See https://stat.ethz.ch/pipermail/bioc-devel/2017-January/010396.html
On 01/31/2017 07:57 AM, Christian Arnold wrote:
Hi,
it appears that in the newest devel version,
fetchExtendedChromInfoFromUCSC is broken (again). I found an earlier
post here:
https://www.mail-archive.com/bioc-devel@r-project.org/msg06193.html,
which however states that this has been fixed already in the previous
version 1.11.2 of the package:
library(GenomeInfoDb)
fetchExtendedChromInfoFromUCSC("mm9")
("mm9")
Error in file(file, "rt") : cannot open connection
In addition: Warning messages:
1: In FUN(genome = names(SUPPORTED_UCSC_GENOMES)[idx], circ_seqs =
supported_genome$circ_seqs, :
NCBI seqlevel was set to NA for mm9 UCSC seqlevel(s) not in the NCBI
assembly: chr1_random, chr3_random, chr4_random, chr5_random, chr7_random,
chr8_random, chr9_random, chr13_random, chr16_random, chr17_random,
chrX_random, chrY_random, chrUn_random
2: In file(file, "rt") :
URL
'https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_000001635.18.assembly.txt':
status was '404 Not Found'
sessionInfo()
R Under development (unstable) (2016-06-30 r70858)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8
LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C
LC_TELEPHONE=C LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
methods base
other attached packages:
[1] GenomeInfoDb_1.11.6 IRanges_2.9.16 S4Vectors_0.13.11
BiocGenerics_0.21.3
loaded via a namespace (and not attached):
[1] tools_3.4.0
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