[Bioc-devel] rtracklayer::import() fails when genome parameter is used
Raymond Cavalcante
rcavalca at umich.edu
Mon Feb 6 16:13:51 CET 2017
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 <rcavalca at 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
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