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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