Michaell Taylor wrote: > > I am having trouble installing RMySQL on a clean install of Fedora Core 4 64 > bit on a dual dual core machine (that is, two dual core processors). Seems > like the LD_LIBRARY_PATH is incorrect, but I don't seem to have it quite > right yet. > > There are a few mentions of this problem in google, but thus far none of the > "fixes" and fixed my problem. I've tried defining the LD_LIBRARY_PATH > environment variable, and setting the PKG_CPPFLAGS, and PKG_LIBS environment > variables as well. No luck so far. > > (initially would not compile, but specification of the PKG_CPPFLAGS, and > PKG_LIBS got the compile to complete without errors). I still cannot load > the library. My error message is: > > > library(RMySQL) > Loading required package: DBI > Error in dyn.load(x, as.logical(local), as.logical(now)) : > unable to load shared library > '/usr/lib64/R/library/RMySQL/libs/RMySQL.so': > /usr/lib64/R/library/RMySQL/libs/RMySQL.so: undefined symbol: > mysql_field_count > Error in library(RMySQL) : .First.lib failed for 'RMySQL' > > > > Trying to install the newest RMySQL on the newest R. > > > version > _ > platform x86_64-redhat-linux-gnu > arch x86_64 > os linux-gnu > system x86_64, linux-gnu > status > major 2 > minor 2.1 > year 2005 > month 12 > day 20 > svn rev 36812 > language R > > ********************* > I find libmysqlclient.so in the following location(s). > > [EMAIL PROTECTED] mtaylor]# locate libmysqlclient.so > /usr/lib/mysql/libmysqlclient.so.14.0.0 > /usr/lib/mysql/libmysqlclient.so.14 > /usr/lib64/mysql/libmysqlclient.so.10.0.0 > /usr/lib64/mysql/libmysqlclient.so.10 > /usr/lib64/mysql/libmysqlclient.so.14.0.0 > /usr/lib64/mysql/libmysqlclient.so.14 > /usr/lib64/mysql/libmysqlclient.so > /usr/lib64/mysql3/mysql/libmysqlclient.so.10.0.0 > /usr/lib64/mysql3/mysql/libmysqlclient.so.10 > /usr/lib64/mysql3/mysql/libmysqlclient.so > > ********************** > > I set the LD_LIBRARY_PATH according to these results, then double checked > that > it was set. (I also set it to /usr/lib64/mysql3/mysql as another iteration) > > [EMAIL PROTECTED] mtaylor]# printenv LD_LIBRARY_PATH > /usr/lib64/mysql3/ > > Just to be sure... > > [EMAIL PROTECTED] mtaylor]# printenv PKG_CPPFLAGS > -I/usr/include/mysql > > [EMAIL PROTECTED] mtaylor]# printenv PKG_LIBS > -L/usr/lib64/mysql > > (also tried PKG_LIBS=-L/usr/lib64/mysql3/mysql and PKG_LIBS=-L/usr/lib/mysql) > > I recompiled the package each time with R CMD INSTALL RMySQL_0.5-7.tar.gz, > but > I always get the same error message. > > ****************** > appears to install .... > > [EMAIL PROTECTED] mtaylor]# R CMD INSTALL RMySQL_0.5-7.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 > gcc -I/usr/lib64/R/include -I/usr/include/mysql -I/usr/local/include -fPIC > -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m64 -mtune=nocona -c > RS-DBI.c -o RS-DBI.o > gcc -I/usr/lib64/R/include -I/usr/include/mysql -I/usr/local/include -fPIC > -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m64 -mtune=nocona -c > RS-MySQL.c -o RS-MySQL.o > gcc -shared -L/usr/local/lib64 -o RMySQL.so RS-DBI.o RS-MySQL.o > -L/usr/lib/mysql -lz -L/usr/lib64/R/lib -lR > ** R > ** inst > ** save image > . > snip > . > ** building package indices ... > * DONE (RMySQL) > > > [EMAIL PROTECTED] mtaylor]# /sbin/ldconfig -v | grep mysql > /usr/lib/mysql: > libmysqlclient.so.14 -> libmysqlclient.so.14.0.0 > libmysqlclient_r.so.14 -> libmysqlclient_r.so.14.0.0 > /usr/lib64/mysql: > libmysqlclient_r.so.10 -> libmysqlclient_r.so.10.0.0 > libmysqlclient.so.14 -> libmysqlclient.so.14.0.0 > libmysqlclient_r.so.14 -> libmysqlclient_r.so.14.0.0 > libmysqlclient.so.10 -> libmysqlclient.so.10.0.0 > > just to make sure the headers are actually in the specified location... > > [EMAIL PROTECTED] mtaylor]# ls /usr/include/mysql > chardefs.h m_ctype.h my_dir.h my_no_pthread.h mysql_embed.h > my_xml.h rlshell.h sslopt-longopts.h > errmsg.h m_string.h my_getopt.h my_pthread.h mysql.h > raid.h > rltypedefs.h sslopt-vars.h > history.h my_alloc.h my_global.h my_semaphore.h mysql_time.h > readline.h sql_common.h tilde.h > keycache.h my_config.h my_list.h mysql_com.h mysql_version.h > rlmbutil.h sql_state.h typelib.h > keymaps.h my_dbug.h my_net.h mysqld_error.h my_sys.h > rlprivate.h sslopt-case.h xmalloc.h > > > There is a dial in here somewhere that I think I am turning the wrong > direction - just can't see it. Any experience with this one? > > > -- > ======================================= > Michaell Taylor, PhD. > Principal > Boxwood Means, Inc. > 203.653.4100 > > ______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
We did have similar problems, but it turned out to be a MySQL installation problem -- for unknown reasons (to me, at least) the symbolic link to libmysqlclient.so.14 was pointing nowhere. After re-installing the client and devel RPMS things worked fine: export PKG_LIBS='-L/usr/lib64/mysql -lmysqlclient' export PKG_CPPFLAGS=-I/usr/include/mysql R CMD INSTALL -l /tmp/R RMySQL_0.5-7.tar.gz ... > library(RMySQL, lib.loc="/tmp/R") Loading required package: DBI > sessionInfo() R version 2.2.1, 2005-12-20, x86_64-unknown-linux-gnu attached base packages: [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" [7] "base" other attached packages: RMySQL DBI "0.5-7" "0.1-9" Hope this helps, -- David ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
