Hi J?rn, [cc'ing the mailing list] J?rn Dietrich wrote: > Hi all, > I have the same problem by using the function getSeq() and I am using > the new release of R. > > sessionInfo() R version 2.9.1 (2009-06-26) > x86_64-unknown-linux-gnu > > Does any one have an idea? Unfortunately, some people are still experiencing this problem even after they've upgraded to a recent version of R release/devel. There was definitely a PROTECT/UNPROTECT bug in the reg.finalizer() code, and that bug has been fixed in R release/devel one month ago. After this fix, I did some (light) testing and was not able to get the annoying 'formal argument "envir" matched by multiple actual arguments' error anymore, so I concluded that the issue was solved... Kasper contacted me off-list recently because he was still getting the error. With the details he provided, I was able to isolate another PROTECT/UNPROTECT issue, but this time in the setGeneric/setMethod C code (methods package). I've sent a bug report to R-devel but haven't heard back from them yet: https://stat.ethz.ch/pipermail/r-devel/2009-July/053973.html I'll post here again as soon as I have something new. Thanks for your patience with this issue! Cheers, H. > Best wishes > Joern > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319