Hi, I noticed that following: > append(DNAStringSet(), list(DNAString("aaaa"), DNAString("catc"))) [[1]] 4-letter "DNAString" instance seq: AAAA [[3A2]] 4-letter "DNAString" instance seq: CATC [[3]] A DNAStringSet instance of length 0 I guess, the last element shouldn't be there -- or not? Regards, Philip P.S.: > sessionInfo() R version 2.11.1 (2010-05-31) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=de_DE.UTF-8 [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicRanges_1.0.7 Biostrings_2.16.9 IRanges_1.6.6 loaded via a namespace (and not attached): [1] Biobase_2.8.0 BSgenome_1.16.2 -- | Philip Kensche <pkensche at="" cmbi.ru.nl=""> | http://www.cmbi.ru.nl/~pkensche | | Center for Molecular and Biomolecular Informatics | http://www2.cmbi.ru.nl | | phone +31 (0)24 36 19693 | fax +31 (0)24 36 19395

On 08/10/2010 03:01 AM, Philip Kensche wrote: > Hi, > > I noticed that following: > >> append(DNAStringSet(), list(DNAString("aaaa"), DNAString("catc"))) > > [[1]] > 4-letter "DNAString" instance > seq: AAAA > > [[3A2]] > 4-letter "DNAString" instance > seq: CATC > > [[3]] > A DNAStringSet instance of length 0 > > I guess, the last element shouldn't be there -- or not? this has to do with what base::append does when the first argument is zero length, > base::append function (x, values, after = length(x)) { lengx <- length(x) if (!after) c(values, x) else if (after >= lengx) c(x, values) else c(x[1L:after], values, x[(after + 1L):lengx]) } <environment: namespace:base=""> which leads to some inconsistent behavior, e.g., dropping zero-length atomic vectors but not other data structures > append(numeric(), list(1)) [[1]] [1] 1 > append(new.env(), list(1)) [[1]] [1] 1 [[2]] <environment: 0x461a508=""> I'm not sure what the reason for this behavior is; I might have expected list(numeric(), 1) in the first case, list(new.env(), 1) in the second. is that '[[3A2]]' in your output correct? It suggests some kind of memory corruption (in R?) but I can't reproduce it. Martin > > > Regards, > > Philip > > > > > P.S.: > > >> sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-pc-linux-gnu > > locale: > [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C > [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=de_DE.UTF-8 > [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GenomicRanges_1.0.7 Biostrings_2.16.9 IRanges_1.6.6 > > loaded via a namespace (and not attached): > [1] Biobase_2.8.0 BSgenome_1.16.2 > > -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793