[R-SIG-Mac] RMySQL install failure
P. B. Pynsent
p.b.pynsent at bham.ac.uk
Thu Nov 2 18:49:46 CET 2006
Jeff,
Thank you for this information, unfortunately this made no difference:
$ ls /usr/local/mysql/lib
libdbug.a libmysql.imp
libmysqlclient_r.a libmysys.a
libmygcc.a libmysqlclient.a
libmystrings.a libz.a
$ export PKG_CPPFLAGS="-I/usr/local/mysql/include"
$ export PKG_LIBS="-L/usr/local/mysql/lib -lmysqlclient"
$ sudo R CMD INSTALL RMySQL_0.5-10.tar.gz
* 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
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'
** Removing '/Library/Frameworks/R.framework/Versions/2.4/Resources/
library/RMySQL'
Thanks,
Paul
On 2 Nov 2006, at 02:39, Jeff Ryan wrote:
> Ricardo,
>
> What does your /users/rrodriguez/Desktop/mysql-5.0.27 directory look
> like? Can you find the libmysqlclient anywhere using
> Spotlight/find/locate...?
>
> my lib directory put down by the MySQL binary install (I **think** it
> was a binary install - my only mac at the moment is a weak ibook, that
> takes so long to compile anything on I don't usually bother) looks
> like:
>
> [veblen:~] jryan% ls /usr/local/mysql/lib
> libdbug.a libmysqlclient.a libmysys.a
> libmygcc.a libmysqlclient_r.a libz.a
> libmysql.imp libmystrings.a
>
> Actually now that I think of it I may have been using the DarwinPorts
> version - though it really shouldn't matter at this stage - that would
> be another error if there was some sort of compat problem.
>
> if you can locate it - use the export procedure as you did before -
> only point to the directory that you find it in. You may need to
> build it from scratch. Like I said previously, NOTHING has caused me
> more headaches than getting RMySQL to build.
>
> Keep us posted.
> Jeff
> On 11/1/06, Ricardo Rodríguez - Your EPEC ICT Team
> <webmaster at environmentalchange.net> wrote:
>>
>>
>> On Nov 1, 2006, at 3:04 PM, P. B. Pynsent wrote:
>>
>> I wonder if anybody has successfully got the RMySQL installation
>> working?
>>
>> I have followed the instructions (both approaches) given on the build
>> failure CRAN site but still get a configuration error.
>>
>> WARNING: ignoring environment value of R_HOME
>> * Installing *source* package 'RMySQL' ...
>> creating cache ./config.cache
>> checking how to run the C preprocessor...
>> The downloaded packages are in
>> /private/tmp/RtmpNiFrHt/downloaded_packages
>> /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.
>>
>> ** Removing '/Users/paul/Library/R/library/RMySQL'
>> ** Restoring previous
>> '/Users/paul/Library/R/library/RMySQL'
>> ERROR: configuration failed for package 'RMySQL'
>>
>>
>> R.version
>> _
>> platform powerpc-apple-darwin8.7.0
>> arch powerpc
>> os darwin8.7.0
>> system powerpc, darwin8.7.0
>> status
>> major 2
>> minor 4.0
>> year 2006
>> month 10
>> day 03
>> svn rev 39566
>> language R
>> version.string R version 2.4.0 (2006-10-03)
>>
>> Mac OS 10.4.8 4 x 2.5GHz G5
>>
>> A similar error message is produced on my MacBook Pro running R
>> 2.4.0.
>>
>> zlib is in /usr/lib. I should be grateful for any suggestions.
>>
>> Many thanks,
>>
>> Paul
>>
>>
>> P. B. Pynsent,
>> Research & Teaching Centre,
>> Royal Orthopaedic Hospital,
>> Northfield,
>> Birmingham, B31 2AP,
>> U. K.
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>>
>> Hi, Paul,
>>
>> I'm also struggling to get RMySQL up and running over here. My
>> installation:
>>
>> > R.version
>> _
>> platform i386-apple-darwin8.6.1
>> arch i386
>> os darwin8.6.1
>> system i386, darwin8.6.1
>> status
>> major 2
>> minor 3.1
>> year 2006
>> month 06
>> day 01
>> svn rev 38247
>> language R
>> version.string Version 2.3.1 (2006-06-01)
>>
>> I have luckily receive a message from Jeff Ryan pointing to the
>> key of the
>> problem: to get a MySQL distribution including headers and the client
>> library. He speaks about a "developer distribution", but I am not
>> able to
>> find such a thing for Mac/Intel (neither for Mac/PPC!) I am
>> currently trying
>> the source distribution trying to build it here, but I'm facing a
>> number of
>> problems so far.
>>
>> As for the compression libraries, I've installed the XTools
>> package included
>> with the installation DVD bundled with our last MacBooks.
>>
>> By downloading mysql-5.0.27.tar.gz, exploding it and exporting the
>> concerned
>> variables as following, I get the messages included below...
>>
>> export
>> PKG_CPPFLAGS="-I/users/rrodriguez/Desktop/mysql-5.0.27/include"
>> export
>> PKG_LIBS="-L/users/rrodriguez/Desktop/mysql-5.0.27/lib
>> -lmysqlclient"
>> R CMD INSTALL RMySQL_0.5-9.tar.gz
>>
>> ricardo-rodriguezs-computer:/Users/rrodriguez/Desktop root#
>> R CMD INSTALL RMySQL_0.5-9.tar.gz
>> * Installing *source* package 'RMySQL' ...
>> creating cache ./config.cache
>> checking how to run the C preprocessor... cc -E
>> checking for compress in -lz... yes
>> checking for getopt_long in -lc... yes
>> checking for mysql_init in -lmysqlclient... no
>> checking for mysql.h... no
>> updating cache ./config.cache
>> creating ./config.status
>> creating src/Makevars
>> ** libs
>> ** arch - i386
>> gcc-4.0 -arch i386
>> -I/Library/Frameworks/R.framework/Resources/include
>> -I/Library/Frameworks/R.framework/Resources/include/i386
>> -I/users/rrodriguez/Desktop/mysql-5.0.27/include -msse3
>> -D__NO_MATH_INLINES -fPIC -fno-common -g -O2 -std=gnu99 -
>> march=pentium-m
>> -mtune=prescott -c RS-DBI.c -o RS-DBI.o
>> gcc-4.0 -arch i386
>> -I/Library/Frameworks/R.framework/Resources/include
>> -I/Library/Frameworks/R.framework/Resources/include/i386
>> -I/users/rrodriguez/Desktop/mysql-5.0.27/include -msse3
>> -D__NO_MATH_INLINES -fPIC -fno-common -g -O2 -std=gnu99 -
>> march=pentium-m
>> -mtune=prescott -c RS-MySQL.c -o RS-MySQL.o
>> gcc-4.0 -arch i386 -flat_namespace -bundle -undefined suppress
>> -L/usr/local/lib -o RMySQL.so RS-DBI.o RS-MySQL.o
>> -L/users/rrodriguez/Desktop/mysql-5.0.27/lib -lmysqlclient
>> -lz -L/Library/Frameworks/R.framework/Resources/lib/i386
>> -lR
>> /usr/bin/ld: warning -L: directory name
>> (/users/rrodriguez/Desktop/mysql-5.0.27/lib) does not exist
>> /usr/bin/ld: can't locate file for: -lmysqlclient
>> collect2: ld returned 1 exit status
>> make: *** [RMySQL.so] Error 1
>> chmod:
>> /Library/Frameworks/R.framework/Versions/2.3/Resources/library/
>> RMySQL/libs/i386/*:
>> No such file or directory
>> ERROR: compilation failed for package 'RMySQL'
>> ** Removing
>> '/Library/Frameworks/R.framework/Versions/2.3/Resources/library/
>> RMySQL'
>> ricardo-rodriguezs-computer:/Users/rrodriguez/Desktop root#
>>
>> In fact there is no /iib folder where the compilation process is
>> calling for
>> it. I am guessing I must first build MySQL, then install it, then
>> build
>> RMySQL, but I am afraid that my programer skills are too poor to
>> solve this
>> issue!
>>
>> Currently I'm running MySQL max 5.0.27 for Mac/Intel in this box. By
>> pointing PKG_CPPFLAGS and PKG_LIBS to this directory I get a much,
>> much
>> longer error log!
>>
>> Any input will be welcome! Thanks,
>>
>> --
>> Ricardo Rodríguez
>> Your EPEC ICT Team
>>
>>
>>
>>
P. B. Pynsent,
Research & Teaching Centre,
Royal Orthopaedic Hospital,
Northfield,
Birmingham, B31 2AP,
U. K.
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