[Bioc-devel] rtracklayer::import() fails when genome parameter is used
Martin Morgan
martin.morgan at roswellpark.org
Mon Feb 6 17:23:39 CET 2017
On 02/06/2017 10:13 AM, Raymond Cavalcante wrote:
> 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”
you have a mixture of 'release' (even-numbered y in x.y.z) and 'devel'
(odd-numbered y in x.y.z) Bioconductor packages, which is a recipe for
disaster. (Well, disaster might be overstating it a bit...). Use
BiocInstaller::biocValid() to sort this out (use
BiocInstaller::biocLite() to manage your packages) and report on whether
this solves your problem.
Martin
>
> 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
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
This email message may contain legally privileged and/or...{{dropped:2}}
More information about the Bioc-devel
mailing list