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Question: rhdf5 package fails to install
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gravatar for trombe.piju
2.1 years ago by
Sweden
trombe.piju0 wrote:

Hi,

I am having a problem when trying to install the rhdf5 package. My R release is 3.1.2 which is running on a Linux system.

My code is the following:

rm(list = ls())
download.file("http://bioconductor.org/biocLite.R", destfile = "biocLite.R")
source("biocLite.R")
biocLite("rhdf5")

and here is the installation report:

BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.5), R version 3.1.2.
Installing package(s) 'rhdf5'
trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/rhdf5_2.10.0.tar.gz'
Content type 'application/x-gzip' length 5355635 bytes (5.1 Mb)
opened URL

downloaded 5678 bytes

Error in readBin(con, "raw", n = 512L) : 
  negative length vectors are not allowed

Do you have a fix for this problem?

Best Regards,

Pierre-Julien

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by trombe.piju0
1

You are not installing rhdf5 in the recommended way. See its landing page for the recommended way. It's also recommended to upgrade to R-3.2 and Bioconductor 3.2. 

I'm just guessing but does your institution have a proxy or firewall?

 

 

ADD REPLYlink written 2.1 years ago by Dan Tenenbaum ♦♦ 8.2k

Yes, my institution has a proxy and firewall...

I tried to install the package the recommended way but I get the same error message. As for upgrading R, I asked but it may take some time before our IT guys grant me the permission to do so.

Anyway, thanks for the help Dan!

ADD REPLYlink written 2.1 years ago by trombe.piju0
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