Re: [R] rimage package broken with fedora upgrade

From: John Kornak <john.kornak_at_ucsf.edu>
Date: Mon 01 Jan 2007 - 23:26:45 GMT

Thanks to Jonathan and Oleg for their suggestions/comments. Their responses are added at the end of this email.

I tried Oleg's suggestion of giving me write permissions on /usr/lib/R/library. This didn't seem to work (I tried various combinations of changing permissions and ownership but nothing worked). Anyway, before changing permissions the library would not work when R was fired up as root. I am by no means a linux/unix expert and maybe there is some method of giving me write permissions that would have solved the problem.

Jonathan was right that his was essentially a different problem. I already had fftw2 installed.

My (heavy-handed) solution was to bite the bullet and re-install fedora core 6 from scratch. (Apparently the upgrade from fc3 does not work as well as back up + fresh install.) After running yum update, I then installed R by clicking the relevant R RPM in CRAN. I subsequently installed fftw2 and fftw2-devel (using "yum install package_name") (the development package is needed) and installed rimage using install.packages("rimage") within R and everything is now fine. Note that it is also necessary to install libjpeg and libjpeg-devel if you do not already have it.

I hope that this helps others that want

I am looking forward to playing with Oleg's EBimage package.

Thanks again and Happy New Year to all!

Cheers

John

-- 
John Kornak,PhD
Assistant Professor
Departments of Radiology, and Epidemiology & Biostatistics
University of California, San Francisco
Box 0946
San Francisco, CA 94143
Tel: (415) 353-4740
fax: (415) 353-9423
Email: john.kornak@ucsf.edu



Jonathan Baron wrote:

> Responding to the original post, which I did not save.
>
>> On 31/12/06, John Kornak <john.kornak@ucsf.edu> wrote: >>> >>> Dear R list members >>> >>> I would be grateful if anyone could guide me to a solution for fixing my >>> rimage package problem described below. >>> >>> I recently upgraded my machine from fedora core 3 to fedora core 6 and >>> then upgraded R from version 2.3.1 from version 2.4.1. >>> >>> I then fired up R, tried to load the rimage library and received the >>> following messages: >>> >>> > library(rimage) >>> Error in dyn.load(x, as.logical(local), as.logical(now)) : >>> unable to load shared library >>> '/usr/lib/R/library/rimage/libs/rimage.so': >>> /usr/lib/R/library/rimage/libs/rimage.so: cannot restore segment prot >>> after reloc: Permission denied >>> Error in library(rimage) : .First.lib failed for 'rimage' Jonathan Baron wrote:
>
> I had the same problem, but, unfortunately, a slightly different error
> message. My error message said:
>
>> library(rimage)
> Error in dyn.load(x, as.logical(local), as.logical(now)) :
> unable to load shared library
> '/usr/lib/R/library/rimage/libs/rimage.so':
> libfftw.so.2: cannot open shared object file: No such file or
> directory
> Error in library(rimage) : .First.lib failed for 'rimage'
>
> So I took the hint and said
>
> yum install libfftw.so.2
>
> and this installed libfftw,
> which cured the problem.
>
> But you did not get this error message about libfftw.
>
> Jon
>
Oleg Sklyar wrote: Cannot help you much with that as the thing seems to compile normally. As you use a global R installation, try giving yourself write permissions in /usr/lib/R/library, this might help. Otherwise, try installing R from source in your home or elsewhere where you have all write permissions and check it again. Anyway, I wanted also to advertise my package because you use rimage: http://bioconductor.org/packages/2.0/bioc/html/EBImage.html The difference is - it supports up to 95 image formats and implements many image processing methods. In fact you can combine this with functions from rimage. If interested, go for a development version above and it works on Fedora 6 Zod and 2.4.1 - did try just today. Best regards, Oleg ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Received on Tue Jan 02 10:35:33 2007

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