Posted by Peter Carr on Thursday, September 18, 2014 at 04:52PM
Changes to Startup Env Impact R Modules on Broad Hosted Servers: As a result of the software update on August 14, we modified the startup environment for the server. This was necessary because the server now requires Java 7. It was previously using Java 6. Surprisingly, this necessitated a change to the R configuration. You may notice slight changes to the behavior of your R modules. For example, the ATLANTISInputs module failed with this error message:
/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_3.0.2/lib64/R/bin/exec/R: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
The workaround is to change the command line for your R modules to use the preferred command line substitution parameter. For example, for an R 3.0 module use <R3.0_Rscript>. For an R 2.15 module use <R2.15_Rscript>. Please contact us for further assistance. Thanks! Originally posted on gpbroad at 4pm on Monday Aug 25
Posted by GenePattern Team on Wednesday, July 23, 2014 at 12:56PM
GenePattern downtime 7/25 - 7/28: Because of systems maintenance at the Broad, the following job queue interruptions will take place between 5 PM on Friday, July 25 and 10 AM Monday, July 28.
5 PM Friday, July 25 - The job queue will be suspended. All new job submissions will remain PENDING until after the system maintenance period. This should allow most running jobs to complete before the system shutdown on Monday
8 AM Monday, July 28 - All running jobs will be terminated, unceremoniously.
8 AM Monday, July 28 - The GenePattern server will be shut down for system maintenance.
approximately 10 AM Monday, July 28 - The GenePattern server will resume normal operations.
Please feel free to contact us if you have any questions or concerns
Visualizers have been fixed for Java 7 - read our blog for more information
Improved the performance of large uploads via the Files tab
Size and date of uploaded files are now visible in the Files tab
Full details about 3.8.2, including hardware/software requirements and known issues can be found in our release notes.
We are continuting to work on updates to our documentation which reflect the latest version of GenePattern. That being said, do let us know if you find anything to be out of date. We'll be happy to provide you with up-to-date information right away and update the page as soon as possible.