[BioC] zlibbioc on Window -- was: Help installing 'rhdf5' in an "offline" environment

[Wolfgang Huber]

Ole

sounds like a challenging environment.
Did you check the vignette of the zlibbioc package (available from http://www.bioconductor.org/packages/release/bioc/html/zlibbioc.html ) - perhaps you need to go into the configure file zlibbioc/src/zlib-1.2.5/configure and adapt.
And/or, run the configure manually and see where it fails (it looks like the output you posted is truncated / missing important information).
 
Wolfgang







Il giorno Jul 30, 2014, alle ore 6:01 EDT, Ole Rogeberg <ole.rogeberg at gmail.com> ha scritto:

> I would like to install rhdf5 in a secured, Windows-based server
> environment that (for security reasons) cannot access outside servers or
> websites. As the environment is "offline" in this sense, I cannot use the
> recommended procedure involving biocLite.R and the bioconductor repository
> directly for installing the rhdf5 package.
> 
> I can upload specific files to the offline environment, but not install
> software directly myself (lack write-access to the relevant folders on the
> server where software is located). However, the system administrator has
> placed a mirror of CRAN in the "offline" environment, and installing new
> CRAN packages in R is unproblematic.
> 
> For rhdf5 I have tried:
> 
> 1. Install rhdf5 directly: Uploading the rhdf5_2.8.0.tar.gz file and
> installing it from the package manager in RStudio. This gives the message
> that "ERROR: dependency 'zlibbioc' is not available for package 'rhdf5'"
> 
> 2. Installing required packages that rhdf5 relies on: Uploading and
> installing zlibbioc in the same manner. This gives me a warning that "This
> package has a configure script. It probably needs manual configuration" -
> followed by a compilation error (see full R-message here
> <http://screencast.com/t/2bTXvwuZ>).
> 
> I am unable to figure out what the "status 127" error message refers to, or
> if this is even a sensible way to proceed.
> 
> Has anyone got a simple solution that I can implement or (if needed) a more
> technical solution I can forward to my system administrator?
> 
> Sincerely,
> 
> Ole Rogeberg
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor