rhdf5 package fails to install
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Entering edit mode
@trombepiju-8987
Last seen 5.9 years ago
Sweden

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

rhdf5 hdf5 • 2.8k views
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Entering edit mode

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?

 

 

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Entering edit mode

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!

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