CODEWITHSUNDEEP
rbioinformaticsbioconductor
G. Aughey
G. Aughey

Reputation: 1

Installing R bioconductor genome package

I've been trying to use a tool called seqplots to analyse some sequencing data. This tool runs through bioconductor and requires installing genome packages. The bioconductor website gives the following installation instructions:

To install this package, start R and enter:

source("https://bioconductor.org/biocLite.R")
biocLite("BSgenome.Dmelanogaster.UCSC.dm6")`

If I enter this in the R terminal I get the following:

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.4 Revised (2016-03-16
r70336).
Installing package(s) ‘BSgenome.Dmelanogaster.UCSC.dm6’
installing the source package ‘BSgenome.Dmelanogaster.UCSC.dm6’

trying URL 'https://bioconductor.org/packages/3.2/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm6_1.4.1.tar.gz'
Content type 'application/x-gzip' length 34147677 bytes (32.6 MB)
downloaded 32.6 MB

'\\icnas4.cc.ic.ac.uk\gaughey'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
* installing *source* package 'BSgenome.Dmelanogaster.UCSC.dm6' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
Warning in library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE) :
  there is no package called 'BSgenome.Dmelanogaster.UCSC.dm6'
Error: loading failed
Execution halted
*** arch - x64
Warning in library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE) :
  there is no package called 'BSgenome.Dmelanogaster.UCSC.dm6'
Error: loading failed
Execution halted
ERROR: loading failed for 'i386', 'x64'
* removing '\\icnas4.cc.ic.ac.uk/gaughey/R/win-library/3.2/BSgenome.Dmelanogaster.UCSC.dm6'

The downloaded source packages are in
    ‘C:\Users\gaughey\AppData\Local\Temp\Rtmpcdmz8E\downloaded_packages’`

I've tried installing other genomes with similar results, and am at a loss as to what to do to resolve this issue. Can anyone help with this? It's very possible that I am overlooking something simple - I am a complete novice with R (or any programming for that matter). I would greatly appreciate any help.

Thanks, Gabriel

Upvotes: 0

Views: 399

Answers (2)

Fábio
Fábio

Reputation: 829

I recommend you should try to run biocLite("BSgenome") and library(BSgenome) (it stores the full genome sequences of a given organism) before try biocLite(pkgs = "BSgenome.Hsapiens.NCBI.GRCh38", dependencies = TRUE).

Upvotes: 0

taniguti
taniguti

Reputation: 38

Seens like is the same problem described here, here and here.

I have no experience on using R in Windows machines, but hope it can help.

Upvotes: 1

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