From pgilbert at bank-banque-canada.ca  Thu Oct 13 18:32:00 2005
From: pgilbert at bank-banque-canada.ca (Paul Gilbert)
Date: Thu, 13 Oct 2005 12:32:00 -0400
Subject: [Rd] Installing R-2.2.0 package
In-Reply-To: <599089EF29304C44AF1D84B1C223AC63032EF4F3@groamrexm03.amer.pfizer.com>
References: <599089EF29304C44AF1D84B1C223AC63032EF4F3@groamrexm03.amer.pfizer.com>
Message-ID: <434E8C00.9000106@bank-banque-canada.ca>

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
>>    
>>
>
>  
>



[Rd] Installing R-2.2.0 package
Paul Gilbert