R devel - Mar 2010 - Installation problem with 2.10 and Solaris 10 (PR#14227)

Full_Name: John Noble
Version: 2.10
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.  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.  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

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

  Thanks, john noble
  VCU 
  jnoble at vcu.edu

  Solaris 10, SPARC

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)
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