FAQ
Dear list,

I've just installed R-2.2.0 under Solaris and have a question about
installing packages. If a package fails to install for any reason and I go
to install another package, I get this message:

$ R-2.2.0-64bit --vanilla CMD INSTALL ~/srca/cran/RSQLite_0.4-0.tar.gz
ERROR: failed to lock directory
'/app/openpkg/lib/R-2.2.0-64bit/lib/R/library' for modifying
Try removing '/app/openpkg/lib/R-2.2.0-64bit/lib/R/library/00LOCK'

I can remove the lock directory by hand, and then the next package installs,
but this makes it quite difficult to download and install a batch of
packages from CRAN or Biocondctor! Is this lock directory a new feature with
R-2.2.0? Is there a work around in the R build itself or the installation
scripts?

Much thanks!!!
---------------------
David P Dean
Research Informatics
PGRD Groton Labs
(860)-441-5053
david.p.dean at pfizer.com
----------------------------------------------------------------------
LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}}

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  • Uwe Ligges at Oct 13, 2005 at 3:12 pm

    Dean, David P wrote:

    Dear list,

    I've just installed R-2.2.0 under Solaris and have a question about
    installing packages. If a package fails to install for any reason and I go
    to install another package, I get this message:

    $ R-2.2.0-64bit --vanilla CMD INSTALL ~/srca/cran/RSQLite_0.4-0.tar.gz
    ERROR: failed to lock directory
    '/app/openpkg/lib/R-2.2.0-64bit/lib/R/library' for modifying
    Try removing '/app/openpkg/lib/R-2.2.0-64bit/lib/R/library/00LOCK'

    I can remove the lock directory by hand, and then the next package installs,
    but this makes it quite difficult to download and install a batch of
    packages from CRAN or Biocondctor! Is this lock directory a new feature with
    R-2.2.0? Is there a work around in the R build itself or the installation
    scripts?
    No, not a new feature in R-2.2.0, it has been there for some time now.
    After a *successful* installation, the 00LOCK directory should be
    deleted by the installation tools themselves.
    After an unsuccessful installation, the installation tools should
    restore the stuff in the 00LOCK directory.
    Do you abort the installtion manually (this is the only way I figured
    out how not to remove 00LOCK automatically)?

    Uwe Ligges


    Much thanks!!!
    ---------------------
    David P Dean
    Research Informatics
    PGRD Groton Labs
    (860)-441-5053
    david.p.dean at pfizer.com
    ----------------------------------------------------------------------
    LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}}

    ______________________________________________
    R-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/r-devel
  • Paul Gilbert at Oct 13, 2005 at 3:19 pm

    Uwe Ligges wrote:
    Dean, David P wrote:


    Dear list,

    I've just installed R-2.2.0 under Solaris and have a question about
    installing packages. If a package fails to install for any reason and I go
    to install another package, I get this message:

    $ R-2.2.0-64bit --vanilla CMD INSTALL ~/srca/cran/RSQLite_0.4-0.tar.gz
    ERROR: failed to lock directory
    '/app/openpkg/lib/R-2.2.0-64bit/lib/R/library' for modifying
    Try removing '/app/openpkg/lib/R-2.2.0-64bit/lib/R/library/00LOCK'

    I can remove the lock directory by hand, and then the next package installs,
    but this makes it quite difficult to download and install a batch of
    packages from CRAN or Biocondctor! Is this lock directory a new feature with
    R-2.2.0? Is there a work around in the R build itself or the installation
    scripts?
    No, not a new feature in R-2.2.0, it has been there for some time now.
    I have the impression the feature behaves slightly differently as of
    R-2.2.0. Now the 00LOCK file is not removed in Solaris when there is an
    unsuccessful install. (In Linux I think it does get removed.)

    Paul Gilbert
    After a *successful* installation, the 00LOCK directory should be
    deleted by the installation tools themselves.
    After an unsuccessful installation, the installation tools should
    restore the stuff in the 00LOCK directory.
    Do you abort the installtion manually (this is the only way I figured
    out how not to remove 00LOCK automatically)?

    Uwe Ligges




    Much thanks!!!
    ---------------------
    David P Dean
    Research Informatics
    PGRD Groton Labs
    (860)-441-5053
    david.p.dean at pfizer.com
    ----------------------------------------------------------------------
    LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}}

    ______________________________________________
    R-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/r-devel
    ______________________________________________
    R-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/r-devel
  • Uwe Ligges at Oct 13, 2005 at 3:31 pm

    Paul Gilbert wrote:

    Uwe Ligges wrote:
    Dean, David P wrote:


    Dear list,

    I've just installed R-2.2.0 under Solaris and have a question about
    installing packages. If a package fails to install for any reason and
    I go
    to install another package, I get this message:

    $ R-2.2.0-64bit --vanilla CMD INSTALL
    ~/srca/cran/RSQLite_0.4-0.tar.gz ERROR: failed to lock directory
    '/app/openpkg/lib/R-2.2.0-64bit/lib/R/library' for modifying
    Try removing '/app/openpkg/lib/R-2.2.0-64bit/lib/R/library/00LOCK'

    I can remove the lock directory by hand, and then the next package
    installs,
    but this makes it quite difficult to download and install a batch of
    packages from CRAN or Biocondctor! Is this lock directory a new
    feature with
    R-2.2.0? Is there a work around in the R build itself or the
    installation
    scripts?

    No, not a new feature in R-2.2.0, it has been there for some time now.
    I have the impression the feature behaves slightly differently as of
    R-2.2.0. Now the 00LOCK file is not removed in Solaris when there is an
    unsuccessful install. (In Linux I think it does get removed.)
    Yes, under both Linux and Windows it is removed.

    Can anybody else check on Solaris, please? Or can David Dean debug on
    his machine?

    In particular, we need exact system information, because it seems to be
    an OS/platform specific problem.

    Uwe Ligges



    Paul Gilbert
    After a *successful* installation, the 00LOCK directory should be
    deleted by the installation tools themselves.
    After an unsuccessful installation, the installation tools should
    restore the stuff in the 00LOCK directory.
    Do you abort the installtion manually (this is the only way I figured
    out how not to remove 00LOCK automatically)?

    Uwe Ligges




    Much thanks!!!
    --------------------- David P Dean
    Research Informatics
    PGRD Groton Labs
    (860)-441-5053
    david.p.dean at pfizer.com
    ----------------------------------------------------------------------
    LEGAL NOTICE\ Unless expressly stated otherwise, this
    messag...{{dropped}}

    ______________________________________________
    R-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/r-devel

    ______________________________________________
    R-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/r-devel
  • Prof Brian Ripley at Oct 13, 2005 at 3:42 pm
    It works on Solaris 8 for me, and this is checked as part of the
    alpha/beta process.

    The code is the same on Linux and Solaris, after all, so this would have
    to be a Solaris shell bug.
    On Thu, 13 Oct 2005, Uwe Ligges wrote:

    Paul Gilbert wrote:

    Uwe Ligges wrote:
    Dean, David P wrote:


    Dear list,

    I've just installed R-2.2.0 under Solaris and have a question about
    installing packages. If a package fails to install for any reason and
    I go
    to install another package, I get this message:

    $ R-2.2.0-64bit --vanilla CMD INSTALL
    ~/srca/cran/RSQLite_0.4-0.tar.gz ERROR: failed to lock directory
    '/app/openpkg/lib/R-2.2.0-64bit/lib/R/library' for modifying
    Try removing '/app/openpkg/lib/R-2.2.0-64bit/lib/R/library/00LOCK'

    I can remove the lock directory by hand, and then the next package
    installs,
    but this makes it quite difficult to download and install a batch of
    packages from CRAN or Biocondctor! Is this lock directory a new
    feature with
    R-2.2.0? Is there a work around in the R build itself or the
    installation
    scripts?

    No, not a new feature in R-2.2.0, it has been there for some time now.
    I have the impression the feature behaves slightly differently as of
    R-2.2.0. Now the 00LOCK file is not removed in Solaris when there is an
    unsuccessful install. (In Linux I think it does get removed.)
    Yes, under both Linux and Windows it is removed.

    Can anybody else check on Solaris, please? Or can David Dean debug on
    his machine?

    In particular, we need exact system information, because it seems to be
    an OS/platform specific problem.

    Uwe Ligges



    Paul Gilbert
    After a *successful* installation, the 00LOCK directory should be
    deleted by the installation tools themselves.
    After an unsuccessful installation, the installation tools should
    restore the stuff in the 00LOCK directory.
    Do you abort the installtion manually (this is the only way I figured
    out how not to remove 00LOCK automatically)?

    Uwe Ligges




    Much thanks!!!
    --------------------- David P Dean
    Research Informatics
    PGRD Groton Labs
    (860)-441-5053
    david.p.dean at pfizer.com
    ----------------------------------------------------------------------
    LEGAL NOTICE\ Unless expressly stated otherwise, this
    messag...{{dropped}}

    ______________________________________________
    R-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/r-devel

    ______________________________________________
    R-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/r-devel
    ______________________________________________
    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
  • Dean, David P at Oct 13, 2005 at 4:02 pm

    From: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk]
    Sent: Thursday, October 13, 2005 11:42 AM
    To: Uwe Ligges
    Cc: Paul Gilbert; r-devel at r-project.org; Dean, David P
    Subject: Re: [Rd] Installing R-2.2.0 package

    It works on Solaris 8 for me, and this is checked as part of the
    alpha/beta process.

    The code is the same on Linux and Solaris, after all, so this would have
    to be a Solaris shell bug.
    I'm on Solaris 8 as well. R is compiled for 64-bits, but I wouldn't expect
    that to be a factor. R was built and is run in an environment created with
    OpenPKG and containing GNU equivalents to many utilities -- so it's not a
    stock Solaris setup.

    I'm not familiar with R internals but will be happy to try to debug if I
    can. Does the installer call out to the shell somehow? Where would I start
    to look for the relevant code?

    Thanks!
    David Dean
    On Thu, 13 Oct 2005, Uwe Ligges wrote:

    Paul Gilbert wrote:

    Uwe Ligges wrote:
    Dean, David P wrote:


    Dear list,

    I've just installed R-2.2.0 under Solaris and have a question about
    installing packages. If a package fails to install for any reason and
    I go
    to install another package, I get this message:

    $ R-2.2.0-64bit --vanilla CMD INSTALL
    ~/srca/cran/RSQLite_0.4-0.tar.gz ERROR: failed to lock directory
    '/app/openpkg/lib/R-2.2.0-64bit/lib/R/library' for modifying
    Try removing '/app/openpkg/lib/R-2.2.0-64bit/lib/R/library/00LOCK'

    I can remove the lock directory by hand, and then the next package
    installs,
    but this makes it quite difficult to download and install a batch of
    packages from CRAN or Biocondctor! Is this lock directory a new
    feature with
    R-2.2.0? Is there a work around in the R build itself or the
    installation
    scripts?

    No, not a new feature in R-2.2.0, it has been there for some time now.
    I have the impression the feature behaves slightly differently as of
    R-2.2.0. Now the 00LOCK file is not removed in Solaris when there is an
    unsuccessful install. (In Linux I think it does get removed.)
    Yes, under both Linux and Windows it is removed.

    Can anybody else check on Solaris, please? Or can David Dean debug on
    his machine?

    In particular, we need exact system information, because it seems to be
    an OS/platform specific problem.

    Uwe Ligges



    Paul Gilbert
    After a *successful* installation, the 00LOCK directory should be
    deleted by the installation tools themselves.
    After an unsuccessful installation, the installation tools should
    restore the stuff in the 00LOCK directory.
    Do you abort the installtion manually (this is the only way I figured
    out how not to remove 00LOCK automatically)?

    Uwe Ligges




    Much thanks!!!
    --------------------- David P Dean
    Research Informatics
    PGRD Groton Labs
    (860)-441-5053
    david.p.dean at pfizer.com
    ---------------------------------------------------------------------
    -
    LEGAL NOTICE\ Unless expressly stated otherwise, this
    messag...{{dropped}}

    ______________________________________________
    R-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/r-devel

    ______________________________________________
    R-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/r-devel
    ______________________________________________
    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
  • Prof Brian Ripley at Oct 13, 2005 at 4:20 pm

    On Thu, 13 Oct 2005, Dean, David P wrote:

    From: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk]
    Sent: Thursday, October 13, 2005 11:42 AM
    To: Uwe Ligges
    Cc: Paul Gilbert; r-devel at r-project.org; Dean, David P
    Subject: Re: [Rd] Installing R-2.2.0 package

    It works on Solaris 8 for me, and this is checked as part of the
    alpha/beta process.

    The code is the same on Linux and Solaris, after all, so this would have
    to be a Solaris shell bug.
    I'm on Solaris 8 as well. R is compiled for 64-bits, but I wouldn't expect
    that to be a factor.
    I tested this on a 64-bit setup, as it happens.
    R was built and is run in an environment created with
    OpenPKG and containing GNU equivalents to many utilities -- so it's not a
    stock Solaris setup.
    I hope /bin/sh is Solaris and not bash.
    I'm not familiar with R internals but will be happy to try to debug if I
    can. Does the installer call out to the shell somehow? Where would I start
    to look for the relevant code?
    INSTALL _is_ a shell script.

    Rather than mess about with past code, can you first please try the
    current R-patched (see the FAQ) as I will shortly not have R-2.2.0 on
    Solaris but rather R-patched (I already have R-devel in 4 flavours).
    Thanks!
    David Dean
    On Thu, 13 Oct 2005, Uwe Ligges wrote:

    Paul Gilbert wrote:

    Uwe Ligges wrote:
    Dean, David P wrote:


    Dear list,

    I've just installed R-2.2.0 under Solaris and have a question about
    installing packages. If a package fails to install for any reason and
    I go
    to install another package, I get this message:

    $ R-2.2.0-64bit --vanilla CMD INSTALL
    ~/srca/cran/RSQLite_0.4-0.tar.gz ERROR: failed to lock directory
    '/app/openpkg/lib/R-2.2.0-64bit/lib/R/library' for modifying
    Try removing '/app/openpkg/lib/R-2.2.0-64bit/lib/R/library/00LOCK'

    I can remove the lock directory by hand, and then the next package
    installs,
    but this makes it quite difficult to download and install a batch of
    packages from CRAN or Biocondctor! Is this lock directory a new
    feature with
    R-2.2.0? Is there a work around in the R build itself or the
    installation
    scripts?

    No, not a new feature in R-2.2.0, it has been there for some time now.
    I have the impression the feature behaves slightly differently as of
    R-2.2.0. Now the 00LOCK file is not removed in Solaris when there is an
    unsuccessful install. (In Linux I think it does get removed.)
    Yes, under both Linux and Windows it is removed.

    Can anybody else check on Solaris, please? Or can David Dean debug on
    his machine?

    In particular, we need exact system information, because it seems to be
    an OS/platform specific problem.

    Uwe Ligges



    Paul Gilbert
    After a *successful* installation, the 00LOCK directory should be
    deleted by the installation tools themselves.
    After an unsuccessful installation, the installation tools should
    restore the stuff in the 00LOCK directory.
    Do you abort the installtion manually (this is the only way I figured
    out how not to remove 00LOCK automatically)?

    Uwe Ligges




    Much thanks!!!
    --------------------- David P Dean
    Research Informatics
    PGRD Groton Labs
    (860)-441-5053
    david.p.dean at pfizer.com
    ---------------------------------------------------------------------
    -
    LEGAL NOTICE\ Unless expressly stated otherwise, this
    messag...{{dropped}}

    ______________________________________________
    R-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/r-devel

    ______________________________________________
    R-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/r-devel
    ______________________________________________
    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
    ______________________________________________
    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
  • Paul Gilbert at Oct 13, 2005 at 4:32 pm
    I'm using SunOS 5.8, R compiled as a 32 bit app, and I didn't intend to
    set up anything special. Below is an example installing RMySQL (twice).
    The error the second time is because of the lock file. I think

    ERROR: configuration failed for package 'RMySQL'
    /apps/asd/unix/gnu/R/SunOS-sparc32/R-2.2.0/bin/INSTALL: test: argument
    expected

    may be a clue.


    (BTW. If there is a simple answer to the libz problem then I would
    appreciate hearing.)

    Paul Gilbert
    install.packages(c("RMySQL"), Sys.getenv("R_LIBS"), repos =
    "http://cran.at.r-project.org")
    trying URL 'http://cran.at.r-project.org/src/contrib/RMySQL_0.5-5.tar.gz'
    Content type 'application/x-tar' length 280328 bytes
    opened URL
    ==================================================
    downloaded 273Kb

    * Installing *source* package 'RMySQL' ...
    creating cache ./config.cache
    checking how to run the C preprocessor... /lib/cpp
    checking for compress in -lz... no
    checking for getopt_long in -lc... no
    checking for mysql_init in -lmysqlclient... no
    checking for mysql.h... no
    checking for mysql_init in -lmysqlclient... no
    checking for mysql_init in -lmysqlclient... no
    checking for mysql_init in -lmysqlclient... no
    checking for mysql_init in -lmysqlclient... no
    checking for mysql_init in -lmysqlclient... no

    Configuration error:
    Could not locate the library "libz" required by MySQL.

    INSTRUCTIONS:

    The "libz" library is required by the MySQL client library
    in order to compress/uncompress connections between clients
    and the MySQL engine.

    Make sure you have "libz" installed properly and/or included
    in your $LD_LIBRARY_PATH. Perhaps it is not in any of the
    standard directories (e.g., /usr/lib/, /usr/local/lib)?

    Aborting the installation of RMySQL.

    ERROR: configuration failed for package 'RMySQL'
    /apps/asd/unix/gnu/R/SunOS-sparc32/R-2.2.0/bin/INSTALL: test: argument
    expected

    The downloaded packages are in
    /tmp/Rtmp26660/downloaded_packages
    Warning message:
    installation of package 'RMySQL' had non-zero exit status in:
    install.packages(c("RMySQL"), Sys.getenv("R_LIBS"), repos =
    "http://cran.at.r-project.org")
    install.packages(c("RMySQL"), Sys.getenv("R_LIBS"), repos =
    "http://cran.at.r-project.org")
    trying URL 'http://cran.at.r-project.org/src/contrib/RMySQL_0.5-5.tar.gz'
    Content type 'application/x-tar' length 280328 bytes
    opened URL
    ==================================================
    downloaded 273Kb

    ERROR: failed to lock directory
    '/home/asd9/gnu/R/SunOS-sparc32/R-2.2.0/site-library' for modifying
    Try removing '/home/asd9/gnu/R/SunOS-sparc32/R-2.2.0/site-library/00LOCK'

    The downloaded packages are in
    /tmp/Rtmp26660/downloaded_packages
    Warning message:
    installation of package 'RMySQL' had non-zero exit status in:
    install.packages(c("RMySQL"), Sys.getenv("R_LIBS"), repos =
    "http://cran.at.r-project.org")
    >


    Dean, David P wrote:
    From: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk]
    Sent: Thursday, October 13, 2005 11:42 AM
    To: Uwe Ligges
    Cc: Paul Gilbert; r-devel at r-project.org; Dean, David P
    Subject: Re: [Rd] Installing R-2.2.0 package

    It works on Solaris 8 for me, and this is checked as part of the
    alpha/beta process.

    The code is the same on Linux and Solaris, after all, so this would have
    to be a Solaris shell bug.
    I'm on Solaris 8 as well. R is compiled for 64-bits, but I wouldn't expect
    that to be a factor. R was built and is run in an environment created with
    OpenPKG and containing GNU equivalents to many utilities -- so it's not a
    stock Solaris setup.

    I'm not familiar with R internals but will be happy to try to debug if I
    can. Does the installer call out to the shell somehow? Where would I start
    to look for the relevant code?

    Thanks!
    David Dean

    On Thu, 13 Oct 2005, Uwe Ligges wrote:


    Paul Gilbert wrote:


    Uwe Ligges wrote:


    Dean, David P wrote:




    Dear list,

    I've just installed R-2.2.0 under Solaris and have a question about
    installing packages. If a package fails to install for any reason and
    I go
    to install another package, I get this message:

    $ R-2.2.0-64bit --vanilla CMD INSTALL
    ~/srca/cran/RSQLite_0.4-0.tar.gz ERROR: failed to lock directory
    '/app/openpkg/lib/R-2.2.0-64bit/lib/R/library' for modifying
    Try removing '/app/openpkg/lib/R-2.2.0-64bit/lib/R/library/00LOCK'

    I can remove the lock directory by hand, and then the next package
    installs,
    but this makes it quite difficult to download and install a batch of
    packages from CRAN or Biocondctor! Is this lock directory a new
    feature with
    R-2.2.0? Is there a work around in the R build itself or the
    installation
    scripts?

    No, not a new feature in R-2.2.0, it has been there for some time now.


    I have the impression the feature behaves slightly differently as of
    R-2.2.0. Now the 00LOCK file is not removed in Solaris when there is an
    unsuccessful install. (In Linux I think it does get removed.)
    Yes, under both Linux and Windows it is removed.

    Can anybody else check on Solaris, please? Or can David Dean debug on
    his machine?

    In particular, we need exact system information, because it seems to be
    an OS/platform specific problem.

    Uwe Ligges





    Paul Gilbert


    After a *successful* installation, the 00LOCK directory should be
    deleted by the installation tools themselves.
    After an unsuccessful installation, the installation tools should
    restore the stuff in the 00LOCK directory.
    Do you abort the installtion manually (this is the only way I figured
    out how not to remove 00LOCK automatically)?

    Uwe Ligges






    Much thanks!!!
    --------------------- David P Dean
    Research Informatics
    PGRD Groton Labs
    (860)-441-5053
    david.p.dean at pfizer.com
    ---------------------------------------------------------------------
    -

    LEGAL NOTICE\ Unless expressly stated otherwise, this
    messag...{{dropped}}

    ______________________________________________
    R-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/r-devel

    ______________________________________________
    R-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/r-devel


    ______________________________________________
    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
  • Prof Brian Ripley at Oct 13, 2005 at 4:41 pm

    On Thu, 13 Oct 2005, Paul Gilbert wrote:

    I'm using SunOS 5.8, R compiled as a 32 bit app, and I didn't intend to
    set up anything special. Below is an example installing RMySQL (twice).
    The error the second time is because of the lock file. I think

    ERROR: configuration failed for package 'RMySQL'
    /apps/asd/unix/gnu/R/SunOS-sparc32/R-2.2.0/bin/INSTALL: test: argument
    expected

    may be a clue.
    Please try R-patched, as I think it might already have been fixed (by
    adding quotes for a different reason).
    (BTW. If there is a simple answer to the libz problem then I would
    appreciate hearing.)
    Simple: install it.
    Paul Gilbert
    install.packages(c("RMySQL"), Sys.getenv("R_LIBS"), repos =
    "http://cran.at.r-project.org")
    trying URL 'http://cran.at.r-project.org/src/contrib/RMySQL_0.5-5.tar.gz'
    Content type 'application/x-tar' length 280328 bytes
    opened URL
    ==================================================
    downloaded 273Kb

    * Installing *source* package 'RMySQL' ...
    creating cache ./config.cache
    checking how to run the C preprocessor... /lib/cpp
    checking for compress in -lz... no
    checking for getopt_long in -lc... no
    checking for mysql_init in -lmysqlclient... no
    checking for mysql.h... no
    checking for mysql_init in -lmysqlclient... no
    checking for mysql_init in -lmysqlclient... no
    checking for mysql_init in -lmysqlclient... no
    checking for mysql_init in -lmysqlclient... no
    checking for mysql_init in -lmysqlclient... no

    Configuration error:
    Could not locate the library "libz" required by MySQL.

    INSTRUCTIONS:

    The "libz" library is required by the MySQL client library
    in order to compress/uncompress connections between clients
    and the MySQL engine.

    Make sure you have "libz" installed properly and/or included
    in your $LD_LIBRARY_PATH. Perhaps it is not in any of the
    standard directories (e.g., /usr/lib/, /usr/local/lib)?

    Aborting the installation of RMySQL.

    ERROR: configuration failed for package 'RMySQL'
    /apps/asd/unix/gnu/R/SunOS-sparc32/R-2.2.0/bin/INSTALL: test: argument
    expected

    The downloaded packages are in
    /tmp/Rtmp26660/downloaded_packages
    Warning message:
    installation of package 'RMySQL' had non-zero exit status in:
    install.packages(c("RMySQL"), Sys.getenv("R_LIBS"), repos =
    "http://cran.at.r-project.org")
    install.packages(c("RMySQL"), Sys.getenv("R_LIBS"), repos =
    "http://cran.at.r-project.org")
    trying URL 'http://cran.at.r-project.org/src/contrib/RMySQL_0.5-5.tar.gz'
    Content type 'application/x-tar' length 280328 bytes
    opened URL
    ==================================================
    downloaded 273Kb

    ERROR: failed to lock directory
    '/home/asd9/gnu/R/SunOS-sparc32/R-2.2.0/site-library' for modifying
    Try removing '/home/asd9/gnu/R/SunOS-sparc32/R-2.2.0/site-library/00LOCK'

    The downloaded packages are in
    /tmp/Rtmp26660/downloaded_packages
    Warning message:
    installation of package 'RMySQL' had non-zero exit status in:
    install.packages(c("RMySQL"), Sys.getenv("R_LIBS"), repos =
    "http://cran.at.r-project.org")

    Dean, David P wrote:
    From: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk]
    Sent: Thursday, October 13, 2005 11:42 AM
    To: Uwe Ligges
    Cc: Paul Gilbert; r-devel at r-project.org; Dean, David P
    Subject: Re: [Rd] Installing R-2.2.0 package

    It works on Solaris 8 for me, and this is checked as part of the
    alpha/beta process.

    The code is the same on Linux and Solaris, after all, so this would have
    to be a Solaris shell bug.
    I'm on Solaris 8 as well. R is compiled for 64-bits, but I wouldn't expect
    that to be a factor. R was built and is run in an environment created with
    OpenPKG and containing GNU equivalents to many utilities -- so it's not a
    stock Solaris setup.

    I'm not familiar with R internals but will be happy to try to debug if I
    can. Does the installer call out to the shell somehow? Where would I start
    to look for the relevant code?

    Thanks!
    David Dean

    On Thu, 13 Oct 2005, Uwe Ligges wrote:


    Paul Gilbert wrote:


    Uwe Ligges wrote:


    Dean, David P wrote:




    Dear list,

    I've just installed R-2.2.0 under Solaris and have a question about
    installing packages. If a package fails to install for any reason and
    I go
    to install another package, I get this message:

    $ R-2.2.0-64bit --vanilla CMD INSTALL
    ~/srca/cran/RSQLite_0.4-0.tar.gz ERROR: failed to lock directory
    '/app/openpkg/lib/R-2.2.0-64bit/lib/R/library' for modifying
    Try removing '/app/openpkg/lib/R-2.2.0-64bit/lib/R/library/00LOCK'

    I can remove the lock directory by hand, and then the next package
    installs,
    but this makes it quite difficult to download and install a batch of
    packages from CRAN or Biocondctor! Is this lock directory a new
    feature with
    R-2.2.0? Is there a work around in the R build itself or the
    installation
    scripts?

    No, not a new feature in R-2.2.0, it has been there for some time now.


    I have the impression the feature behaves slightly differently as of
    R-2.2.0. Now the 00LOCK file is not removed in Solaris when there is an
    unsuccessful install. (In Linux I think it does get removed.)
    Yes, under both Linux and Windows it is removed.

    Can anybody else check on Solaris, please? Or can David Dean debug on
    his machine?

    In particular, we need exact system information, because it seems to be
    an OS/platform specific problem.

    Uwe Ligges





    Paul Gilbert


    After a *successful* installation, the 00LOCK directory should be
    deleted by the installation tools themselves.
    After an unsuccessful installation, the installation tools should
    restore the stuff in the 00LOCK directory.
    Do you abort the installtion manually (this is the only way I figured
    out how not to remove 00LOCK automatically)?

    Uwe Ligges






    Much thanks!!!
    --------------------- David P Dean
    Research Informatics
    PGRD Groton Labs
    (860)-441-5053
    david.p.dean at pfizer.com
    ---------------------------------------------------------------------
    -

    LEGAL NOTICE\ Unless expressly stated otherwise, this
    messag...{{dropped}}

    ______________________________________________
    R-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/r-devel

    ______________________________________________
    R-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/r-devel


    ______________________________________________
    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
    ______________________________________________
    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
  • Dean, David P at Oct 13, 2005 at 7:38 pm

    From: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk]
    Sent: Thursday, October 13, 2005 12:21 PM
    To: Dean, David P
    Cc: Uwe Ligges; r-devel at r-project.org; Paul Gilbert
    Subject: Re: [Rd] Installing R-2.2.0 package
    On Thu, 13 Oct 2005, Dean, David P wrote:

    From: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk]
    Sent: Thursday, October 13, 2005 11:42 AM
    To: Uwe Ligges
    Cc: Paul Gilbert; r-devel at r-project.org; Dean, David P
    Subject: Re: [Rd] Installing R-2.2.0 package

    It works on Solaris 8 for me, and this is checked as part of the
    alpha/beta process.

    The code is the same on Linux and Solaris, after all, so this would
    have
    to be a Solaris shell bug.
    I'm on Solaris 8 as well. R is compiled for 64-bits, but I wouldn't expect
    that to be a factor.
    I tested this on a 64-bit setup, as it happens.
    R was built and is run in an environment created with
    OpenPKG and containing GNU equivalents to many utilities -- so it's not a
    stock Solaris setup.
    I hope /bin/sh is Solaris and not bash.
    I'm not familiar with R internals but will be happy to try to debug if I
    can. Does the installer call out to the shell somehow? Where would I start
    to look for the relevant code?
    INSTALL _is_ a shell script.

    Rather than mess about with past code, can you first please try the
    current R-patched (see the FAQ) as I will shortly not have R-2.2.0 on
    Solaris but rather R-patched (I already have R-devel in 4 flavours).
    Thanks!
    David Dean
    OK, I'll try the current patched. I did locate the INSTALL script and added
    a -x flag to see what is going on. (This is in the stock 2.2.0):

    + do_exit_on_error
    remove_R_package_dir=yes
    + test -z
    /net/gsun374/app/openpkg/lib/R-2.2.0-64bit/lib/R/bin/INSTALL: test: argument
    expected

    I think this line in do_exit_on_error causes an abend if bundlepkg isn't
    set:

    If test -z ${bundlepkg}; do

    Cheers,
    David Dean
    ----------------------------------------------------------------------
    LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}}
  • Prof Brian Ripley at Oct 13, 2005 at 7:47 pm

    On Thu, 13 Oct 2005, Dean, David P wrote:

    From: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk]
    Sent: Thursday, October 13, 2005 12:21 PM
    To: Dean, David P
    Cc: Uwe Ligges; r-devel at r-project.org; Paul Gilbert
    Subject: Re: [Rd] Installing R-2.2.0 package
    On Thu, 13 Oct 2005, Dean, David P wrote:

    From: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk]
    Sent: Thursday, October 13, 2005 11:42 AM
    To: Uwe Ligges
    Cc: Paul Gilbert; r-devel at r-project.org; Dean, David P
    Subject: Re: [Rd] Installing R-2.2.0 package

    It works on Solaris 8 for me, and this is checked as part of the
    alpha/beta process.

    The code is the same on Linux and Solaris, after all, so this would
    have
    to be a Solaris shell bug.
    I'm on Solaris 8 as well. R is compiled for 64-bits, but I wouldn't expect
    that to be a factor.
    I tested this on a 64-bit setup, as it happens.
    R was built and is run in an environment created with
    OpenPKG and containing GNU equivalents to many utilities -- so it's not a
    stock Solaris setup.
    I hope /bin/sh is Solaris and not bash.
    I'm not familiar with R internals but will be happy to try to debug if I
    can. Does the installer call out to the shell somehow? Where would I start
    to look for the relevant code?
    INSTALL _is_ a shell script.

    Rather than mess about with past code, can you first please try the
    current R-patched (see the FAQ) as I will shortly not have R-2.2.0 on
    Solaris but rather R-patched (I already have R-devel in 4 flavours).
    Thanks!
    David Dean
    OK, I'll try the current patched. I did locate the INSTALL script and added
    a -x flag to see what is going on. (This is in the stock 2.2.0):

    + do_exit_on_error
    remove_R_package_dir=yes
    + test -z
    /net/gsun374/app/openpkg/lib/R-2.2.0-64bit/lib/R/bin/INSTALL: test: argument
    expected

    I think this line in do_exit_on_error causes an abend if bundlepkg isn't
    set:

    If test -z ${bundlepkg}; do
    It is in R-patched, and indeed it has quotes too.


    --
    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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