Installing R-2.2.0 package
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 ---------------------------------------------------------------------
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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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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