[R] RMySQL installation
Janet Young
jayoung at fhcrc.org
Fri Dec 21 23:27:01 CET 2007
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
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