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}}
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
> 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
> 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 DeanOK, 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}}