Hej Bioc! When I want to get the alphabetByCycle for an AAStringSet, I get "Error in alphabetByCycle(aa) : unknown class ?AAString?". Here is a toy example: > aa <- AAStringSet(c("ARN","DCQ")) > aa A AAStringSet instance of length 2 width seq [1] 3 ARN [2] 3 DCQ > alphabetByCycle(aa) Error in alphabetByCycle(aa) : unknown class ?AAString' My sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=C [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] RColorBrewer_1.0-5 ShortRead_1.20.0 Rsamtools_1.14.2 lattice_0.20-24 GenomicRanges_1.14.0 Biostrings_2.30.0 [7] XVector_0.2.0 IRanges_1.20.0 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] Biobase_2.22.0 bitops_1.0-6 grid_3.0.2 hwriter_1.3 latticeExtra_0.6-26 stats4_3.0.2 [7] tools_3.0.2 zlibbioc_1.8.0 Cheers, Nico --------------------------------------------------------------- Nicolas Delhomme Nathaniel Street Lab Department of Plant Physiology Ume? Plant Science Center Tel: +46 90 786 7989 Email: nicolas.delhomme at plantphys.umu.se SLU - Ume? universitet Ume? S-901 87 Sweden

On 12/17/2013 04:11 AM, Nicolas Delhomme wrote: > Hej Bioc! > > When I want to get the alphabetByCycle for an AAStringSet, I get "Error in alphabetByCycle(aa) : unknown class ?AAString?". > this is enabled in ShortRead 1.21.8, thanks Nico. Martin > Here is a toy example: >> aa <- AAStringSet(c("ARN","DCQ")) >> aa > A AAStringSet instance of length 2 > width seq > [1] 3 ARN > [2] 3 DCQ >> alphabetByCycle(aa) > Error in alphabetByCycle(aa) : unknown class ?AAString' > > My sessionInfo() > > R version 3.0.2 (2013-09-25) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=C > [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] RColorBrewer_1.0-5 ShortRead_1.20.0 Rsamtools_1.14.2 lattice_0.20-24 GenomicRanges_1.14.0 Biostrings_2.30.0 > [7] XVector_0.2.0 IRanges_1.20.0 BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] Biobase_2.22.0 bitops_1.0-6 grid_3.0.2 hwriter_1.3 latticeExtra_0.6-26 stats4_3.0.2 > [7] tools_3.0.2 zlibbioc_1.8.0 > > Cheers, > > Nico > > --------------------------------------------------------------- > Nicolas Delhomme > > Nathaniel Street Lab > Department of Plant Physiology > Ume? Plant Science Center > > Tel: +46 90 786 7989 > Email: nicolas.delhomme at plantphys.umu.se > SLU - Ume? universitet > Ume? S-901 87 Sweden > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- 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