Installing R-2.2.0 package

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
---------------------------------------------------------------------

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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)
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