Grokbase Groups R r-devel March 2010
FAQ
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

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  • Prof Brian Ripley at Mar 3, 2010 at 8:40 am

    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
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    --
    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

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