Question: annotate incompatible with RdbiPgSQL !?!
10.1 years ago by
Philip Lijnzaad • 160
Philip Lijnzaad • 160 wrote:
Dear all, I took a while to 'solve' the following problem. I need to use both RdbiPgSQL and geneplotter. The latter loads, directly or indirectly, all of annotate AnnotationDbi DBI RSQLite xtable lattice I used to have an old version of annotate that I didn't bother upgrading and worked fine. I recently did however, resulting in the indirect loading of DBI. This, in turn, is incompatible with Rdbi, resulting in connection errors: Error in function (classes, fdef, mtable) : unable to find an inherited method for function "dbConnect", for signature "PgSQL" I solved it by first library()-ing DBI, then Rdbi and RdbiPgSQL. However, I don't think this is very satisfactory. The ordering of libary() statements should be irrelevant and secondly, if I would just like to plot a few genes, it is overkill to also load complete database connection code. Would a dependency "Suggests: DBI etc." , rather than "Depends: DBI etc." not be more than enough for the annotate package? Kind regards, Philip -- Philip Lijnzaad, PhD Holstege Genomics Laboratory Dept. of Biomedical Genetics University Medical Center (UMC), Utrecht Stratenum room 2.211 (on Mondays and Thursdays not in after 15.00) MSN chat (*NOT* email): email@example.com P.O. Box 85060, 3508 AB Utrecht (Universiteitsweg 100, 3584 CG Utrecht) The Netherlands tel: +31 (0)8875 68464 fax: +31 (0)8875 68479 [[alternative HTML version deleted]]
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