<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 24 Mar 2015, at 11:24, Josh Moore <<a href="mailto:josh@glencoesoftware.com" class="">josh@glencoesoftware.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Hi José,</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">On Tue, Mar 24, 2015 at 10:59 AM, José Salavert Torres</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class=""><</span><a href="mailto:josator@ebi.ac.uk" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">josator@ebi.ac.uk</a><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">> wrote:</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">Sorry, I can not execute the second command, I do not have root permissions on the OMERO machine.<br class=""></blockquote><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Hmmm....do you have access to the server logs? Can you put us in</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">contact with your server administrator?</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Thanks,</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">~Josh</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">(I had to build and manually install every dependency).<br class=""><br class="">omero admin diagnostics<br class=""><br class="">================================================================================<br class="">OMERO Diagnostics 5.1.0-m2-ice35-SNAPSHOT<br class="">================================================================================<br class=""><br class="">Commands: java -version 1.6.0 (/usr/bin/java)<br class="">Commands: python -V 2.6.6 (/nfs/public/rw/pdbe/mol2cell/software/python2.6-virt-env/bin/python -- 2 others)<br class="">Commands: icegridnode --version 3.5.1 (/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/bin/icegridnode)<br class="">Commands: icegridadmin --version 3.5.1 (/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/bin/icegridadmin)<br class="">Commands: psql --version 8.4.20 (/usr/bin/psql)<br class=""><br class="">Server: icegridnode running<br class="">Server: Blitz-0 active (pid = 4104, enabled)<br class="">Server: DropBox active (pid = 4116, enabled)<br class="">Server: FileServer active (pid = 4123, enabled)<br class="">Server: Indexer-0 active (pid = 4125, enabled)<br class="">Server: MonitorServer active (pid = 4124, enabled)<br class="">Server: OMERO.Glacier2 active (pid = 4126, enabled)<br class="">Server: OMERO.IceStorm inactive (disabled)<br class="">Server: PixelData-0 active (pid = 4129, enabled)<br class="">Server: Processor-0 active (pid = 4127, enabled)<br class="">Server: Tables-0 inactive (disabled)<br class="">Server: TestDropBox inactive (enabled)<br class=""><br class="">Log dir: /nfs/public/rw/pdbe/mol2cell/omero/development/openmicroscopy/dist/var/log exists<br class=""><br class="">Log files: Blitz-0.log 17.0 MB errors=1 warnings=912<br class="">Log files: Blitz-0.log.1 524.0 MB errors=65 warnings=9855<br class="">Log files: Blitz-0.log.2 524.0 MB errors=3900 warnings=6595<br class="">Log files: DropBox.log 41.0 KB errors=20 warnings=19<br class="">Log files: FileServer.log 7.0 KB errors=2 warnings=0<br class="">Log files: Indexer-0.log 2.0 MB errors=162 warnings=590<br class="">Log files: MonitorServer.log 20.0 KB errors=3 warnings=0<br class="">Log files: OMEROweb.log 1.0 MB errors=316 warnings=294<br class="">Log files: OMEROweb_request.log 176.0 KB errors=205 warnings=290<br class="">Log files: PixelData-0.log 419.0 KB errors=23 warnings=290<br class="">Log files: Processor-0.log 109.0 KB errors=46 warnings=30<br class="">Log files: Tables-0.log n/a<br class="">Log files: TestDropBox.log n/a<br class="">Log files: master.err 78.0 KB errors=53 warnings=53<br class="">Log files: master.out 0.0 KB errors=1 warnings=0<br class="">Log files: Total size 1070.65 MB<br class=""><br class=""><br class="">Environment:OMERO_HOME=(unset)<br class="">Environment:OMERO_NODE=(unset)<br class="">Environment:OMERO_MASTER=(unset)<br class="">Environment:OMERO_TEMPDIR=(unset)<br class="">Environment:PATH=/nfs/public/rw/pdbe/mol2cell/software/python2.6-virt-env/bin:/nfs/public/rw/pdbe/mol2cell/software/IMOD/IMOD/bin:/nfs/public/rw/pdbe/mol2cell/software/bin:/nfs/public/rw/pdbe/mol2cell/omero/development/openmicroscopy/dist/bin:/nfs/public/rw/pdbe/mol2cell/software/hdf5-1.8.14-linux-centos6-x86_64-gcc447-shared/bin:/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/bin:/usr/lib64/ccache:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/net/isilonP/public/rw/homes/pdb_em/bin<br class="">Environment:PYTHONPATH=/nfs/public/rw/pdbe/mol2cell/omero/development/openmicroscopy/dist/lib/python:/nfs/public/rw/pdbe/mol2cell/software/python2.6-virt-env/lib/python2.6:/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/python::/net/isilonP/public/rw/homes/pdb_em/python-2.6-libraries<br class="">Environment:ICE_HOME=/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1<br class="">Environment:LD_LIBRARY_PATH=/nfs/public/rw/pdbe/mol2cell/software/IMOD/IMOD/lib:/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/lib64:/nfs/public/rw/pdbe/mol2cell/software/hdf5-1.8.14-linux-centos6-x86_64-gcc447-shared/lib:<br class="">Environment:DYLD_LIBRARY_PATH=/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/lib:<br class=""><br class="">OMERO SSL port:4064<br class="">OMERO TCP port:4063<br class="">OMERO data dir:'/nfs/public/rw/pdbe/mol2cell/omero/development/var/OMERO.data' Exists? True Is writable? True<br class="">OMERO temp dir:'/net/isilonP/public/rw/homes/pdb_em/omero/tmp' Exists? True Is writable? True (Size: 0)<br class=""><br class="">JVM settings: Blitz -Xmx602m -XX:MaxPermSize=512m<br class="">JVM settings: Indexer -Xmx401m -XX:MaxPermSize=512m<br class="">JVM settings: Pixeldata -Xmx602m -XX:MaxPermSize=512m<br class="">JVM settings: Repository -Xmx401m -XX:MaxPermSize=512m<br class=""><br class="">OMERO.web status... [RUNNING] (PID 4375)<br class=""><br class=""><br class=""><br class=""><br class=""><br class=""><blockquote type="cite" class="">On 23 Mar 2015, at 18:54, Josh Moore <<a href="mailto:josh@glencoesoftware.com" class="">josh@glencoesoftware.com</a>> wrote:<br class=""><br class="">Hi José,<br class=""><br class="">On Mon, Mar 23, 2015 at 2:11 PM, José Salavert Torres <<a href="mailto:josator@ebi.ac.uk" class="">josator@ebi.ac.uk</a>> wrote:<br class=""><blockquote type="cite" class="">Dear OMERO users:<br class=""><br class="">I was able to do the import before but now without changing configuration or anything it fails from any machine (even localhost). However Romero insight is working properly. Can you help me?:<br class=""></blockquote>...<br class=""><blockquote type="cite" class="">2015-03-23 10:40:43,444 2219 [ main] ERROR ome.formats.importer.ImportLibrary - Error on import<br class="">java.lang.RuntimeException: Cannot exclusively use the managed repository.<br class=""> at ome.formats.importer.ImportLibrary.checkManagedRepo(ImportLibrary.java:709) ~[blitz.jar:na]<br class=""> at ome.formats.importer.ImportLibrary.createImport(ImportLibrary.java:316) ~[blitz.jar:na]<br class=""> at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:465) ~[blitz.jar:na]<br class=""> at ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:271) ~[blitz.jar:na]<br class=""> at ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:216) [blitz.jar:na]<br class=""> at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:752) [blitz.jar:na]<br class="">2015-03-23 10:40:43,444 2219 [ main] INFO ome.formats.importer.ImportLibrary - Exiting on error<br class=""></blockquote><br class="">This looks like there is some server error. Could you provide use the output of:<br class=""><br class="">$ bin/omero admin diagnostics<br class=""><br class="">as well as:<br class=""><br class=""><br class="">$ bin/omero -s root@localhost fs repos<br class=""><br class="">e.g.<br class=""><br class=""># | Id | UUID | Type | Path<br class="">---+-------+--------------------------------------+---------+-------------------------------------------------------------------<br class="">0 | 17 | ce1e2766-089f-4555-a52a-f75746fd44da | Public |<br class="">/repositories/OMERO-5.0-latest-deploy<br class="">1 | 18 | ScriptRepo | Script |<br class="">/opt/hudson/workspace/OMERO-5.1-merge-deploy/src/dist/lib/scripts<br class="">2 | 10901 | a5a2b4b3-d146-4ccc-98fa-7353a1ba023b | Managed |<br class="">/repositories/OMERO-5.1-merge-deploy/ManagedRepository<br class="">3 | 18651 | 34b38044-0ff6-4019-8f97-4e0093f5a3c3 | Public |<br class="">/repositories/OMERO-5.0-latest-deploy<br class="">4 | 18701 | 640d985e-0ba5-47a6-bacb-42b7cf60354b | Public |<br class="">/repositories/OMERO-5.1-merge-deploy<br class="">(5 rows)<br class=""><br class="">Cheers,<br class="">~Josh<br class="">_______________________________________________<br class="">ome-users mailing list<br class=""><a href="mailto:ome-users@lists.openmicroscopy.org.uk" class="">ome-users@lists.openmicroscopy.org.uk</a><br class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br class=""></blockquote><br class="">_______________________________________________<br class="">ome-users mailing list<br class=""><a href="mailto:ome-users@lists.openmicroscopy.org.uk" class="">ome-users@lists.openmicroscopy.org.uk</a><br class=""><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br class=""></blockquote><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">ome-users mailing list</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">ome-users@lists.openmicroscopy.org.uk</a><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a></div></blockquote></div><br class=""></div></body></html>