From ripley at stats.ox.ac.uk  Thu Oct 13 18:41:58 2005
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Thu, 13 Oct 2005 17:41:58 +0100 (BST)
Subject: [Rd] Installing R-2.2.0 package
In-Reply-To: <434E8C00.9000106@bank-banque-canada.ca>
References: <599089EF29304C44AF1D84B1C223AC63032EF4F3@groamrexm03.amer.pfizer.com>
	<434E8C00.9000106@bank-banque-canada.ca>
Message-ID: <Pine.LNX.4.61.0510131740210.7130@gannet.stats>

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



[Rd] Installing R-2.2.0 package
Prof Brian Ripley