GenomeInfoDb::Seqinfo() error 404 on the function
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Entering edit mode
@bastienherve-12262
Last seen 4.6 years ago

Hi,

I'm trying to use Seqinfo() function from GenomeInfoDb package, sadly, i got an URL error when I execute the function

I currently use R version 3.3.2 with GenomeInfoDb package version 1.10.2

> library(GenomeInfoDb)
> library(Rsamtools)

> sessionInfo()

R version 3.3.2 (2016-10-31)
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              
 [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] Rsamtools_1.26.1     Biostrings_2.42.1    XVector_0.14.0      
[4] GenomicRanges_1.26.2 GenomeInfoDb_1.10.2  IRanges_2.8.1       
[7] S4Vectors_0.12.1     BiocGenerics_0.20.0 

loaded via a namespace (and not attached):
[1] zlibbioc_1.20.0    tools_3.3.2        BiocParallel_1.8.1 bitops_1.0-6 

> Seqinfo(genome="hg38")
Error in file(file, "rt") : cannot open connection
In addition: Warning message:
In file(file, "rt") :
  URL 'https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_000001405.26.assembly.txt': status was '404 Not Found'

I got the same problem with others genomes like hg19... And yes, my internet connection is on.

When I copy paste the URL in a web browser i got an error, so I think that the link is just broke. I need a work around on this problem. By modifying the URL path ? Using an other function ?

Thanks for your time !

 

 
GenomeInfoDb Seqinfo 404 error • 896 views
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Entering edit mode

Thanks for bringing this up. We're aware of the issue and are currently working on a fix. See

https://stat.ethz.ch/pipermail/bioc-devel/2017-February/010435.html

We'll let you know when the fix is available.

H.

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Entering edit mode
@herve-pages-1542
Last seen 14 hours ago
Seattle, WA, United States

This is fixed now: https://stat.ethz.ch/pipermail/bioc-devel/2017-February/010454.html

Cheers,

H.

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Entering edit mode
@bastienherve-12262
Last seen 4.6 years ago

Works, thank you !

Regards

Bastien

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