From ripley at stats.ox.ac.uk  Wed Mar  3 09:40:58 2010
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Wed, 3 Mar 2010 08:40:58 +0000 (GMT)
Subject: [Rd] Installation problem with 2.10 and Solaris 10 (PR#14227)
In-Reply-To: <20100302213508.93193282EF29@mail.pubhealth.ku.dk>
References: <20100302213508.93193282EF29@mail.pubhealth.ku.dk>
Message-ID: <alpine.LFD.2.00.1003030806000.11176@gannet.stats.ox.ac.uk>

On Tue, 2 Mar 2010, jnoble at vcu.edu wrote:

> Full_Name: John Noble
> Version: 2.10

There is no such version of R (see the posting guide for the need for 
accurate reporting of version numbers).  In 2.10.1, the unpacking is 
usually done by either by

tar xf

or

gzip -dc | tar xf

so the behaviour of gzip -d without -c is not relevant.

As R 2.10.0 and 2.10.1 have been built on many Solaris 10 systems, by 
far the most likely issue is a configuration problem on yours.

One possible workaround (not needed on our Solaris boxes) is to set 
the environment variable TAR to a GNU version of tar that supports 
unpacking compressed archives directly: R will then call that tar.

> OS: Solaris 10 SPARC
> Submission from: (NULL) (128.172.190.27)
>
>
>
>  The make of Recommended fails.  All sections of Make work up to 
> this point and the compiled version of R appears to be correct. 
> Only when adding the recommended modules does the problem appear.

Do you mean the 'recommended packages': there are 'modules' and that 
is not what is being installed at this stage?

> The best I can figure the problem appears to be related to the fact 
> that gzip will not decompress linked files without the "-f" option.

Not the whole story ... but what version of gzip is this?

> Sample output follows:
>
> # make
> make[1]: Entering directory `/home/jnoble/R-2.10.1/src/library/Recommended'
> begin installing recommended package boot
> ERROR: cannot extract package from 'boot.tgz'
> make[1]: *** [boot.ts] Error 1
> make[1]: Leaving directory `/home/jnoble/R-2.10.1/src/library/Recommended'
> make: *** [recommended-packages] Error 2
>
>  The boot.ts.out file contains:
>
> # more boot.ts.out
>  ERROR: cannot extract package from 'boot.tgz'
>
>  If I try to run the command that the Makefile appears to be running
> by hand I get the following:
>
> # ../../../bin/R CMD INSTALL -l "../../../library" boot.tgz
>  ERROR: cannot extract package from 'boot.tgz'
>
> Oddly, the following happens with the latest gzip:
>
> gzip -d boot.tgz
> gzip: boot.tgz: Number of symbolic links encountered during path name traversal
> exceeds MAXSYMLINKS

That is as expected, but where did you get the idea that gzip -d is 
used in that fashion?  The most likely command used,

gzip -dc boot.tgz | tar xf -

works for e.g. gzip 1.3.5 (which is what our Solaris 10 system has in 
/usr/bin) and 1.3.12.

>  This can be corrected with the "-f" option but I can't pass that into "R".

Actually, you can: the gzip command used is set by R_GZIPCMD.  But 
you do not want to here.

>
>  Thanks, john noble
>  VCU
>  jnoble at vcu.edu
>
>  Solaris 10, SPARC
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595



[Rd] Installation problem with 2.10 and Solaris 10 (PR#14227)
Prof Brian Ripley