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Entering edit mode
@npantelireis16-14851
Last seen 3.3 years ago

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,  :
installation path not writeable, unable to update packages: MASS, mgcv, rpart
Old packages: 'GenomicRanges'
Update all/some/none? [a/s/n]: n

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Entering edit mode
Mike Smith ★ 5.0k
@mike-smith
Last seen 10 hours ago
EMBL Heidelberg / de.NBI

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I don't know why biocLite() would try to find an out-of-date version, perhaps you were just very unlucky with the timing.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')
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Entering edit mode
@npantelireis16-14851
Last seen 3.3 years ago

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