2

I'm trying to install the the RMySQL package using

bash > R ... > install.packages('RMySQL', repos='http://cran.us.r-project.org')

and get the following output with an error at the end:

Installing package into ‘/usr/local/lib/R/3.2/site-library’ (as ‘lib’ is unspecified) trying URL 'http://cran.us.r-project.org/src/contrib/RMySQL_0.10.6.tar.gz' Content type 'application/x-gzip' length 52407 bytes (51 KB) ================================================== downloaded 51 KB * installing *source* package ‘RMySQL’ ... ** package ‘RMySQL’ successfully unpacked and MD5 sums checked Found mysql_config cflags and libs! Using PKG_CFLAGS=-I/usr/local/mysql/include -g -fno-omit-frame-pointer -fno-strict-aliasing -arch x86_64 Using PKG_LIBS=-L/usr/local/mysql/lib -lmysqlclient ** libs clang -I/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/include -DNDEBUG -I/usr/local/mysql/include -g -fno-omit-frame-pointer -fno-strict-aliasing -arch x86_64 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -fPIC -g -O2 -c RMySQL-init.c -o RMySQL-init.o clang -I/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/include -DNDEBUG -I/usr/local/mysql/include -g -fno-omit-frame-pointer -fno-strict-aliasing -arch x86_64 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -fPIC -g -O2 -c connection.c -o connection.o clang -I/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/include -DNDEBUG -I/usr/local/mysql/include -g -fno-omit-frame-pointer -fno-strict-aliasing -arch x86_64 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -fPIC -g -O2 -c db-apply.c -o db-apply.o clang -I/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/include -DNDEBUG -I/usr/local/mysql/include -g -fno-omit-frame-pointer -fno-strict-aliasing -arch x86_64 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -fPIC -g -O2 -c driver.c -o driver.o clang -I/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/include -DNDEBUG -I/usr/local/mysql/include -g -fno-omit-frame-pointer -fno-strict-aliasing -arch x86_64 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -fPIC -g -O2 -c exception.c -o exception.o clang -I/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/include -DNDEBUG -I/usr/local/mysql/include -g -fno-omit-frame-pointer -fno-strict-aliasing -arch x86_64 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -fPIC -g -O2 -c fields.c -o fields.o clang -I/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/include -DNDEBUG -I/usr/local/mysql/include -g -fno-omit-frame-pointer -fno-strict-aliasing -arch x86_64 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -fPIC -g -O2 -c result.c -o result.o clang -I/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/include -DNDEBUG -I/usr/local/mysql/include -g -fno-omit-frame-pointer -fno-strict-aliasing -arch x86_64 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -fPIC -g -O2 -c utils.c -o utils.o clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/openssl/lib -o RMySQL.so RMySQL-init.o connection.o db-apply.o driver.o exception.o fields.o result.o utils.o -L/usr/local/mysql/lib -lmysqlclient -F/usr/local/Cellar/r/3.2.2_1/R.framework/.. -framework R -lintl -Wl,-framework -Wl,CoreFoundation installing to /usr/local/lib/R/3.2/site-library/RMySQL/libs ** R ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/usr/local/lib/R/3.2/site-library/RMySQL/libs/RMySQL.so': dlopen(/usr/local/lib/R/3.2/site-library/RMySQL/libs/RMySQL.so, 6): Library not loaded: libmysqlclient.18.dylib Referenced from: /usr/local/lib/R/3.2/site-library/RMySQL/libs/RMySQL.so Reason: image not found Error: loading failed Execution halted ERROR: loading failed * removing ‘/usr/local/lib/R/3.2/site-library/RMySQL’ The downloaded source packages are in ‘/private/var/folders/87/wkgwm0754tn9csz8295qjmmc000bxz/T/RtmpxlEAlo/downloaded_packages’ Warning message: In install.packages("RMySQL", repos = "http://cran.us.r-project.org") : installation of package ‘RMySQL’ had non-zero exit status > > install.packages('RMySQL', repos='http://cran.us.r-project.org') Installing package into ‘/usr/local/lib/R/3.2/site-library’ (as ‘lib’ is unspecified) trying URL 'http://cran.us.r-project.org/src/contrib/RMySQL_0.10.6.tar.gz' Content type 'application/x-gzip' length 52407 bytes (51 KB) ================================================== downloaded 51 KB * installing *source* package ‘RMySQL’ ... ** package ‘RMySQL’ successfully unpacked and MD5 sums checked Found mysql_config cflags and libs! Using PKG_CFLAGS=-I/usr/local/mysql/include -g -fno-omit-frame-pointer -fno-strict-aliasing -arch x86_64 Using PKG_LIBS=-L/usr/local/mysql/lib -lmysqlclient ** libs clang -I/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/include -DNDEBUG -I/usr/local/mysql/include -g -fno-omit-frame-pointer -fno-strict-aliasing -arch x86_64 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -fPIC -g -O2 -c RMySQL-init.c -o RMySQL-init.o clang -I/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/include -DNDEBUG -I/usr/local/mysql/include -g -fno-omit-frame-pointer -fno-strict-aliasing -arch x86_64 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -fPIC -g -O2 -c connection.c -o connection.o clang -I/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/include -DNDEBUG -I/usr/local/mysql/include -g -fno-omit-frame-pointer -fno-strict-aliasing -arch x86_64 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -fPIC -g -O2 -c db-apply.c -o db-apply.o clang -I/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/include -DNDEBUG -I/usr/local/mysql/include -g -fno-omit-frame-pointer -fno-strict-aliasing -arch x86_64 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -fPIC -g -O2 -c driver.c -o driver.o clang -I/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/include -DNDEBUG -I/usr/local/mysql/include -g -fno-omit-frame-pointer -fno-strict-aliasing -arch x86_64 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -fPIC -g -O2 -c exception.c -o exception.o clang -I/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/include -DNDEBUG -I/usr/local/mysql/include -g -fno-omit-frame-pointer -fno-strict-aliasing -arch x86_64 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -fPIC -g -O2 -c fields.c -o fields.o clang -I/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/include -DNDEBUG -I/usr/local/mysql/include -g -fno-omit-frame-pointer -fno-strict-aliasing -arch x86_64 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -fPIC -g -O2 -c result.c -o result.o clang -I/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/include -DNDEBUG -I/usr/local/mysql/include -g -fno-omit-frame-pointer -fno-strict-aliasing -arch x86_64 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -fPIC -g -O2 -c utils.c -o utils.o clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/openssl/lib -o RMySQL.so RMySQL-init.o connection.o db-apply.o driver.o exception.o fields.o result.o utils.o -L/usr/local/mysql/lib -lmysqlclient -F/usr/local/Cellar/r/3.2.2_1/R.framework/.. -framework R -lintl -Wl,-framework -Wl,CoreFoundation installing to /usr/local/lib/R/3.2/site-library/RMySQL/libs ** R ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/usr/local/lib/R/3.2/site-library/RMySQL/libs/RMySQL.so': dlopen(/usr/local/lib/R/3.2/site-library/RMySQL/libs/RMySQL.so, 6): Library not loaded: libmysqlclient.18.dylib Referenced from: /usr/local/lib/R/3.2/site-library/RMySQL/libs/RMySQL.so Reason: image not found Error: loading failed Execution halted ERROR: loading failed * removing ‘/usr/local/lib/R/3.2/site-library/RMySQL’ The downloaded source packages are in ‘/private/var/folders/87/wkgwm0754tn9csz8295qjmmc000bxz/T/RtmpxlEAlo/downloaded_packages’ Warning message: In install.packages("RMySQL", repos = "http://cran.us.r-project.org") : installation of package ‘RMySQL’ had non-zero exit status

Any idea?

Improve this question
2
  • 1
    Can you give us some details on your Linux platform? This works reliably on Debian/Ubuntu... And FWIW I am having more luck with MariaDB rather than MySQL; the package will happily take either. Commented Sep 7, 2015 at 19:16
  • How did you install /usr/local/mysql/? Is that brew? Commented Sep 7, 2015 at 20:49

1 Answer 1

Reset to default
2

You need to give more details about your installation. I guess you are using a homebrew version of R? You are strongly recommended to use the official R package for mac instead, which is what the CRAN build servers (and most users) are using.

That said, there seems to be something odd with your libmysqlclient installation. Assuming this is brew, try reinstalling:

brew remove mysql-connector-c brew upgrade brew install mysql-connector-c

Verify that libmysqlclient.18.dylib is installed:

ls /usr/local/opt/mysql-connector-c/lib

Alternatively you can try linking to mariadb:

brew remove mysql-connector-c brew install mariadb

If this doesn't work it might be a bug in the brew version of R. The compiler fails to record the path to libmysqlclient.18.dylib. Maybe R not passing the correct RPATH flags to the linker.

Improve this answer
Sign up to request clarification or add additional context in comments.

1 Comment

Thanks. It is Homebrew. But after (re-)installing mysql-connector-c, and re-attempting to install the package (install.packages('RMySQL', repos='http://cran.us.r-project.org')), I still see the same error.

Start asking to get answers

Find the answer to your question by asking.

Ask question

Explore related questions

See similar questions with these tags.