[R] RMySQL installation

From: Janet Young <jayoung_at_fhcrc.org>
Date: Fri, 21 Dec 2007 14:27:01 -0800


Hi,

I am having trouble getting RMySQL running on a solaris machine. [43] bedrock:/home/jayoung/source_codes/R/other_packages> uname -a SunOS bedrock 5.10 Generic_118833-36 sun4v sparc SUNW,Sun-Fire-T200

I thought I had finally managed to get it installed, albeit with some warnings that I didn't understand (it took me a while to find where our mysql libraries were), but when I tried to load it within R I got an error:

 > library(RMySQL)
Error in dyn.load(file, ...) :

   unable to load shared library '/home/btrask/traskdata/lib/R/ library/RMySQL/libs/RMySQL.so':

   ld.so.1: R: fatal: relocation error: file /home/btrask/traskdata/ lib/R/library/RMySQL/libs/RMySQL.so: symbol mysql_more_results: referenced symbol not found
Error: package/namespace load failed for 'RMySQL'

I'm not a sysadmin and don't know any C, so I don't really understand this error, but I'm wondering whether we might have an older, incompatible version of mysql?
[42] bedrock:/home/jayoung/source_codes/R/other_packages> mysql -V mysql Ver 12.22 Distrib 4.0.24, for sun-solaris2.10 (sparc)

Or am I somehow failing to specify some of the necessary libraries in LD_LIBRARY_PATH or some other thing R is using to look for libraries?

I've pasted the command I used for installation, and the output of the build process below, as well as the output of sessionInfo.

Thanks in advance for any help,

Janet Young


Dr. Janet Young (Trask lab)

Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., C3-168,
P.O. Box 19024, Seattle, WA 98109-1024, USA.

tel: (206) 667 1471 fax: (206) 667 6524
email: jayoung_at_fhcrc.org

http://www.fhcrc.org/labs/trask/


[13] bedrock:/home/jayoung/source_codes/R/other_packages> R CMD INSTALL --configure-args='--with-mysql-inc=/usr/sfw/include/mysql -- with-mysql-lib=/usr/sfw/lib' RMySQL_0.6-0.tar.gz * Installing to library '/home/btrask/traskdata/lib/R/library' * Installing *source* package 'RMySQL' ... checking for gcc... gcc
checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables...
checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -E checking for compress in -lz... yes
checking for getopt_long in -lc... yes
checking for mysql_init in -lmysqlclient... no checking for egrep... egrep
checking for ANSI C header files... yes
checking for sys/types.h... yes

checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes

checking for stdint.h... yes
checking for unistd.h... yes
checking mysql.h usability... no
checking mysql.h presence... no
checking for mysql.h... no
configure: creating ./config.status
config.status: creating src/Makevars
** libs
cc -I/home/btrask/traskdata/lib/R/include -I/home/btrask/traskdata/ lib/R/include -I/usr/sfw/include/mysql -I/usr/local/include -KPIC -g -c RS-DBI.c -o RS-DBI.o
"RS-DBI.c", line 1177: warning: assignment type mismatch:

         pointer to char "=" pointer to const char
"RS-DBI.c", line 1190: warning: implicit function declaration: isalpha
"RS-DBI.c", line 1228: warning: assignment type mismatch:

         pointer to char "=" pointer to const char cc -I/home/btrask/traskdata/lib/R/include -I/home/btrask/traskdata/ lib/R/include -I/usr/sfw/include/mysql -I/usr/local/include -KPIC -g -c RS-MySQL.c -o RS-MySQL.o
"RS-MySQL.c", line 134: warning: implicit function declaration:
mysql_more_results
"RS-MySQL.c", line 161: warning: implicit function declaration:
mysql_next_result
"RS-MySQL.c", line 387: warning: assignment type mismatch:

         pointer to char "=" pointer to const char
"RS-MySQL.c", line 389: warning: assignment type mismatch:

         pointer to char "=" pointer to const char
"RS-MySQL.c", line 391: warning: assignment type mismatch:

         pointer to char "=" pointer to const char
"RS-MySQL.c", line 393: warning: assignment type mismatch:

         pointer to char "=" pointer to const char
"RS-MySQL.c", line 395: warning: assignment type mismatch:

         pointer to char "=" pointer to const char cc -G -L/usr/local/lib -o RMySQL.so RS-DBI.o RS-MySQL.o -L/usr/sfw/ lib -lmysqlclient -lz -L/home/btrask/traskdata/lib/R/lib -lR

** R
** inst
** preparing package for lazy loading

Loading required package: DBI
Creating a new generic function for "format" in "RMySQL" Creating a new generic function for "print" in "RMySQL" ** help
  >>> Building/Updating help pages for package 'RMySQL'
      Formats: text html latex example
   MySQL                             text    html    latex   example
   MySQLConnection-class             text    html    latex   example
   MySQLDriver-class                 text    html    latex   example
   MySQLObject-class                 text    html    latex   example
   MySQLResult-class                 text    html    latex   example
   RMySQL-package                    text    html    latex   example
   S4R                               text    html    latex   example
   dbApply-methods                   text    html    latex   example
   dbApply                           text    html    latex   example
   dbBuildTableDefinition            text    html    latex
   dbCallProc-methods                text    html    latex
   dbCommit-methods                  text    html    latex   example
   dbConnect-methods                 text    html    latex   example
Note: unmatched right brace in 'dbDataType-methods' on or after line 24
   dbDataType-methods                text    html    latex   example
   dbDriver-methods                  text    html    latex   example
   dbEscapeStrings-methods           text    html    latex   example
   dbEscapeStrings                   text    html    latex   example
   dbGetInfo-methods                 text    html    latex   example
   dbListTables-methods              text    html    latex   example
   dbNextResult-methods              text    html    latex   example
   dbNextResult                      text    html    latex   example
   dbObjectId-class                  text    html    latex   example
   dbReadTable-methods               text    html    latex   example
   dbSendQuery-methods               text    html    latex   example
   dbSetDataMappings-methods         text    html    latex   example
   fetch-methods                     text    html    latex   example
   isIdCurrent                       text    html    latex   example
   make.db.names-methods             text    html    latex   example
   mysqlDBApply                      text    html    latex   example
   mysqlSupport                      text    html    latex
   safe.write                        text    html    latex   example
   summary-methods                   text    html    latex
** building package indices ...
* DONE (RMySQL)

[1] bedrock:/home/jayoung> R

R version 2.6.1 Patched (2007-12-02 r43572) Copyright (C) 2007 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.

 > library(DBI)
 > library(RMySQL)
Error in dyn.load(file, ...) :

   unable to load shared library '/home/btrask/traskdata/lib/R/ library/RMySQL/libs/RMySQL.so':

   ld.so.1: R: fatal: relocation error: file /home/btrask/traskdata/ lib/R/library/RMySQL/libs/RMySQL.so: symbol mysql_more_results: referenced symbol not found
Error: package/namespace load failed for 'RMySQL'  > sessionInfo()
R version 2.6.1 Patched (2007-12-02 r43572) sparc-sun-solaris2.10

locale:
/en_US.ISO8859-15/C/C/en_US.ISO8859-15/en_US.ISO8859-15/C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] DBI_0.2-4  > q()
Save workspace image? [y/n/c]: n

[2] bedrock:/home/jayoung> printenv LD_LIBRARY_PATH /opt/SUNWspro/lib:/usr/lib:/opt/SUNWspro/lib:/usr/openwin/lib:/usr/ lib:/usr/local/lib:/opt/hpnpl/lib:/opt/sfw/lib:/usr/local/emacs/lib:/ usr/local/ImageMagick:/home/btrask/traskdata/lib/R/library/RSPerl/ libs:/home/btrask/traskdata/lib/R/lib:/usr/sfw/lib:/opt/local/apps/ gdbm-1.7.3/lib:/home/jayoung/traskdata/lib/R/bin:/home/jayoung/ traskdata/lib/R/lib:/home/jayoung/traskdata/lib/RSPerl/libs:/home/ jayoung/traskdata/lib/RSPerl:/home/jayoung/traskdata/lib/RSPerl/scripts



R-help_at_r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Fri 21 Dec 2007 - 22:31:22 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Fri 21 Dec 2007 - 23:30:19 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.