James MacDonald <jmacdon at="" med.umich.edu=""> writes: > Hi Sebastian, > > I don't know if there is a method to check for mis-matched packages, but > there is a simple way to update your packages so in truth there should > be no need for such checking. Beyond Jim's suggestions, there isn't much users can do. However, package developers can add specific version requirements to the packages listed in the Depends field of their DESCRIPTION file. This will then generate an error if the package is loaded and the wrong version of a dependency is installed. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user/

Hi Seth, Would it be worth to put a check in biocLite.R or create a similar script that users could run to check for a version mismatch for a BioC release? If you have it output the results of sessionInfo() and put in the FAQ to run it before asking a question, it could help solve the problem. Francois > Beyond Jim's suggestions, there isn't much users can do. However, > package developers can add specific version requirements to the > packages listed in the Depends field of their DESCRIPTION file. This > will then generate an error if the package is loaded and the wrong > version of a dependency is installed. > > + seth >

Hi, Seth Falcon wrote: >> I don't know if there is a method to check for mis-matched packages, but >> there is a simple way to update your packages so in truth there should >> be no need for such checking. > > Beyond Jim's suggestions, there isn't much users can do. However, > package developers can add specific version requirements to the > packages listed in the Depends field of their DESCRIPTION file. This > will then generate an error if the package is loaded and the wrong > version of a dependency is installed. Thanks to you both for your explanations. Updating everything as suggested by James did work as well. However, I guess as the annotation packages being used by gcrma() are loaded in a dynamic manner and packages for other species have different versions (?) this static dependency check via the DESCRIPTION file won't work? In an application one would try to catch the problem at run time in order to give the user a meaningful error message. Especially, if a new version depends on a feature not available in previous versions. But I don't know this is worth the effort here. Ciao, Sebastian