[Bioc-devel] GenomeInfoDb::fetchExtendedChromInfoFromUCSC broken again?

[Martin Morgan]

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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