > ^ > 10 errors > [EMAIL PROTECTED]:~/bin/biojava/biojava-live_1.6/demos$ > > > Richard Holland wrote: >> >> Hello. >> >> Before typing the javac instruction, type the following to check what >> your classpath actually contains: >> >> echo $CLASSPATH >> >> If this doesn't immediately 'look right' (i.e. it has curly braces or >> variable names embedded in it, or doesn't match where you think the >> files are), then this'll be where the problem is. >> >> If you can't see any obvious problems with it, then post it as a reply >> to this message and we can take a closer look. >> >> cheers, >> Richard >> >> >> 2008/7/26 James Carman <[EMAIL PROTECTED]>: >> >>> >>> Try export CLASSPATH=$CLASSPATH:... >>> >>> Basically, remove the "squiggly braces" >>> >>> >>> On Sat, Jul 26, 2008 at 6:41 AM, Peter Robinson >>> <[EMAIL PROTECTED]> wrote: >>> >>>> >>>> Hi Biojava, >>>> >>>> I am entirely new to Biojava and have limited Java experience (C is more >>>> my >>>> thing), and so this is almost certainly a dumb question, but I cannot >>>> seem >>>> to find an answer in the online docs. I am running debian 4 linux and >>>> have: >>>> >>>> java version "1.6.0_06" >>>> Java(TM) SE Runtime Environment (build 1.6.0_06-b02) >>>> Java HotSpot(TM) Server VM (build 10.0-b22, mixed mode) >>>> >>>> >>>> >>>> I have downloaded the biojava code, unpacked it, and set the CLASSPATH >>>> in >>>> bashrc : >>>> >>>> BIOJAVA_BASE=/home/peter/bin/biojava/biojava-live_1.6 >>>> export CLASSPATH=${BIOJAVA_BASE}/biojava.jar >>>> export CLASSPATH=${CLASSPATH}:${BIOJAVA_BASE}/commons-cli.jar >>>> export >>>> CLASSPATH=${CLASSPATH}:${BIOJAVA_BASE}/commons-collections-2.1.jar >>>> export CLASSPATH=${CLASSPATH}:${BIOJAVA_BASE}/bytecode.jar >>>> export CLASSPATH=${CLASSPATH}:${BIOJAVA_BASE}/commons-dbcp-1.1.jar >>>> export CLASSPATH=${CLASSPATH}:${BIOJAVA_BASE}/commons-pool-1.1.jar >>>> export CLASSPATH=${CLASSPATH}:. >>>> >>>> >>>> This also goes through without error from the command line. However, >>>> when I >>>> try to compile one of the test programs as instructed on the page: >>>> http://biojava.org/wiki/BioJava:GetStarted >>>> >>>> [EMAIL PROTECTED]:~/bin/biojava/biojava-live_1.6/demos$ javac >>>> seq/TestEmbl.java >>>> >>>> >>>> I get a bunch of errors, apparently javac cannot find the imports it >>>> needs. >>>> (see bottom of this mail). >>>> >>>> I would greatly appreciate any tips how to get started here! >>>> Thanks, Peter >>>> >>>> >>>> >>>> >>>> [EMAIL PROTECTED]:~/bin/biojava/biojava-live_1.6/demos$ javac >>>> seq/TestEmbl.java >>>> seq/TestEmbl.java:25: package org.biojavax does not exist >>>> import org.biojavax.Namespace; >>>> ^ >>>> seq/TestEmbl.java:26: package org.biojavax does not exist >>>> import org.biojavax.RichObjectFactory; >>>> ^ >>>> seq/TestEmbl.java:27: package org.biojavax.bio.seq does not exist >>>> import org.biojavax.bio.seq.RichSequence; >>>> ^ >>>> seq/TestEmbl.java:28: package org.biojavax.bio.seq does not exist >>>> import org.biojavax.bio.seq.RichSequenceIterator; >>>> ^ >>>> seq/TestEmbl.java:48: cannot find symbol >>>> symbol : class Namespace >>>> location: class seq.TestEmbl >>>> Namespace ns = RichObjectFactory.getDefaultNamespace(); >>>> ^ >>>> seq/TestEmbl.java:48: cannot find symbol >>>> symbol : variable RichObjectFactory >>>> location: class seq.TestEmbl >>>> Namespace ns = RichObjectFactory.getDefaultNamespace(); >>>> ^ >>>> seq/TestEmbl.java:50: cannot find symbol >>>> symbol : class RichSequenceIterator >>>> location: class seq.TestEmbl >>>> RichSequenceIterator seqI = >>>> ^ >>>> seq/TestEmbl.java:51: package RichSequence does not exist >>>> RichSequence.IOTools.readEMBLDNA(br, ns); >>>> ^ >>>> seq/TestEmbl.java:54: cannot find symbol >>>> symbol : class RichSequence >>>> location: class seq.TestEmbl >>>> RichSequence seq = seqI.nextRichSequence(); >>>> ^ >>>> seq/TestEmbl.java:57: package RichSequence does not exist >>>> RichSequence.IOTools.writeEMBL(System.out, seq, ns); >>>> ^ >>>> 10 errors >>>> [EMAIL PROTECTED]:~/bin/biojava/biojava-live_1.6/demos$ java -version >>>> java version "1.6.0_06" >>>> Java(TM) SE Runtime Environment (build 1.6.0_06-b02) >>>> Java HotSpot(TM) Server VM (build 10.0-b22, mixed mode) >>>> [EMAIL PROTECTED]:~/bin/biojava/biojava-live_1.6/demos$ javac >>>> seq/TestEmbl.java >>>> seq/TestEmbl.java:25: package org.biojavax does not exist >>>> import org.biojavax.Namespace; >>>> ^ >>>> seq/TestEmbl.java:26: package org.biojavax does not exist >>>> import org.biojavax.RichObjectFactory; >>>> ^ >>>> seq/TestEmbl.java:27: package org.biojavax.bio.seq does not exist >>>> import org.biojavax.bio.seq.RichSequence; >>>> ^ >>>> seq/TestEmbl.java:28: package org.biojavax.bio.seq does not exist >>>> import org.biojavax.bio.seq.RichSequenceIterator; >>>> ^ >>>> seq/TestEmbl.java:48: cannot find symbol >>>> symbol : class Namespace >>>> location: class seq.TestEmbl >>>> Namespace ns = RichObjectFactory.getDefaultNamespace(); >>>> ^ >>>> seq/TestEmbl.java:48: cannot find symbol >>>> symbol : variable RichObjectFactory >>>> location: class seq.TestEmbl >>>> Namespace ns = RichObjectFactory.getDefaultNamespace(); >>>> ^ >>>> seq/TestEmbl.java:50: cannot find symbol >>>> symbol : class RichSequenceIterator >>>> location: class seq.TestEmbl >>>> RichSequenceIterator seqI = >>>> ^ >>>> seq/TestEmbl.java:51: package RichSequence does not exist >>>> RichSequence.IOTools.readEMBLDNA(br, ns); >>>> ^ >>>> seq/TestEmbl.java:54: cannot find symbol >>>> symbol : class RichSequence >>>> location: class seq.TestEmbl >>>> RichSequence seq = seqI.nextRichSequence(); >>>> ^ >>>> seq/TestEmbl.java:57: package RichSequence does not exist >>>> RichSequence.IOTools.writeEMBL(System.out, seq, ns); >>>> ^ >>>> 10 errors >>>> [EMAIL PROTECTED]:~/bin/biojava/biojava-live_1.6/demos$ >>>> >>>> _______________________________________________ >>>> Biojava-l mailing list - Biojava-l@lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>>> >>>> >>> >>> _______________________________________________ >>> Biojava-l mailing list - Biojava-l@lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>> >>> >> >> >> >> > > _______________________________________________ > Biojava-l mailing list - Biojava-l@lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - Biojava-l@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l