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

[Christian Arnold]

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