VisBio

From Keith.Neil at sanofi-aventis.com Fri Dec 1 12:47:19 2006 From: Keith.Neil at sanofi-aventis.com (Keith.Neil at sanofi-aventis.com) Date: Fri, 1 Dec 2006 13:47:19 +0100 Subject: [ome-users] Problem with import from imageJ and problem with Java web start Message-ID: <612A88792104254D8494B330B9B1420E06FE05@TLPW31.f2.enterprise> First, I have this error when I try and import images into a new OME instance from ImageJ: An exception has occurred: org.openmicroscopy.ds.RemoteServerErrorException: error executing RPC `dispatch'. DBD::Pg::st execute failed: ERROR: null value in column "module_execution_id" violates not-null constraint at /usr/lib/perl5/site_perl/5.8.8/OME/Factory.pm line 858 OME::Factory::newObject('OME::Factory=HASH(0xb4cb4d4)', 'OME::SemanticType::__DisplayChannel', 'HASH(0xbbdc810)') called at /usr/lib/perl5/site_perl/5.8.8/OME/Factory.pm line 1022 OME::Factory::newAttribute('OME::Factory=HASH(0xb4cb4d4)', 'OME::SemanticType=HASH(0xaa05b88)', 'undef', 'undef', 'HASH(0xbbdc810)') called at /usr/lib/perl5/site_perl/5.8.8/OME/Remote/DTO/GenericAssembler.pm line 290 OME::Remote::DTO::GenericAssembler::__updateDTO('OME::Remote::DTO::GenericAssembler', 'OME::SemanticType::__DisplayChannel', 'HASH(0xbbdc810)', 'HASH(0xa277ec8)') called at /usr/lib/perl5/site_perl/5.8.8/OME/Remote/DTO/GenericAssembler.pm line 329 OME::Remote::DTO::GenericAssembler::updateDTO('OME::Remote::DTO::GenericAssembler', '@DisplayChannel' , 'HASH(0xbbdc810)') called at /usr/lib/perl5/site_perl/5.8.8/OME/Remote/Facades/GenericFacade.pm line 133 OME::Remote::Facades::GenericFacade::updateObject('OME::Remote::Facades::GenericFacade', '@DisplayChannel' , 'HASH(0xbbdc810)') called at /usr/lib/perl5/site_perl/5.8.8/OME/Remote/Facade.pm line 181 eval {...} called at /usr/lib/perl5/site_perl/5.8.8/OME/Remote/Facade.pm line 175 OME::Remote::Facade::dispatch('OME::Remote::Facade', 'f5333f330b6b334240c9ba28a1e70961', 'updateObject', '@DisplayChannel' , 'HASH(0xbbdc810)') called at /usr/lib/perl5/site_perl/5.8.8/OME/Remote/RPC2.pm line 142 eval {...} called at /usr/lib/perl5/site_perl/5.8.8/OME/Remote/RPC2.pm line 141 OME::Remote::RPC2::serve('OME::Remote::RPC2=HASH(0xb96a9d8)', ' VisBio UW-Madison LOCI A biological visualization tool designed for easy visualization and analysis of multidimensional image data

ome-image=key:f5333f330b6b334240c9ba28a1e70961 at xxx.xx.xx.xxxxx:1

(I edited out the machine name...) Can I put the visbio package on a local machine and alter the java webstart xml to point to this? Any doc to do this? Thanks very much for your help! Keith -------------- next part -------------- An HTML attachment was scrubbed... URL: From ctrueden at wisc.edu Mon Dec 4 19:19:02 2006 From: ctrueden at wisc.edu (Curtis Rueden) Date: Mon, 4 Dec 2006 13:19:02 -0600 Subject: [ome-users] Problem with import from imageJ and problem with Java web start In-Reply-To: <612A88792104254D8494B330B9B1420E06FE05@TLPW31.f2.enterprise> References: <612A88792104254D8494B330B9B1420E06FE05@TLPW31.f2.enterprise> Message-ID: <857a86450612041119q2de0d902t6984f6f034eef7cf@mail.gmail.com> Hi Keith, Sorry to hear of your troubles. Please note that both the ImageJ/OME connectivity and VisBio Web Start support are somewhat in flux right now, and currently being actively developed to be more robust. We expect to have a better VisBio JWS link by version 2.6.1, and are nearly done fixing some known problems with the Java remote interface to OME. In the meantime, though, both of these features have significant problems. > First, I have this error when I try and import images into a new OME > instance from ImageJ: I tested the currently released version of the OME Plugin for ImageJ with the latest version of OME from CVS, on my Ubuntu Dapper system with DBD::Pg 1.43 installed, and was able to upload an image successfully. You are running OME 2.6.0rc3, right? And what version of DBD::Pg are you using? Some of the versions past 1.43 are known to be incompatible with OME. > Second, > > I have a problem running the Visbio program using the java web start within > our proxy firewall, the test applications work ok after entering the > firewall proxy user + password. Both OME 2.6.0rc3 has an old Web Start configuration for VisBio hardcoded in. The simplest way to fix this is to change the source code of OME/src/perl2/OME/Web/VisBio.pm to match the new configuration (see http://www.loci.wisc.edu/visbio/jws/visbio.jnlp for the current configuration). The OME 2.6.0 final release will match the current VisBio configuration, but still be hardcoded. We are also evaluating how to make the VisBio link more robust for the next release, OME 2.6.1. We will probably provide an extra level of indirection in the JNLP generation (calling a perl script that lives on the LOCI server to do so), and we may also bundle a version of VisBio with the OME release as a fallback, or even the default. > Can I put the visbio package on a local machine and alter the java webstart > xml to point to this? Any doc to do this? Yes, it should be fairly straightforward. Just change the VisBio.pm file to your liking, and put the necessary JAR files on your own server. You can copy them from the LOCI server if you wish, or get the code from the Subversion repository (third-party JARs are in there, and the LOCI code can be compiled from source using ant). The only trick if you don't copy them from the LOCI server's jws folder directly is: the JARs must be signed using the jarsigner tool. Feel free to email me with any questions about configuring VisBio and OME for Web Start, and I can point you in the right direction. -Curtis On 12/1/06, Keith.Neil at sanofi-aventis.com wrote: > > > > > First, I have this error when I try and import images into a new OME > instance from ImageJ: > > An exception has occurred: > org.openmicroscopy.ds.RemoteServerErrorException: error > executing RPC `dispatch'. > DBD::Pg::st execute failed: ERROR: null value in column > "module_execution_id" violates not-null constraint > at /usr/lib/perl5/site_perl/5.8.8/OME/Factory.pm line 858 > OME::Factory::newObject('OME::Factory=HASH(0xb4cb4d4)', > 'OME::SemanticType::__DisplayChannel', 'HASH(0xbbdc810)') > called at /usr/lib/perl5/site_perl/5.8.8/OME/Factory.pm > line 1022 > OME::Factory::newAttribute('OME::Factory=HASH(0xb4cb4d4)', > 'OME::SemanticType=HASH(0xaa05b88)', 'undef', 'undef', > 'HASH(0xbbdc810)') called at > /usr/lib/perl5/site_perl/5.8.8/OME/Remote/DTO/GenericAssembler.pm > line 290 > OME::Remote::DTO::GenericAssembler::__updateDTO('OME::Remote::DTO::GenericAssembler', > 'OME::SemanticType::__DisplayChannel', 'HASH(0xbbdc810)', > 'HASH(0xa277ec8)') called at > /usr/lib/perl5/site_perl/5.8.8/OME/Remote/DTO/GenericAssembler.pm > line 329 > OME::Remote::DTO::GenericAssembler::updateDTO('OME::Remote::DTO::GenericAssembler', > '@DisplayChannel', 'HASH(0xbbdc810)') called at > /usr/lib/perl5/site_perl/5.8.8/OME/Remote/Facades/GenericFacade.pm > line 133 > OME::Remote::Facades::GenericFacade::updateObject('OME::Remote::Facades::GenericFacade', > '@DisplayChannel', 'HASH(0xbbdc810)') called at > /usr/lib/perl5/site_perl/5.8.8/OME/Remote/Facade.pm line > 181 > eval {...} called at > /usr/lib/perl5/site_perl/5.8.8/OME/Remote/Facade.pm line > 175 > OME::Remote::Facade::dispatch('OME::Remote::Facade', > 'f5333f330b6b334240c9ba28a1e70961', 'updateObject', > '@DisplayChannel', 'HASH(0xbbdc810)') called at > /usr/lib/perl5/site_perl/5.8.8/OME/Remote/RPC2.pm line 142 > eval {...} called at > /usr/lib/perl5/site_perl/5.8.8/OME/Remote/RPC2.pm line 141 > OME::Remote::RPC2::serve('OME::Remote::RPC2=HASH(0xb96a9d8)', > ' encoding="ISO-8859-1"?> /usr/lib/perl5/site_perl/5.8.8/OME/Remote/Apache2/XMLRPC.pm > line 31 > OME::Remote::Apache2::XMLRPC::handler('Apache2::RequestRec=SCALAR(0xbb05100)') > called at -e line 0 > eval {...} called at -e line 0 > > > Second, > > I have a problem running the Visbio program using the java web start within > our proxy firewall, the test applications work ok after entering the > firewall proxy user + password. The Visbio program generates the following > exception:JNLPException[category: Erreur de t?l?chargement : Exception: > java.io.IOException: HTTP response 404 : LaunchDesc: null ] > at > com.sun.javaws.cache.DownloadProtocol.doDownload(Unknown > Source) > at > com.sun.javaws.cache.DownloadProtocol.getDownloadSize(Unknown > Source) > at com.sun.javaws.LaunchDownload.downloadJarFiles(Unknown > Source) > at > com.sun.javaws.LaunchDownload.downloadEagerorAll(Unknown > Source) > at com.sun.javaws.Launcher.downloadResources(Unknown > Source) > at com.sun.javaws.Launcher.handleApplicationDesc(Unknown > Source) > at com.sun.javaws.Launcher.handleLaunchFile(Unknown > Source) > at com.sun.javaws.Launcher.run(Unknown Source) > at java.lang.Thread.run(Unknown Source) > > > Une erreur est survenue au cours du lancement ou de l'ex?cution de > l'application. > > Titre : VisBio > Fournisseur : UW-Madison LOCI > Cat?gorie : Erreur de t?l?chargement > > Impossible de charger la ressource : > http://www.loci.wisc.edu/visbio/jws/bio_formats.jar > > > > > spec="1.0+" > codebase="http://www.loci.wisc.edu/visbio/jws"> > > VisBio > UW-Madison LOCI > href="http://www.loci.wisc.edu/visbio/index.html"/> > A biological visualization tool designed for easy > visualization and analysis of multidimensional image > data > > > > > > > > > > > > > > > > > > > > > > > ome-image=key:f5333f330b6b334240c9ba28a1e70961 at xxx.xx.xx.xxxxx:1 > > > > > (I edited out the machine name...) > > Can I put the visbio package on a local machine and alter the java webstart > xml to point to this? Any doc to do this? > > > > Thanks very much for your help! > > > > Keith > _______________________________________________ > ome-users mailing list > ome-users at lists.openmicroscopy.org.uk > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users > > > From igg at nih.gov Thu Dec 7 17:36:04 2006 From: igg at nih.gov (Ilya Goldberg) Date: Thu, 7 Dec 2006 12:36:04 -0500 Subject: [ome-users] OME 2.6.0 Release Message-ID: The OME development team is proud to announce the official release of OME 2.6.0! Download for generic UNIX: http://cvs.openmicroscopy.org.uk/snapshots/ome-2.6.0.tar.gz Or, a graphical installation wizard for OS X (universal native PPC/ Intel): http://cvs.openmicroscopy.org.uk/snapshots/ome-installer-2.6.0.dmg The OS X installer includes all software dependencies for both architectures, so its a large (~40 Mb) download. Thanks to all who contributed, and helped us test the release candidates! We will be updating our website (http://openmicroscopy.org) in the next day or so to reflect this new official release. The major changes in this release (with respect to OME 2.4.0) were in the web interface, access control, and connectivity with other applications. Reports indicate that this release is also much easier to install than OME 2.4.0. The web interface was revamped to make it entirely HTML template- based. The templates are indexed by the DB, so each user can have their own collection of templates to view specific types or collections of information. Since templates are mostly just HTML, the user interface can be changed without having to program. The UI allows switching templates on the fly with a drop-down menu. Access to objects is now controlled through provenance instead of containership. That's a fancy way to say that objects are now owned by those who crated them rather than by those who own the objects they're contained in. The other way was not only more convoluted to say, it lead to many more inconsistencies. Two-way integration with Excel (OME-Excel.xls) allows populating spreadsheets directly from a live OME server using a VisualBasic library included in src/Excel/OME-Excel.xls. A spreadsheet importer allows bulk annotation of images as well as populating generic structured data - either from native Excel documents or tab-delimited text files. Connectivity with Matlab is much improved and more robust. Images managed by OME can be accessed from matlab using matlab's imread() function. Extensive testing and validation of OME Analysis Modules implemented as functions in matlab (i.e. ".m" files). Most matlab functions can be used unchanged both in "pure matlab" and in OME (with appropriate XML wrappers). Among other features included: * Better VisBio support. * Guest access. * Encryption of passwords in transit over http. * Graphical OS X Installation "Wizard". * More robust, easier installation on supported platforms. * Substantially improved latency and performance for remote access. * A simplified URL-based API to get OME data as tab-delimited text tables (basis for OME-Excel.xls). * Improved import format support * Simplified and more robust data curation: Deletion of images, datasets, users and module execution results with the ome commander * New web and command-line wizards make it easy to convert spreadsheets into structured OME annotation * More useable and flexible 3+4 D segmentation with FindSpots. * Integrated on-line help! Anticipated major features in our next release - 2.6.1: * Integration with LDAP (Thanks to Mike McCaughey of Vanderbilt) * Integration with LOCI's BioFormats (adds support for tons of new image types) * Improvements to integration with LOCI's VisBio * Better (slightly) security over http to prevent some forms of session stealing. * Allow use of pre-compiled MATLAB modules (i.e. without a MATLAB license). * Robust distributed image analysis over many network-connected "nodes". Much of this functionality is already in CVS (HEAD), so we anticipate this release will be in early 2007. Enjoy! From imagesincho at gmail.com Mon Dec 11 01:49:35 2006 From: imagesincho at gmail.com (InCho Chong) Date: Sun, 10 Dec 2006 17:49:35 -0800 Subject: [ome-users] Image File import issues Message-ID: <83f3579e0612101749n7d87c02an45238ce884d69ee1@mail.gmail.com> We have started with some basic image import at the hosiptal and found following errors trying to import TIF images: 8-bit single channel TIF or TIFF files Browser: IMPORT screen lists files in /OME/ome_images ADD TO QUEUE is OK IMPORT FILES gives following error Died at /usr/lib/perl5/site_perl/5.8.5/OME/Image/Server.pm line 414. Command Line: [user_name at ome ome_images]$ ome import test.tiff Importing files 1/4: [IN PROGRESS] Starting import Died at /usr/lib/perl5/site_perl/5.8.5/OME/Image/Server.pm line 414. Exiting... Exiting... [user_name at ome ome_images]$ ome import -d "test" test.tiff Importing files 1/4: [IN PROGRESS] Starting import Died at /usr/lib/perl5/site_perl/5.8.5/OME/Image/Server.pm line 414. Exiting... Exiting... [user_name at ome ome_images]$ Please help. we are not sure why this import is failing. Is there some specific parameters for the data image import? Thanks, -- -InCho From imagesincho at gmail.com Wed Dec 13 06:54:56 2006 From: imagesincho at gmail.com (InCho Chong) Date: Tue, 12 Dec 2006 22:54:56 -0800 Subject: [ome-users] Image File import issues In-Reply-To: <83f3579e0612101749n7d87c02an45238ce884d69ee1@mail.gmail.com> References: <83f3579e0612101749n7d87c02an45238ce884d69ee1@mail.gmail.com> Message-ID: <83f3579e0612122254l356478b6p7d3e8862e67b82b5@mail.gmail.com> This may be caused more by the re-installation of OME to correct server name change. When I restart httpd, I am getting following error. [root at ome init.d]# ./httpd restart Stopping httpd: [ OK ] Starting httpd: [Tue Dec 12 22:53:02 2006] [warn] The ScriptAlias directive in /OME/conf/httpd1.99.omeis.conf at line 2 will probably never match because it overlaps an earlier ScriptAlias. Use of uninitialized value in concatenation (.) or string at /usr/lib/perl5/site_perl/5.8.5/OME/Install/ApacheConfigTask.pm line 75. Processing OME-startup.pl Tring to get a session as the Apache user... Pre-loading SemanticTypes... WARNING: Explicit deletion of OME::Session at /OME/conf/OME-startup.pl line 76 OME::Session __destroySession: $self->__destroySession(); at /OME/conf/OME-startup.pl line 76 Pre-loading classes for OME::Web... Thanks, InCho On 12/10/06, InCho Chong wrote: > We have started with some basic image import at the hosiptal and found > following errors trying to import TIF images: > > 8-bit single channel TIF or TIFF files > > Browser: > > IMPORT screen lists files in /OME/ome_images ADD TO QUEUE is OK IMPORT > FILES gives following error Died at > /usr/lib/perl5/site_perl/5.8.5/OME/Image/Server.pm line 414. > > Command Line: > [user_name at ome ome_images]$ ome import test.tiff Importing files > 1/4: [IN PROGRESS] Starting import Died at > /usr/lib/perl5/site_perl/5.8.5/OME/Image/Server.pm line 414. > Exiting... > Exiting... > [user_name at ome ome_images]$ ome import -d "test" test.tiff Importing files > 1/4: [IN PROGRESS] Starting import Died at > /usr/lib/perl5/site_perl/5.8.5/OME/Image/Server.pm line 414. > Exiting... > Exiting... > [user_name at ome ome_images]$ > > Please help. we are not sure why this import is failing. Is there > some specific parameters for the data image import? > > Thanks, > -- > > -InCho > From igg at nih.gov Thu Dec 14 17:51:17 2006 From: igg at nih.gov (Ilya Goldberg) Date: Thu, 14 Dec 2006 12:51:17 -0500 Subject: [ome-users] Image File import issues In-Reply-To: <83f3579e0612101749n7d87c02an45238ce884d69ee1@mail.gmail.com> References: <83f3579e0612101749n7d87c02an45238ce884d69ee1@mail.gmail.com> Message-ID: It looks like the error originated with the image server (omeis). More detailed errors are in the Apache error log (usually /var/log/ httpd/error_log). Are you using the 2.6.0 release? -Ilya On Dec 10, 2006, at 8:49 PM, InCho Chong wrote: > We have started with some basic image import at the hosiptal and found > following errors trying to import TIF images: > > 8-bit single channel TIF or TIFF files > > Browser: > > IMPORT screen lists files in /OME/ome_images ADD TO QUEUE is OK IMPORT > FILES gives following error Died at > /usr/lib/perl5/site_perl/5.8.5/OME/Image/Server.pm line 414. > > Command Line: > [user_name at ome ome_images]$ ome import test.tiff Importing files > 1/4: [IN PROGRESS] Starting import Died at > /usr/lib/perl5/site_perl/5.8.5/OME/Image/Server.pm line 414. > Exiting... > Exiting... > [user_name at ome ome_images]$ ome import -d "test" test.tiff > Importing files > 1/4: [IN PROGRESS] Starting import Died at > /usr/lib/perl5/site_perl/5.8.5/OME/Image/Server.pm line 414. > Exiting... > Exiting... > [user_name at ome ome_images]$ > > Please help. we are not sure why this import is failing. Is there > some specific parameters for the data image import? > > Thanks, > -- > > -InCho > _______________________________________________ > ome-users mailing list > ome-users at lists.openmicroscopy.org.uk > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users > From igg at nih.gov Fri Dec 15 16:22:16 2006 From: igg at nih.gov (Ilya Goldberg) Date: Fri, 15 Dec 2006 11:22:16 -0500 Subject: [ome-users] Image File import issues In-Reply-To: <83f3579e0612122254l356478b6p7d3e8862e67b82b5@mail.gmail.com> References: <83f3579e0612101749n7d87c02an45238ce884d69ee1@mail.gmail.com> <83f3579e0612122254l356478b6p7d3e8862e67b82b5@mail.gmail.com> Message-ID: A likely problem is that you appear to be using mod_perl 1.99 with Apache 2. You should upgrade mod_perl or down-grade both mod_perl and Apache. mod_perl-1.99 with Apache 2 is unstable. The messages reported by the startup script look to be OK, but you will have nothing but trouble with your current mod_perl/Apache configuration. -Ilya On Dec 13, 2006, at 1:54 AM, InCho Chong wrote: > This may be caused more by the re-installation of OME to correct > server name change. > > When I restart httpd, I am getting following error. > > [root at ome init.d]# ./httpd restart > Stopping httpd: [ OK ] > Starting httpd: [Tue Dec 12 22:53:02 2006] [warn] The ScriptAlias > directive in /OME/conf/httpd1.99.omeis.conf at line 2 will probably > never match because it overlaps an earlier ScriptAlias. > Use of uninitialized value in concatenation (.) or string at > /usr/lib/perl5/site_perl/5.8.5/OME/Install/ApacheConfigTask.pm line > 75. > Processing OME-startup.pl > Tring to get a session as the Apache user... > Pre-loading SemanticTypes... > WARNING: Explicit deletion of OME::Session at /OME/conf/OME- > startup.pl line 76 > OME::Session __destroySession: $self->__destroySession(); > at /OME/conf/OME-startup.pl line 76 > Pre-loading classes for OME::Web... > > Thanks, > InCho > > On 12/10/06, InCho Chong wrote: >> We have started with some basic image import at the hosiptal and >> found >> following errors trying to import TIF images: >> >> 8-bit single channel TIF or TIFF files >> >> Browser: >> >> IMPORT screen lists files in /OME/ome_images ADD TO QUEUE is OK >> IMPORT >> FILES gives following error Died at >> /usr/lib/perl5/site_perl/5.8.5/OME/Image/Server.pm line 414. >> >> Command Line: >> [user_name at ome ome_images]$ ome import test.tiff Importing files >> 1/4: [IN PROGRESS] Starting import Died at >> /usr/lib/perl5/site_perl/5.8.5/OME/Image/Server.pm line 414. >> Exiting... >> Exiting... >> [user_name at ome ome_images]$ ome import -d "test" test.tiff >> Importing files >> 1/4: [IN PROGRESS] Starting import Died at >> /usr/lib/perl5/site_perl/5.8.5/OME/Image/Server.pm line 414. >> Exiting... >> Exiting... >> [user_name at ome ome_images]$ >> >> Please help. we are not sure why this import is failing. Is there >> some specific parameters for the data image import? >> >> Thanks, >> -- >> >> -InCho >> > _______________________________________________ > ome-users mailing list > ome-users at lists.openmicroscopy.org.uk > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users > From jatb86 at gmail.com Wed Dec 20 14:52:44 2006 From: jatb86 at gmail.com (Javier Tibau) Date: Wed, 20 Dec 2006 09:52:44 -0500 Subject: [ome-users] cvs install Message-ID: I lost my id_dsa files so now I can't connect to the cvs server. The problem is I suspect there's something wrong with the anonymous cvs download. When I downloaded as an authenticated user I could install with no problem. Now (anoncvs download) I get some problems with automake/autoconf. automake version: 1.9.6 autoconf version: 2.59 This is my binary builds: **************************************************************************************************************************************** USING C CONFIGURE SCRIPT -- './configure --prefix=/OME --with-omeis-root=/OME/OMEIS' SUCCESS -- OUTPUT: "checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking whether make sets $(MAKE)... yes checking for working aclocal-1.4... missing checking for working autoconf... found checking for working automake-1.4... missing checking for working autoheader... found checking for working makeinfo... missing checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether make sets $(MAKE)... (cached) yes checking for ranlib... ranlib configure: using OMEIS root... /OME/OMEIS configure: using OMEIS JPEG quality default... 80 checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 checking for _LARGE_FILES value needed for large files... no checking for BZ2_bzDecompress in -lbz2... yes checking how to run the C preprocessor... gcc -E checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking bzlib.h usability... yes checking bzlib.h presence... yes checking for bzlib.h... yes checking for png_init_io in -lpng... yes checking png.h usability... yes checking png.h presence... yes checking for png.h... yes checking for jpeg_start_compress in -ljpeg... yes checking jpeglib.h usability... yes checking jpeglib.h presence... yes checking for jpeglib.h... yes checking for TIFFReadScanline in -ltiff... yes checking tiffio.h usability... yes checking tiffio.h presence... yes checking for tiffio.h... yes checking if ssl is wanted... yes OpenSSL found in /usr checking if zlib is wanted... yes checking for inflateEnd in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for inflateEnd in -lz... (cached) yes checking zlib in /usr... ok checking for compat version of Berkeley DB... /usr/include/db_185.h checking for Berkeley DB usability... yes checking for LZW encoder in -ltiff... yes checking for ANSI C header files... (cached) yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for off_t... yes checking for size_t... yes checking for void *... yes checking size of void *... 4 checking for int... yes checking size of int... 4 checking for long... yes checking size of long... 4 checking for long long int... yes checking size of long long int... 8 configure: using off_t format string... "lld" configure: using OID format string... "llu" checking for stdlib.h... (cached) yes checking for unistd.h.. . (cached) yes checking for getpagesize... yes checking for working mmap... yes checking for vprintf... yes checking for _doprnt... no checking for mkdir... yes checking for socket... yes checking for strdup... yes checking for strerror... yes checking for strstr... yes configure: creating ./config.status config.status: creating Makefile config.status: creating zoom/Makefile config.status: creating zoom/lib/Makefile config.status: creating t/Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing default-1 commands " COMPILING MODULE -- 'make' FAILURE -- OUTPUT: "make all-recursive make[1]: Entering directory `/home/jtibau/Projects/OME/src/C/omeis' Making all in zoom make[2]: Entering directory `/home/jtibau/Projects/OME/src/C/omeis/zoom' Making all in lib make[3]: Entering directory `/home/jtibau/Projects/OME/src/C/omeis/zoom/lib' gcc -DHAVE_CONFIG_H -I. -I. -I../.. -DOMEIS_ROOT=\"/OME/OMEIS\" -I../include -I/usr/include/libxml2 -I/usr/include -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c window.c gcc -DHAVE_CONFIG_H -I. -I. -I../.. -DOMEIS_ROOT=\"/OME/OMEIS\" -I../include -I/usr/include/libxml2 -I/usr/include -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c pic.c gcc -DHAVE_CONFIG_H -I. -I. -I../.. -DOMEIS_ROOT=\"/OME/OMEIS\" -I../include -I/usr/include/libxml2 -I/usr/include -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c pic_file.c gcc -DHAVE_CONFIG_H -I. -I. -I../.. -DOMEIS_ROOT=\"/OME/OMEIS\" -I../include -I/usr/include/libxml2 -I/usr/include -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c pic_all.c gcc -DHAVE_CONFIG_H -I. -I. -I../.. -DOMEIS_ROOT=\"/OME/OMEIS\" -I../include -I/usr/include/libxml2 -I/usr/include -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c swap.c gcc -DHAVE_CONFIG_H -I. -I. -I../.. -DOMEIS_ROOT=\"/OME/OMEIS\" -I../include -I/usr/include/libxml2 -I/usr/include -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c tiff.c gcc -DHAVE_CONFIG_H -I. -I. -I../.. -DOMEIS_ROOT=\"/OME/OMEIS\" -I../include -I/usr/include/libxml2 -I/usr/include -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c jpeg.c gcc -DHAVE_CONFIG_H -I. -I. -I../.. -DOMEIS_ROOT=\"/OME/OMEIS\" -I../include -I/usr/include/libxml2 -I/usr/include -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c png.c gcc -DHAVE_CONFIG_H -I. -I. -I../.. -DOMEIS_ROOT=\"/OME/OMEIS\" -I../include -I/usr/include/libxml2 -I/usr/include -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c omeis.c rm -f libpic.a ar cru libpic.a window.o pic.o pic_file.o pic_all.o swap.o tiff.o jpeg.o png.o omeis.o ranlib libpic.a gcc -DHAVE_CONFIG_H -I. -I. -I../.. -DOMEIS_ROOT=\"/OME/OMEIS\" -I../include -I/usr/include/libxml2 -I/usr/include -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c zoom.c gcc -DHAVE_CONFIG_H -I. -I. -I../.. -DOMEIS_ROOT=\"/OME/OMEIS\" -I../include -I/usr/include/libxml2 -I/usr/include -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c scanline.c scanline.c : In function 'scanline_zero': scanline.c:98: warning: incompatible implicit declaration of built-in function 'bzero' gcc -DHAVE_CONFIG_H -I. -I. -I../.. -DOMEIS_ROOT=\"/OME/OMEIS\" -I../include -I/usr/include/libxml2 -I/usr/include -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c filt.c rm -f libzoom.a ar cru libzoom.a zoom.o scanline.o filt.o ranlib libzoom.a make[3]: Leaving directory `/home/jtibau/Projects/OME/src/C/omeis/zoom/lib' make[3]: Entering directory `/home/jtibau/Projects/OME/src/C/omeis/zoom' make[3]: Nothing to be done for `all-am'. make[3]: Leaving directory `/home/jtibau/Projects/OME/src/C/omeis/zoom' make[2]: Leaving directory `/home/jtibau/Projects/OME/src/C/omeis/zoom' Making all in t make[2]: Entering directory `/home/jtibau/Projects/OME/src/C/omeis/t' gcc -DHAVE_CONFIG_H -I. -I. -I.. -DOMEIS_ROOT=\"/OME/OMEIS\" -I../zoom/include -I/usr/include/libxml2 -I/usr/include -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c test-concurrent-write.c gcc -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -L/usr/lib -L/usr/lib -ldb -o test-concurrent-write test-concurrent-write.o -L/usr/lib -lxml2 -lz -lm ../zoom/lib/libzoom.a ../zoom/lib/libpic.a -lz -ltiff -ljpeg -lpng -lbz2 -lssl -lcrypto test-concurrent-write.o: In function `main':/home/jtibau/Projects/OME/src/C/omeis/t/test-concurrent-write.c:82: undefined reference to `OMEIS_ClearError' :/home/jtibau/Projects/OME/src/C/omeis/t/test-concurrent-write.c :88: undefined reference to `NewPixels' :/home/jtibau/Projects/OME/src/C/omeis/t/test-concurrent-write.c:101: undefined reference to `DoPixelIO' :/home/jtibau/Projects/OME/src/C/omeis/t/test-concurrent-write.c :109: undefined reference to `FinishPixels' :/home/jtibau/Projects/OME/src/C/omeis/t/test-concurrent-write.c:117: undefined reference to `freePixelsRep' :/home/jtibau/Projects/OME/src/C/omeis/t/test-concurrent-write.c :110: undefined reference to `OMEIS_ReportError' :/home/jtibau/Projects/OME/src/C/omeis/t/test-concurrent-write.c:102: undefined reference to `OMEIS_ReportError' :/home/jtibau/Projects/OME/src/C/omeis/t/test- concurrent-write.c:65: undefined reference to `OMEIS_ReportError' collect2: ld returned 1 exit status make[2]: *** [test-concurrent-write] Error 1 make[2]: Leaving directory `/home/jtibau/Projects/OME/src/C/omeis/t' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/jtibau/Projects/OME/src/C/omeis' make: *** [all-recursive-am] Error 2 " **************************************************************************************************************************************** First of all at the beginning it looks like it's searching for automake-1.4. I've tried using that version and get pretty much the same undefined reference errors at the end. I'm using ubuntu dapper. I can install from the tarball too w/o problems. Any hints? -- Javier Tibau Research Assistant Center of Vision and Robotics (CVR) ESPOL Guayaquil - Ecuador website: www.cvr.espol.edu.ec -------------- next part -------------- An HTML attachment was scrubbed... URL: