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Question: BiomaRT URLs down? 404 Not Found
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gravatar for n.pantelireis16
4 months ago by
n.pantelireis160 wrote:

New to R so I may be making some very remedial mistake here. However I've been having trouble installing biomaRt onto my version of R 3.4.3 on my local windows computer. 

I've tried to install using bioconductor but it seems to have an issue with URL stating 404 Not Found in the text output.

Hope someone can point me in right direction here. 

Cheers

source ("http://bioconductor.org/biocLite.R")

biocLite("biomaRt") 

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.3 (2017-11-30).
Installing package(s) ‘biomaRt’
trying URL 'https://bioconductor.org/packages/3.6/bioc/bin/windows/contrib/3.4/biomaRt_2.34.1.zip'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'https://bioconductor.org/packages/3.6/bioc/bin/windows/contrib/3.4/biomaRt_2.34.1.zip'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'https://bioconductor.org/packages/3.6/bioc/bin/windows/contrib/3.4/biomaRt_2.34.1.zip': HTTP status was '404 Not Found'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘biomaRt’ failed
installation path not writeable, unable to update packages: MASS, mgcv, rpart
Old packages: 'GenomicRanges'
Update all/some/none? [a/s/n]: n

 

ADD COMMENTlink modified 3 months ago • written 4 months ago by n.pantelireis160
2
gravatar for Mike Smith
4 months ago by
Mike Smith2.7k
EMBL Heidelberg / de.NBI
Mike Smith2.7k wrote:

biomaRt updated to version 2.34.2 in the last few days, and so the version reported in your message is no longer available.  If I run the command in the same version of R I get:

Installing package(s) ‘biomaRt’
trying URL 'https://bioconductor.org/packages/3.6/bioc/bin/windows/contrib/3.4/biomaRt_2.34.2.zip'

I don't know why biocLite() would try to find an out-of-date version, perhaps you were just very unlucky with the timing.  I would suggest giving it another try now, and reporting back here if you're still experiencing problems.

You can also be really explicit and give biocLite() the complete path to the zip file, but this is not normally necessary e.g.

library(BiocInstaller)
biocLite('https://bioconductor.org/packages/3.6/bioc/bin/windows/contrib/3.4/biomaRt_2.34.2.zip')
ADD COMMENTlink modified 4 months ago • written 4 months ago by Mike Smith2.7k
0
gravatar for n.pantelireis16
3 months ago by
n.pantelireis160 wrote:

Thanks Mike! 

I tried the normal install using biocLite("biomaRt) again, it's still trying to access the old URL. 

However, I used the command you recommended specifiying the path and it seems to installed it without a problem. 

Thank you very much!

Best,

Nick

ADD COMMENTlink written 3 months ago by n.pantelireis160
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