Question

Can't install RBGL

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Entering edit mode

chris.strickland • 0

@chrisstrickland-8706

Last seen 8.6 years ago

India

Hi,

I am trying to install the library RBGL. I followed the instructions on http://www.bioconductor.org/packages/release/bioc/html/RBGL.html.

Here is my R console output

source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.0 (BiocInstaller 1.16.5), ?biocLite for help
A new version of Bioconductor is available after installing the most recent version of R; see http://bioconductor.org/install
> biocLite("RBGL")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.5), R version 3.1.0.
Installing package(s) 'RBGL'
trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.1/RBGL_1.42.0.zip'
Content type 'application/zip' length 3132860 bytes (3.0 Mb)
opened URL
downloaded 2.5 Mb

Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
cannot open the connection
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
downloaded length 2610324 != reported length 3132860
2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
cannot open compressed file 'RBGL/DESCRIPTION', probable reason 'No such file or directory'
>

If anybody knows the solution for this could you please let me know.

Thanks,
Chris.

installation • 1.2k views

ADD COMMENT • link 8.6 years ago chris.strickland • 0

0

Entering edit mode

First of all, I am really surprised that the line

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

worked for you in R-3.1.0. Support for https in source() and related commands was just added recently; when I tried it in R-3.1.0 it failed. Do you have a non-default setting for the download.file.method option? What is the result of

getOption("download.file.method")

?

Secondly, I can't reproduce this problem. Does just trying the biocLite() command again fix the problem?

Sometimes errors like this indicate that you are behind a restrictive firewall or proxy. Do you know if that is the case?

You might try setting the download.file.method option to different values (get the possible values from the relevant section of ?options) and then trying the biocLite() command again.

ADD REPLY • link 8.6 years ago Dan Tenenbaum ★ 8.2k

score 0 · Answer 1 · 2015-08-26

I get,

> getOption("download.file.method")
NULL

"Sometimes errors like this indicate that you are behind a restrictive firewall or proxy. Do you know if that is the case?"

This is likely, although I am able to install other software packages, from the CRAN repository.

OK, I worked it out. I had to change mirrors. using chooseBioCmirror()

I tried the Seattle mirror first (it was number 1). I tried biocLite("RBGL") again and it failed again. I then switched to the Australian mirror and biocLite("RBGL") worked.

Thanks for the help.

Chris.