Oops, I got so caught up in the setting up the code I forgot to say what the error was:
Error in match.arg(pruning.mode) : 'arg' should be one of “error”, “coarse”, “fine”, “tidy” Thanks again, Raymond > On Feb 6, 2017, at 10:10 AM, Raymond Cavalcante <rcava...@umich.edu> wrote: > > Hello, > > Perhaps this is related to problems in GenomeInfoDb::Seqinfo() and NCBI > server file structure changes, but rtracklayer::import() is failing when I > specify a genome. > > See below for example code. > > Thanks, > Raymond Cavalcante > > library(annotatr) > > # These fail > file = system.file('extdata', 'test_BED3.bed', package = 'annotatr') > r = annotatr::read_regions(con = file, format = 'bed', genome ='hg19') > gr = rtracklayer::import(con = file, format = 'bed', genome='hg19') > > # These succeed > file = system.file('extdata', 'test_BED3.bed', package = 'annotatr') > r = annotatr::read_regions(con = file, format = 'bed') > gr = rtracklayer::import(con = file, format = 'bed') > > My devtools::session_info() is: > > Session info > ------------------------------------------------------------------- > setting value > version R version 3.3.2 (2016-10-31) > system x86_64, darwin16.1.0 > ui unknown > language (EN) > collate en_US.UTF-8 > tz America/Detroit > date 2017-02-06 > > Packages > ----------------------------------------------------------------------- > package * version date > AnnotationDbi 1.36.1 2017-01-27 > AnnotationHub 2.6.4 2017-01-27 > annotatr * 1.1.7 2017-01-27 > assertthat 0.1 2013-12-06 > Biobase 2.34.0 2016-11-16 > BiocGenerics 0.20.0 2016-11-16 > BiocInstaller 1.24.0 2016-11-16 > BiocParallel 1.8.1 2016-11-16 > biomaRt 2.30.0 2016-11-16 > Biostrings 2.42.1 2017-01-27 > bitops 1.0-6 2013-08-17 > BSgenome 1.42.0 2016-11-16 > colorspace 1.3-1 2016-11-18 > DBI 0.5-1 2016-09-10 > devtools 1.12.0 2016-12-05 > digest 0.6.10 2016-08-02 > dplyr 0.5.0 2016-06-24 > GenomeInfoDb 1.11.7 2017-02-04 > GenomicAlignments 1.10.0 2016-11-16 > GenomicFeatures 1.26.2 2017-01-27 > GenomicRanges 1.26.2 2017-01-27 > ggplot2 2.2.1 2016-12-30 > gtable 0.2.0 2016-02-26 > htmltools 0.3.5 2016-03-21 > httpuv 1.3.3 2015-08-04 > httr 1.2.1 2016-07-03 > interactiveDisplayBase 1.12.0 2016-11-16 > IRanges 2.8.1 2017-01-27 > lattice 0.20-34 2016-09-06 > lazyeval 0.2.0 2016-06-12 > magrittr 1.5 2014-11-22 > Matrix 1.2-8 2017-01-20 > memoise 1.0.0 2016-01-29 > mime 0.5 2016-07-07 > munsell 0.4.3 2016-02-13 > org.Dm.eg.db 3.4.0 2016-11-16 > org.Hs.eg.db 3.4.0 2016-11-16 > org.Mm.eg.db 3.4.0 2016-11-16 > org.Rn.eg.db 3.4.0 2016-11-16 > plyr 1.8.4 2016-06-08 > R6 2.2.0 2016-10-05 > Rcpp 0.12.9 2017-01-14 > RCurl 1.95-4.8 2016-03-01 > readr 1.0.0 2016-08-03 > regioneR 1.6.0 2017-01-27 > reshape2 1.4.2 2016-10-22 > Rsamtools 1.26.1 2016-11-16 > RSQLite 1.1-2 2017-01-08 > rtracklayer 1.34.1 2016-11-16 > S4Vectors 0.12.1 2017-01-26 > scales 0.4.1 2016-11-09 > shiny 0.14.2 2016-11-01 > stringi 1.1.2 2016-10-01 > stringr 1.1.0 2016-08-19 > SummarizedExperiment 1.4.0 2016-11-16 > tibble 1.2 2016-08-26 > TxDb.Dmelanogaster.UCSC.dm3.ensGene 3.2.2 2016-11-16 > TxDb.Dmelanogaster.UCSC.dm6.ensGene 3.3.0 2016-11-16 > TxDb.Hsapiens.UCSC.hg19.knownGene 3.2.2 2016-11-16 > TxDb.Hsapiens.UCSC.hg38.knownGene 3.4.0 2016-11-16 > TxDb.Mmusculus.UCSC.mm10.knownGene 3.4.0 2016-11-16 > TxDb.Mmusculus.UCSC.mm9.knownGene 3.2.2 2016-11-16 > TxDb.Rnorvegicus.UCSC.rn4.ensGene 3.2.2 2016-11-16 > TxDb.Rnorvegicus.UCSC.rn5.refGene 3.4.0 2016-11-16 > TxDb.Rnorvegicus.UCSC.rn6.refGene 3.4.0 2016-11-16 > withr 1.0.2 2016-06-20 > XML 3.98-1.5 2016-11-10 > xtable 1.8-2 2016-02-05 > XVector 0.14.0 2016-11-16 > yaml 2.1.14 2016-11-12 > zlibbioc 1.20.0 2016-11-16 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel