Hello,
After reverting to the release version of GenomeInfoDb (1.10.2) the error
disappears.
In my defense, disaster is overstating it a bit, especially given the context.
GenomeInfoDb::Seqinfo() has been failing because of changes to the NCBI servers
(and still continues to fail). The devel version was installed to test if an
update from Friday had fixed the problem. Turns out that problem is still
present, but a thread for that is ongoing.
In any event, thanks for the quick reply,
Raymond
> On Feb 6, 2017, at 11:23 AM, Martin Morgan <martin.mor...@roswellpark.org>
> wrote:
>
> 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 <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
>>
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>>
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