From markjschreiber at gmail.com Thu Mar 6 01:24:32 2008 From: markjschreiber at gmail.com (Mark Schreiber) Date: Thu, 6 Mar 2008 14:24:32 +0800 Subject: [Biojava-dev] proposal to drop BioSQL Singapore version support from BJ version 1.6 onwards Message-ID: <93b45ca50803052224y5434d6d9t35fa180f33db35ca@mail.gmail.com> Hi all - With the formal release of BioSQL v1.0 (Tokyo) and the new Hibernate ORM mapping to BioSQL offered in BioJava 1.5 (BioJavaX) the older JDBC mappings to the BioSQL (Singapore) are now outdated. We have not been supporting these for some time. Unless people are still actively using these mappings I would propose that we drop them from the upcoming BioJava 1.6. This would remove some cruft from the code base and would also mean we can drop about 4 jar files from the lib (commons-pool etc). Are there any strong arguments for or against? - Mark From ayates at ebi.ac.uk Thu Mar 6 04:10:25 2008 From: ayates at ebi.ac.uk (Andy Yates) Date: Thu, 6 Mar 2008 09:10:25 +0000 Subject: [Biojava-dev] proposal to drop BioSQL Singapore version support from BJ version 1.6 onwards In-Reply-To: <93b45ca50803052224y5434d6d9t35fa180f33db35ca@mail.gmail.com> References: <93b45ca50803052224y5434d6d9t35fa180f33db35ca@mail.gmail.com> Message-ID: +1 Maintaining two apis is always a bad idea On 6 Mar 2008, at 06:24, Mark Schreiber wrote: > Hi all - > > With the formal release of BioSQL v1.0 (Tokyo) and the new Hibernate > ORM mapping to BioSQL offered in BioJava 1.5 (BioJavaX) the older JDBC > mappings to the BioSQL (Singapore) are now outdated. We have not been > supporting these for some time. > > Unless people are still actively using these mappings I would propose > that we drop them from the upcoming BioJava 1.6. This would remove > some cruft from the code base and would also mean we can drop about 4 > jar files from the lib (commons-pool etc). > > Are there any strong arguments for or against? > > - Mark > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev From bugzilla-daemon at portal.open-bio.org Thu Mar 6 18:16:49 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 6 Mar 2008 18:16:49 -0500 Subject: [Biojava-dev] [Bug 2467] New: BioJava : IOTools.writeFasta() : Infinite Exception loop Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2467 Summary: BioJava : IOTools.writeFasta() : Infinite Exception loop Product: BioJava Version: 1.5 Platform: PC OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: seq.io AssignedTo: biojava-dev at biojava.org ReportedBy: benjamin.pavie at gmail.com Opening a non correct fasta file and then write it as Fasta give an infinite Exception loop. Here is an example : public class GeneralReader { public static void main(String[] args) { try { Class.forName("org.biojavax.bio.seq.io.FastaFormat"); } catch (ClassNotFoundException e) { e.printStackTrace(); } try { RichSequenceIterator iter = IOTools.readFile(new File (args[0]), ns); IOTools.writeFasta(System.out, iter, ns); } catch (FileNotFoundException ex) { ex.printStackTrace(); } catch (IOException ex) { ex.printStackTrace(); } } } } When we give as arg[0] a file containing : > MAIDVDRTLAVLRRKLEALGYSDPLEPASLQLVQKLVEDLVHTTDSYTAVKQQCAKQAQEIAAFDTRLESVRQDSVRLQS ENSQLHVLVMQHAERHEREAREHYTAVKRLEDTIAELSYWKHAAAEKLASADKENAGLRKRCEELAKLTDRLASGAATPQ the operation RichSequenceIterator iter = IOTools.readFile(new File (args[0]), ns); works well, but IOTools.writeFasta(System.out, iter, ns); give a infinity loop of exception : org.biojava.bio.BioException: Could not read sequence at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113) at org.biojavax.bio.seq.io.RichStreamReader.nextSequence(RichStreamReader.java:92) at org.biojavax.bio.seq.io.RichStreamWriter.writeStream(RichStreamWriter.java:66) at org.biojavax.bio.seq.RichSequence$IOTools.writeFasta(RichSequence.java:1279) at GeneralReader.main(GeneralReader.java:12) Caused by: java.io.IOException: Stream does not appear to contain FASTA formatted data: > at org.biojavax.bio.seq.io.FastaFormat.readRichSequence(FastaFormat.java:189) at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) ... 4 more org.biojava.bio.BioException: Could not read sequence at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113) at org.biojavax.bio.seq.io.RichStreamReader.nextSequence(RichStreamReader.java:92) at org.biojavax.bio.seq.io.RichStreamWriter.writeStream(RichStreamWriter.java:66) at org.biojavax.bio.seq.RichSequence$IOTools.writeFasta(RichSequence.java:1279) at GeneralReader.main(GeneralReader.java:12) Caused by: java.io.IOException: Stream does not appear to contain FASTA formatted data: MAIDVDRTLAVLRRKLEALGYSDPLEPASLQLVQKLVEDLVHTTDSYTAVKQQCAKQAQEIAAFDTRLESVRQDSVRLQSENSQLHVLVMQHAERHEREAREHYTAVKRLEDTIAELSYWKHAAAEKLASADKENAGLRKRCEELAKLTDRLASGAATPQ at org.biojavax.bio.seq.io.FastaFormat.readRichSequence(FastaFormat.java:182) at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) ... 4 more org.biojava.bio.BioException: Could not read sequence at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113) at org.biojavax.bio.seq.io.RichStreamReader.nextSequence(RichStreamReader.java:92) at org.biojavax.bio.seq.io.RichStreamWriter.writeStream(RichStreamWriter.java:66) at org.biojavax.bio.seq.RichSequence$IOTools.writeFasta(RichSequence.java:1279) at GeneralReader.main(GeneralReader.java:12) Caused by: java.io.IOException: Premature stream end at org.biojavax.bio.seq.io.FastaFormat.readRichSequence(FastaFormat.java:173) at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) ... 4 more etc ... -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Mar 10 05:34:51 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 10 Mar 2008 05:34:51 -0400 Subject: [Biojava-dev] [Bug 2467] BioJava : IOTools.writeFasta() : Infinite Exception loop In-Reply-To: Message-ID: <200803100934.m2A9YpSM000675@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2467 ------- Comment #1 from mark.schreiber at novartis.com 2008-03-10 05:34 EST ------- To clarify the bug is in the exception handling that is going into an infinite loop, one report of the problem is enough. I don't think that there is any need to recognize a Fasta format sequence with no name. This doesn't really qualify as Fasta format in my opinion so I think the parser should be allowed to throw an exception. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Tue Mar 11 12:27:50 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 11 Mar 2008 12:27:50 -0400 Subject: [Biojava-dev] [Bug 2467] BioJava : IOTools.writeFasta() : Infinite Exception loop In-Reply-To: Message-ID: <200803111627.m2BGRoHg023413@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2467 ------- Comment #2 from gwaldon at geneinfinity.org 2008-03-11 12:27 EST ------- I certainly disagree with this. There is no requirement that a fasta file contains a name in its description line. Most definitions only state that ">" is required and some even say that name and description are optional (see Wikipedia). In fact I am sure these files are frequent in html forms when sequences in fasta format are requested and hard drives located at the bench are probably full of them. Therefore no need to throw an exception for something not exceptional. What about adding a mandatory name such as "unknown", "untitled", "unnamed", "noname", "no_name", "notitle", "nameless", "undefined", "undetermined", or "anonymous"? I have no preference but I have used "untitled" in a project. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Mar 12 01:23:33 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 12 Mar 2008 01:23:33 -0400 Subject: [Biojava-dev] [Bug 2467] BioJava : IOTools.writeFasta() : Infinite Exception loop In-Reply-To: Message-ID: <200803120523.m2C5NXWx012177@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2467 ------- Comment #3 from mark.schreiber at novartis.com 2008-03-12 01:23 EST ------- sigh... Don't even get me started on Fasta's so-called "format". I think the best solution to the missing name/accession/gi/description/whatever-else-you-feel-like-putting-behind-the > is to set all of the above to an empty string (""). This would be the closest to what the user put in (ie nothing). Calling it "unknown" or something else actually conveys some information where there was none to begin with. Also someone may intentionally use the word "unknown" which might have meaning to them, us using a default would conflict with this. Additionally roundtripping would be a problem as it would go in with no name and come out with a "unknown". OK, so two bugs to fix. Infinite loop in the exception handling and tolerating description lines with no information. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From darin.london at duke.edu Tue Mar 18 14:16:58 2008 From: darin.london at duke.edu (darin.london at duke.edu) Date: Tue, 18 Mar 2008 13:16:58 -0500 Subject: [Biojava-dev] BOSC 2008 Announcement and Call For Submissions Message-ID: <200803181816.m2IIGwni007236@tenero.duhs.duke.edu> BOSC 2008 Call for Abstracts The 9th annual Bioinformatics Open Source Conference (BOSC 2008) will take place in Toronto, Ontario, Canada, as one of several Special Interest Group (SIG) meetings occurring in conjunction with the 16th annual Intelligent Systems for Molecular Biology Conference (ISMB 2008). The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. Many Open Source bioinformatics packages are widely used by the research community across many application areas and form a cornerstone in enabling research in the genomic and post-genomic era. Open source bioinformatics software has facilitated rapid innovation and dissemination of new computational methods as well as informatics infrastructure. Since the work of the Open Source Bioinformatics Community represents some of the most cutting edge of Bioinformatics in general, the overall theme for the conference this year is "Tackling Hard Problems with Emerging Technologies". Topics under this umbrella include cyberinfrastructure, grid computing and workflow management and discovery, and visualization. We will also have a series of update talks about the main Open Source Bioinformatics Software suites. One of the hallmarks of BOSC is the coming together of the open source developer community in one location. A face-to-face meeting of this community creates synergy where participants can work together to create use cases, prototype working code, or run bootcamps for developers from other projects as short, informal, and hands-on tutorials in new software packages and emerging technologies. In short, BOSC is not just a conference for presentations of completed work, but is a dynamic meeting where collaborative work gets done. This year, BOSC is accepting abstract submissions on the conference theme "Tackling Hard Problems with Emerging Technologies". The conference theme reflects that there are new technologies emerging on both the scientific front (new sequencing technologies, etc.) and the IT front (workflows, mashup/web 2.0, improvements in all of the major programming languages, etc.), which may allow the open source community to solve problems that were previously intractable. Abstracts may be submitted for the following topics. 1. Cyberinfrastructure - We are interested in presentations on topics dealing with the development of infrastructure on the web to facilitate software and data re-use (mashups, or traditional), interoperability and inter-process communication, system/service discovery, and data movement and modeling in distributed systems. This may include peer-to-peer systems of data transfer, Web Services, various flavors of data representation (SOAP, JSON, XML, others), and technologies commonly referred to under the Web 2.0 paradigm (e.g. folksonomies/tagging, user-based content generation, content feeds, and Social Networking). 2. Grid Computing and Workflow Management and Discovery - We particularly invite talks that report progress in making workflow systems easier to use and on how to do distributed-collaborative research , e.g. workflows that encompass the coordination of systems running in different parts of the world. 3. Visualization - Visualization is a maturing area of open source software development. We particularly invite talks that demonstrate innovative visualization systems in the context of workflows. 4. Open Source Software - Speakers will present talks on the use, development, or philosophy of open source software in bioinformatics. 5. Bio* Open Source Project Updates - We invite abstracts from the representatives of the open source projects sponsored by or affiliated to the O|B|F (see Projects). Please consult the official BOSC 2008 website at http://www.open-bio.org/wiki/Upcoming_BOSC_conference for all updates and extra information. Submission Process: All abstracts must be submitted through our Open Conference Systems site (http://events.open-bio.org/BOSC2008/openconf.php). The form will ask for a small Abstract Text to be pasted into it, and a full paper. The small Abstract text should be a summary, while the longer abstract (should provide more details, including the open-source license requirement details) Full-length abstracts are limited to one page with one inch (2.5 cm) margins on the top, sides, and bottom. The full-length abstract should include the title, authors, and affiliations. We prefer your abstract to be in PDF format, although plain t Important Dates: May 11: Abstract submission deadline. June 2: Notification of accepted talks. June 4: Early registration discount cut-off. July 18-19: BOSC 2008! We hope to see you at BOSC 2008! Kam Dahlquist and Darin London BOSC 2008 Co-organizers From ap3 at sanger.ac.uk Wed Mar 26 09:55:15 2008 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Wed, 26 Mar 2008 13:55:15 +0000 Subject: [Biojava-dev] preparations for release 1.6 Message-ID: <78ECCE6A-F8CC-45AA-862B-F7D8BFC65EA0@sanger.ac.uk> Hi, The biojava 1.6 release candidate 1 has been available now for a while and I would like to proceed with releasing the final biojava 1.6. I ran doccheck on the latest SVN and we still could do with some javadoc improvements: http://www.spice-3d.org/doccheck/biojava-svn/biojava/ PackageStatistics.html Please commit any remaining bug fixes to SVN until Friday, April 4th 18:00 GMT I will do the release (and SVN branch) after that. Cheers, Andreas ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK +44 (0) 1223 49 6891 ----------------------------------------------------------------------- -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From Russell.Smithies at agresearch.co.nz Wed Mar 26 22:13:16 2008 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Thu, 27 Mar 2008 15:13:16 +1300 Subject: [Biojava-dev] Bioinformatician wanted Message-ID: Dear colleagues, It would be appreciated if you could bring the following position to the attention of potential candidates. Bioinformatician wanted Many of the world's most amazing scientific discoveries are the result of someone 'taking a closer look'. It's this inquisitive nature and relentless search for answers that fuels scientific advancement. And it's also what we'd like you to apply to us, right now. Mind you, you won't need to look too hard to discover that AgResearch is the best place to break all new ground in your career. At first glance you'll see we are New Zealand's largest research institute -world leaders in pastoral research working at the leading-edge of innovation. Scratch the surface a little more and you'll find all the diversity and intellectual challenge a Bioinformatician could ask for. This is a highly collaborative role where you'll be involved in everything from the analysis of genomic data to the design, development, implementation and testing of bioinformatics tools. Knowledge sharing is a pivotal component of our success, so you can also look forward to acting in consultant capacity (both internally and externally) and the autonomy to contribute to scientific publications. Our people are at the pinnacle in their professions, so with your biological background, higher qualification in bioinformatics or computing and your experience in contributing bioinformatics expertise to research groups, you'll not only fit right in, you'll hit the ground running. An outstanding communicator, time manager and relationship builder, you'll also come to us with a thorough knowledge of Unix, pipeline-development, web based technologies and scripting and programming languages. AgResearch is a unique organisation at the forefront of our field, and as far as your future's concerned, that makes us well worth a closer look. There are many benefits waiting to be discovered here, so isn't it time you experienced them? The job description is available online and applications are invited at www.agresearch.co.nz/recruitment/ Reference AGR661, or contact Nauman Maqbool for further information. Applications close 11 April 2008. Regards, Russell Russell Smithies Bioinformatics Applications Developer T +64 3 489 9085 E russell.smithies at agresearch.co.nz AgResearch Farming Food and Health. First Te Ahuwhenua, Te Kai me te Whai Ora. Tuatahi Invermay Research Centre Puddle Alley, Mosgiel, New Zealand T +64 3 489 3809 F +64 3 489 9174 www.agresearch.co.nz ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From nicolas.desreumaux at obs-banyuls.fr Fri Mar 28 08:30:06 2008 From: nicolas.desreumaux at obs-banyuls.fr (nicolas desreumaux) Date: Fri, 28 Mar 2008 13:30:06 +0100 Subject: [Biojava-dev] BioJava Install Message-ID: <47ECE4CE.8070905@obs-banyuls.fr> Dear All, We have a problem to install BioJava on MacOs 10.4 Below errors : --------------------------------------------------------- Buildfile: build.xml init: [echo] Building biojava-1.5 [echo] Java Home: /System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home [echo] JUnit present: ${junit.present} [echo] JUnit supported by Ant: true [echo] HSQLDB driver present: ${sqlDriver.hsqldb} [echo] XSLT support: true prepare: prepare-tests: prepare-biojava: compile-biojava: [javac] Compiling 366 source files to /Users/pierre/BioJava1.5-all/biojava-1.5/ant-build/classes/biojava [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:316: cannot find symbol [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] proxyIV.add(ByteCode.make_checkcast(ourContextC)); [javac] ^ [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:381: cannot find symbol [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] proxyIV.add(ByteCode.make_checkcast(ourContextC) ); [javac] ^ [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:451: cannot find symbol [javac] symbol : variable TYPE_OBJECT [javac] location: class org.biojava.utils.bytecode.CodeUtils [javac] CodeClass c_baseClass = CodeUtils.TYPE_OBJECT; [javac] ^ [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:462: cannot find symbol [javac] symbol : variable TYPE_OBJECT [javac] location: class org.biojava.utils.bytecode.CodeUtils [javac] = CodeUtils.TYPE_OBJECT.getConstructor(CodeUtils.EMPTY_LIST); [javac] ^ [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:497: cannot find symbol [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] revTIV.add(ByteCode.make_checkcast(c_FeatureTemplate)); [javac] ^ [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:507: cannot find symbol [javac] symbol : method getFields() [javac] location: interface org.biojava.utils.bytecode.CodeClass [javac] for(Iterator fi = c_ourTemplate.getFields().iterator(); [javac] ^ [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:537: cannot find symbol [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] revIV.add(ByteCode.make_checkcast(c_ourTemplate)); [javac] ^ [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:539: cannot find symbol [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] revIV.add(ByteCode.make_checkcast(c_ourContext)); [javac] ^ [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:541: cannot find symbol [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] revIV.add(ByteCode.make_checkcast(c_ourTemplate)); [javac] ^ [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:246: cannot find symbol [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] walkIV.add(ByteCode.make_checkcast(c_ourVisitor)); [javac] ^ [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:275: cannot find symbol [javac] symbol : method forMethod(java.lang.reflect.Method) [javac] location: class org.biojava.utils.bytecode.IntrospectedCodeClass [javac] CodeMethod m_getChild = IntrospectedCodeClass.forMethod(m); [javac] ^ [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:293: cannot find symbol [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] wfiv.add(ByteCode.make_checkcast(c_ourType)); [javac] ^ [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:308: cannot find symbol [javac] symbol : method make_instanceof(org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] wrapperIV.add(ByteCode.make_instanceof(c_ourType)); [javac] ^ [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:339: cannot find symbol [javac] symbol : method forMethod(java.lang.reflect.Method) [javac] location: class org.biojava.utils.bytecode.IntrospectedCodeClass [javac] CodeMethod ourMeth = IntrospectedCodeClass.forMethod(meth); [javac] ^ [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:345: cannot find symbol [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] bodyIV.add(ByteCode.make_checkcast(c_thisFiltType)); [javac] ^ [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:354: cannot find symbol [javac] symbol : method make_instanceof(org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] walkIV.add(ByteCode.make_instanceof(c_thisFiltType)); [javac] ^ [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:376: cannot find symbol [javac] symbol : variable TYPE_OBJECT [javac] location: class org.biojava.utils.bytecode.CodeUtils [javac] CodeUtils.TYPE_OBJECT, [javac] ^ [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:406: cannot find symbol [javac] symbol : variable TYPE_OBJECT [javac] location: class org.biojava.utils.bytecode.CodeUtils [javac] CodeUtils.TYPE_OBJECT, [javac] ^ [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] 18 errors BUILD FAILED /Users/pierre/BioJava1.5-all/biojava-1.5/build.xml:266: Compile failed; see the compiler error output for details. Total time: 17 seconds gwenael-piganeaus-Computer:~/BioJava1.5-all/biojava-1.5 pierre$ ant runtests>tests.txt BUILD FAILED /Users/pierre/BioJava1.5-all/biojava-1.5/build.xml:266: Compile failed; see the compiler error output for details. Total time: 11 seconds --------------------------------------------------------- What can I do to avoid these errors ? Thanks. Best regards, Nicolas Desreumaux From markjschreiber at gmail.com Fri Mar 28 09:20:08 2008 From: markjschreiber at gmail.com (Mark Schreiber) Date: Fri, 28 Mar 2008 21:20:08 +0800 Subject: [Biojava-dev] BioJava Install In-Reply-To: <47ECE4CE.8070905@obs-banyuls.fr> References: <47ECE4CE.8070905@obs-banyuls.fr> Message-ID: <93b45ca50803280620s7f53a6fo542e88e65a025b04@mail.gmail.com> Hi = It looks like you are missing the bytecode.jar from your classpath. - Mark On Fri, Mar 28, 2008 at 8:30 PM, nicolas desreumaux wrote: > Dear All, > > > We have a problem to install BioJava on MacOs 10.4 > > > Below errors : > --------------------------------------------------------- > > Buildfile: build.xml > > init: > [echo] Building biojava-1.5 > [echo] Java Home: /System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home > [echo] JUnit present: ${junit.present} > [echo] JUnit supported by Ant: true > [echo] HSQLDB driver present: ${sqlDriver.hsqldb} > [echo] XSLT support: true > > prepare: > > prepare-tests: > > prepare-biojava: > > compile-biojava: > [javac] Compiling 366 source files to /Users/pierre/BioJava1.5-all/biojava-1.5/ant-build/classes/biojava > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:316: cannot find symbol > [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) > [javac] location: class org.biojava.utils.bytecode.ByteCode > [javac] proxyIV.add(ByteCode.make_checkcast(ourContextC)); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:381: cannot find symbol > [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) > [javac] location: class org.biojava.utils.bytecode.ByteCode > [javac] proxyIV.add(ByteCode.make_checkcast(ourContextC) ); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:451: cannot find symbol > [javac] symbol : variable TYPE_OBJECT > [javac] location: class org.biojava.utils.bytecode.CodeUtils > [javac] CodeClass c_baseClass = CodeUtils.TYPE_OBJECT; > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:462: cannot find symbol > [javac] symbol : variable TYPE_OBJECT > [javac] location: class org.biojava.utils.bytecode.CodeUtils > [javac] = CodeUtils.TYPE_OBJECT.getConstructor(CodeUtils.EMPTY_LIST); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:497: cannot find symbol > [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) > [javac] location: class org.biojava.utils.bytecode.ByteCode > [javac] revTIV.add(ByteCode.make_checkcast(c_FeatureTemplate)); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:507: cannot find symbol > [javac] symbol : method getFields() > [javac] location: interface org.biojava.utils.bytecode.CodeClass > [javac] for(Iterator fi = c_ourTemplate.getFields().iterator(); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:537: cannot find symbol > [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) > [javac] location: class org.biojava.utils.bytecode.ByteCode > [javac] revIV.add(ByteCode.make_checkcast(c_ourTemplate)); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:539: cannot find symbol > [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) > [javac] location: class org.biojava.utils.bytecode.ByteCode > [javac] revIV.add(ByteCode.make_checkcast(c_ourContext)); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:541: cannot find symbol > [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) > [javac] location: class org.biojava.utils.bytecode.ByteCode > [javac] revIV.add(ByteCode.make_checkcast(c_ourTemplate)); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:246: cannot find symbol > [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) > [javac] location: class org.biojava.utils.bytecode.ByteCode > [javac] walkIV.add(ByteCode.make_checkcast(c_ourVisitor)); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:275: cannot find symbol > [javac] symbol : method forMethod(java.lang.reflect.Method) > [javac] location: class org.biojava.utils.bytecode.IntrospectedCodeClass > [javac] CodeMethod m_getChild = IntrospectedCodeClass.forMethod(m); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:293: cannot find symbol > [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) > [javac] location: class org.biojava.utils.bytecode.ByteCode > [javac] wfiv.add(ByteCode.make_checkcast(c_ourType)); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:308: cannot find symbol > [javac] symbol : method make_instanceof(org.biojava.utils.bytecode.CodeClass) > [javac] location: class org.biojava.utils.bytecode.ByteCode > [javac] wrapperIV.add(ByteCode.make_instanceof(c_ourType)); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:339: cannot find symbol > [javac] symbol : method forMethod(java.lang.reflect.Method) > [javac] location: class org.biojava.utils.bytecode.IntrospectedCodeClass > [javac] CodeMethod ourMeth = IntrospectedCodeClass.forMethod(meth); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:345: cannot find symbol > [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) > [javac] location: class org.biojava.utils.bytecode.ByteCode > [javac] bodyIV.add(ByteCode.make_checkcast(c_thisFiltType)); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:354: cannot find symbol > [javac] symbol : method make_instanceof(org.biojava.utils.bytecode.CodeClass) > [javac] location: class org.biojava.utils.bytecode.ByteCode > [javac] walkIV.add(ByteCode.make_instanceof(c_thisFiltType)); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:376: cannot find symbol > [javac] symbol : variable TYPE_OBJECT > [javac] location: class org.biojava.utils.bytecode.CodeUtils > [javac] CodeUtils.TYPE_OBJECT, > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:406: cannot find symbol > [javac] symbol : variable TYPE_OBJECT > [javac] location: class org.biojava.utils.bytecode.CodeUtils > [javac] CodeUtils.TYPE_OBJECT, > [javac] ^ > [javac] Note: Some input files use or override a deprecated API. > [javac] Note: Recompile with -Xlint:deprecation for details. > [javac] 18 errors > > > > BUILD FAILED > /Users/pierre/BioJava1.5-all/biojava-1.5/build.xml:266: Compile failed; see the compiler error output for details. > > Total time: 17 seconds > gwenael-piganeaus-Computer:~/BioJava1.5-all/biojava-1.5 pierre$ ant runtests>tests.txt > > BUILD FAILED > /Users/pierre/BioJava1.5-all/biojava-1.5/build.xml:266: Compile failed; see the compiler error output for details. > > Total time: 11 seconds > > --------------------------------------------------------- > > > What can I do to avoid these errors ? > Thanks. > > Best regards, > > Nicolas Desreumaux > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From markjschreiber at gmail.com Fri Mar 28 09:20:08 2008 From: markjschreiber at gmail.com (Mark Schreiber) Date: Fri, 28 Mar 2008 21:20:08 +0800 Subject: [Biojava-dev] BioJava Install In-Reply-To: <47ECE4CE.8070905@obs-banyuls.fr> References: <47ECE4CE.8070905@obs-banyuls.fr> Message-ID: <93b45ca50803280620s7f53a6fo542e88e65a025b04@mail.gmail.com> Hi = It looks like you are missing the bytecode.jar from your classpath. - Mark On Fri, Mar 28, 2008 at 8:30 PM, nicolas desreumaux wrote: > Dear All, > > > We have a problem to install BioJava on MacOs 10.4 > > > Below errors : > --------------------------------------------------------- > > Buildfile: build.xml > > init: > [echo] Building biojava-1.5 > [echo] Java Home: /System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home > [echo] JUnit present: ${junit.present} > [echo] JUnit supported by Ant: true > [echo] HSQLDB driver present: ${sqlDriver.hsqldb} > [echo] XSLT support: true > > prepare: > > prepare-tests: > > prepare-biojava: > > compile-biojava: > [javac] Compiling 366 source files to /Users/pierre/BioJava1.5-all/biojava-1.5/ant-build/classes/biojava > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:316: cannot find symbol > [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) > [javac] location: class org.biojava.utils.bytecode.ByteCode > [javac] proxyIV.add(ByteCode.make_checkcast(ourContextC)); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:381: cannot find symbol > [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) > [javac] location: class org.biojava.utils.bytecode.ByteCode > [javac] proxyIV.add(ByteCode.make_checkcast(ourContextC) ); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:451: cannot find symbol > [javac] symbol : variable TYPE_OBJECT > [javac] location: class org.biojava.utils.bytecode.CodeUtils > [javac] CodeClass c_baseClass = CodeUtils.TYPE_OBJECT; > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:462: cannot find symbol > [javac] symbol : variable TYPE_OBJECT > [javac] location: class org.biojava.utils.bytecode.CodeUtils > [javac] = CodeUtils.TYPE_OBJECT.getConstructor(CodeUtils.EMPTY_LIST); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:497: cannot find symbol > [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) > [javac] location: class org.biojava.utils.bytecode.ByteCode > [javac] revTIV.add(ByteCode.make_checkcast(c_FeatureTemplate)); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:507: cannot find symbol > [javac] symbol : method getFields() > [javac] location: interface org.biojava.utils.bytecode.CodeClass > [javac] for(Iterator fi = c_ourTemplate.getFields().iterator(); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:537: cannot find symbol > [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) > [javac] location: class org.biojava.utils.bytecode.ByteCode > [javac] revIV.add(ByteCode.make_checkcast(c_ourTemplate)); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:539: cannot find symbol > [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) > [javac] location: class org.biojava.utils.bytecode.ByteCode > [javac] revIV.add(ByteCode.make_checkcast(c_ourContext)); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:541: cannot find symbol > [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) > [javac] location: class org.biojava.utils.bytecode.ByteCode > [javac] revIV.add(ByteCode.make_checkcast(c_ourTemplate)); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:246: cannot find symbol > [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) > [javac] location: class org.biojava.utils.bytecode.ByteCode > [javac] walkIV.add(ByteCode.make_checkcast(c_ourVisitor)); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:275: cannot find symbol > [javac] symbol : method forMethod(java.lang.reflect.Method) > [javac] location: class org.biojava.utils.bytecode.IntrospectedCodeClass > [javac] CodeMethod m_getChild = IntrospectedCodeClass.forMethod(m); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:293: cannot find symbol > [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) > [javac] location: class org.biojava.utils.bytecode.ByteCode > [javac] wfiv.add(ByteCode.make_checkcast(c_ourType)); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:308: cannot find symbol > [javac] symbol : method make_instanceof(org.biojava.utils.bytecode.CodeClass) > [javac] location: class org.biojava.utils.bytecode.ByteCode > [javac] wrapperIV.add(ByteCode.make_instanceof(c_ourType)); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:339: cannot find symbol > [javac] symbol : method forMethod(java.lang.reflect.Method) > [javac] location: class org.biojava.utils.bytecode.IntrospectedCodeClass > [javac] CodeMethod ourMeth = IntrospectedCodeClass.forMethod(meth); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:345: cannot find symbol > [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) > [javac] location: class org.biojava.utils.bytecode.ByteCode > [javac] bodyIV.add(ByteCode.make_checkcast(c_thisFiltType)); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:354: cannot find symbol > [javac] symbol : method make_instanceof(org.biojava.utils.bytecode.CodeClass) > [javac] location: class org.biojava.utils.bytecode.ByteCode > [javac] walkIV.add(ByteCode.make_instanceof(c_thisFiltType)); > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:376: cannot find symbol > [javac] symbol : variable TYPE_OBJECT > [javac] location: class org.biojava.utils.bytecode.CodeUtils > [javac] CodeUtils.TYPE_OBJECT, > [javac] ^ > [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:406: cannot find symbol > [javac] symbol : variable TYPE_OBJECT > [javac] location: class org.biojava.utils.bytecode.CodeUtils > [javac] CodeUtils.TYPE_OBJECT, > [javac] ^ > [javac] Note: Some input files use or override a deprecated API. > [javac] Note: Recompile with -Xlint:deprecation for details. > [javac] 18 errors > > > > BUILD FAILED > /Users/pierre/BioJava1.5-all/biojava-1.5/build.xml:266: Compile failed; see the compiler error output for details. > > Total time: 17 seconds > gwenael-piganeaus-Computer:~/BioJava1.5-all/biojava-1.5 pierre$ ant runtests>tests.txt > > BUILD FAILED > /Users/pierre/BioJava1.5-all/biojava-1.5/build.xml:266: Compile failed; see the compiler error output for details. > > Total time: 11 seconds > > --------------------------------------------------------- > > > What can I do to avoid these errors ? > Thanks. > > Best regards, > > Nicolas Desreumaux > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From nicolas.desreumaux at obs-banyuls.fr Fri Mar 28 09:48:21 2008 From: nicolas.desreumaux at obs-banyuls.fr (nicolas desreumaux) Date: Fri, 28 Mar 2008 13:48:21 -0000 Subject: [Biojava-dev] BioJava Install In-Reply-To: <93b45ca50803280620s7f53a6fo542e88e65a025b04@mail.gmail.com> References: <47ECE4CE.8070905@obs-banyuls.fr> <93b45ca50803280620s7f53a6fo542e88e65a025b04@mail.gmail.com> Message-ID: <47ECF714.5060008@obs-banyuls.fr> Hi Thanks for your answer. bytecode.jar is in my classpath and the other .jar too "export CLASSPATH=/home/thomas/biojava.jar:/home/thomas/bytecode.jar: /home/thomas/commons-cli.jar: /home/thomas/commons-collections-2.1.jar: /home/thomas/commons-dbcp-1.1.jar:/home/thomas/commons-pool-1.1.jar:." $CLASSPATH contains these files. Nicolas Mark Schreiber a ?crit : > Hi = > > It looks like you are missing the bytecode.jar from your classpath. > > - Mark > > On Fri, Mar 28, 2008 at 8:30 PM, nicolas desreumaux > wrote: > >> Dear All, >> >> >> We have a problem to install BioJava on MacOs 10.4 >> >> >> Below errors : >> --------------------------------------------------------- >> >> Buildfile: build.xml >> >> init: >> [echo] Building biojava-1.5 >> [echo] Java Home: /System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home >> [echo] JUnit present: ${junit.present} >> [echo] JUnit supported by Ant: true >> [echo] HSQLDB driver present: ${sqlDriver.hsqldb} >> [echo] XSLT support: true >> >> prepare: >> >> prepare-tests: >> >> prepare-biojava: >> >> compile-biojava: >> [javac] Compiling 366 source files to /Users/pierre/BioJava1.5-all/biojava-1.5/ant-build/classes/biojava >> [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:316: cannot find symbol >> [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) >> [javac] location: class org.biojava.utils.bytecode.ByteCode >> [javac] proxyIV.add(ByteCode.make_checkcast(ourContextC)); >> [javac] ^ >> [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:381: cannot find symbol >> [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) >> [javac] location: class org.biojava.utils.bytecode.ByteCode >> [javac] proxyIV.add(ByteCode.make_checkcast(ourContextC) ); >> [javac] ^ >> [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:451: cannot find symbol >> [javac] symbol : variable TYPE_OBJECT >> [javac] location: class org.biojava.utils.bytecode.CodeUtils >> [javac] CodeClass c_baseClass = CodeUtils.TYPE_OBJECT; >> [javac] ^ >> [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:462: cannot find symbol >> [javac] symbol : variable TYPE_OBJECT >> [javac] location: class org.biojava.utils.bytecode.CodeUtils >> [javac] = CodeUtils.TYPE_OBJECT.getConstructor(CodeUtils.EMPTY_LIST); >> [javac] ^ >> [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:497: cannot find symbol >> [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) >> [javac] location: class org.biojava.utils.bytecode.ByteCode >> [javac] revTIV.add(ByteCode.make_checkcast(c_FeatureTemplate)); >> [javac] ^ >> [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:507: cannot find symbol >> [javac] symbol : method getFields() >> [javac] location: interface org.biojava.utils.bytecode.CodeClass >> [javac] for(Iterator fi = c_ourTemplate.getFields().iterator(); >> [javac] ^ >> [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:537: cannot find symbol >> [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) >> [javac] location: class org.biojava.utils.bytecode.ByteCode >> [javac] revIV.add(ByteCode.make_checkcast(c_ourTemplate)); >> [javac] ^ >> [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:539: cannot find symbol >> [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) >> [javac] location: class org.biojava.utils.bytecode.ByteCode >> [javac] revIV.add(ByteCode.make_checkcast(c_ourContext)); >> [javac] ^ >> [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:541: cannot find symbol >> [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) >> [javac] location: class org.biojava.utils.bytecode.ByteCode >> [javac] revIV.add(ByteCode.make_checkcast(c_ourTemplate)); >> [javac] ^ >> [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:246: cannot find symbol >> [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) >> [javac] location: class org.biojava.utils.bytecode.ByteCode >> [javac] walkIV.add(ByteCode.make_checkcast(c_ourVisitor)); >> [javac] ^ >> [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:275: cannot find symbol >> [javac] symbol : method forMethod(java.lang.reflect.Method) >> [javac] location: class org.biojava.utils.bytecode.IntrospectedCodeClass >> [javac] CodeMethod m_getChild = IntrospectedCodeClass.forMethod(m); >> [javac] ^ >> [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:293: cannot find symbol >> [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) >> [javac] location: class org.biojava.utils.bytecode.ByteCode >> [javac] wfiv.add(ByteCode.make_checkcast(c_ourType)); >> [javac] ^ >> [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:308: cannot find symbol >> [javac] symbol : method make_instanceof(org.biojava.utils.bytecode.CodeClass) >> [javac] location: class org.biojava.utils.bytecode.ByteCode >> [javac] wrapperIV.add(ByteCode.make_instanceof(c_ourType)); >> [javac] ^ >> [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:339: cannot find symbol >> [javac] symbol : method forMethod(java.lang.reflect.Method) >> [javac] location: class org.biojava.utils.bytecode.IntrospectedCodeClass >> [javac] CodeMethod ourMeth = IntrospectedCodeClass.forMethod(meth); >> [javac] ^ >> [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:345: cannot find symbol >> [javac] symbol : method make_checkcast(org.biojava.utils.bytecode.CodeClass) >> [javac] location: class org.biojava.utils.bytecode.ByteCode >> [javac] bodyIV.add(ByteCode.make_checkcast(c_thisFiltType)); >> [javac] ^ >> [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:354: cannot find symbol >> [javac] symbol : method make_instanceof(org.biojava.utils.bytecode.CodeClass) >> [javac] location: class org.biojava.utils.bytecode.ByteCode >> [javac] walkIV.add(ByteCode.make_instanceof(c_thisFiltType)); >> [javac] ^ >> [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:376: cannot find symbol >> [javac] symbol : variable TYPE_OBJECT >> [javac] location: class org.biojava.utils.bytecode.CodeUtils >> [javac] CodeUtils.TYPE_OBJECT, >> [javac] ^ >> [javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:406: cannot find symbol >> [javac] symbol : variable TYPE_OBJECT >> [javac] location: class org.biojava.utils.bytecode.CodeUtils >> [javac] CodeUtils.TYPE_OBJECT, >> [javac] ^ >> [javac] Note: Some input files use or override a deprecated API. >> [javac] Note: Recompile with -Xlint:deprecation for details. >> [javac] 18 errors >> >> >> >> BUILD FAILED >> /Users/pierre/BioJava1.5-all/biojava-1.5/build.xml:266: Compile failed; see the compiler error output for details. >> >> Total time: 17 seconds >> gwenael-piganeaus-Computer:~/BioJava1.5-all/biojava-1.5 pierre$ ant runtests>tests.txt >> >> BUILD FAILED >> /Users/pierre/BioJava1.5-all/biojava-1.5/build.xml:266: Compile failed; see the compiler error output for details. >> >> Total time: 11 seconds >> >> --------------------------------------------------------- >> >> >> What can I do to avoid these errors ? >> Thanks. >> >> Best regards, >> >> Nicolas Desreumaux >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> >> > >