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...including bitmap devices and rgl, that we are still working on. Amongst the package issues shown up are - unterminated final lines in src/Makevars[.in] cause failures. - there are many packages which require GNU make and fail to declare it. These include Cairo JavaGD Rcpp RcppExamples RInside farmR highlight phyclust png rJava. - the assumption that 'tar' accepts compressed archives (gdata). - 60-odd C++ -using packages are not correct C++, often because they use GNU extensions or have missing headers (and C++ requires headers for prototypes), or use C99 functions that are not in...

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I'm in the process of converting some S3 methods to S4 methods. I have this function : setGeneric("enrichmentCalc", function(rs, organism, seqLen, ...){standardGeneric("enrichmentCalc")}) setMethod("enrichmentCalc", c("GenomeDataList", "BSgenome"), function(rs, organism, seqLen, ...) { ... ... ... })

...(0.2-3), DEoptim (2.0-4), DescribeDisplay (0.2.2), deSolve (1.7), DiagnosisMed (0.2.3), diffractometry (0.1-02), DoE.base (0.9-17), dplR (1.2.9), dti (0.9-0), dynGraph (0.99100403), e1071 (1.5-23), eha (1.2-18), epitools (0.5-5), estout (1.0.1-1), extracat (1.0-1), extremevalues (2.0), far (0.6-3), farmR (1.1), FD (1.0-7), flashClust (1.00), flexmix (2.2-5), fmri (1.4-0), forensim (1.1-4), FrF2 (1.1), ftsa (1.5), fxregime (1.0-0), GAMens (1.1.1), gcExplorer (0.9-3), GEOmap (1.5-4), GeoXp (1.4.2), GeoXp (1.4.3), ggplot2 (0.8.7), gmt (1.1-4), gRapHD (0.1.6), gRbase (1.3.4), gsDesign (2.2-11), gstat (...