Fedora: MariaDB vs mariadb

[bowerth]

Hello -
many thanks for the package -
I could install on Fedora 25 after installation of mariadb-devel, as explained in the readme.
Soon afterwards, I noticed the current stable version 10.1 does not support JSON functions and I installed the release candidate version 10.2 according to https://downloads.mariadb.org/mariadb/repositories/#mirror=babylon-fr&distro=Fedora&distro_release=fedora25-amd64--fedora25&version=10.2

RMySQL works like charm. However, if I attempt to re-install RMySQL (from CRAN or GitHub), I receive the error /usr/bin/ld: cannot find -lmariadb

>  install.packages("RMySQL")
Installing package into ‘/home/xps13/R/x86_64-redhat-linux-gnu-library/3.3’
(as ‘lib’ is unspecified)
trying URL 'http://cran.univ-paris1.fr/src/contrib/RMySQL_0.10.11.tar.gz'
Content type 'application/x-gzip' length 54186 bytes (52 KB)
==================================================
downloaded 52 KB

* installing *source* package ‘RMySQL’ ...
** package ‘RMySQL’ successfully unpacked and MD5 sums checked
Found mysql_config cflags and libs!
Using PKG_CFLAGS=-I/usr/include/mysql -I/usr/include/mysql/mysql
Using PKG_LIBS=-L/usr/lib64/ -lmariadb -lpthread -ldl -lm -lssl -lcrypto
** libs
gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/include/mysql -I/usr/include/mysql/mysql -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c RMySQL-init.c -o RMySQL-init.o
gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/include/mysql -I/usr/include/mysql/mysql -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c connection.c -o connection.o
gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/include/mysql -I/usr/include/mysql/mysql -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c db-apply.c -o db-apply.o
gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/include/mysql -I/usr/include/mysql/mysql -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c driver.c -o driver.o
gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/include/mysql -I/usr/include/mysql/mysql -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c exception.c -o exception.o
gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/include/mysql -I/usr/include/mysql/mysql -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c fields.c -o fields.o
gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/include/mysql -I/usr/include/mysql/mysql -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c result.c -o result.o
gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/include/mysql -I/usr/include/mysql/mysql -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c utils.c -o utils.o
utils.c: In function ‘RS_DBI_newEntry’:
utils.c:131:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
   for(i = 0; i < length; i++)
   ^~~
utils.c:136:5: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘for’
     return indx;
     ^~~~~~
gcc -m64 -shared -L/usr/lib64/R/lib -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o RMySQL.so RMySQL-init.o connection.o db-apply.o driver.o exception.o fields.o result.o utils.o -L/usr/lib64/ -lmariadb -lpthread -ldl -lm -lssl -lcrypto -L/usr/lib64/R/lib -lR
/usr/bin/ld: cannot find -lmariadb
collect2: error: ld returned 1 exit status
/usr/share/R/make/shlib.mk:6: recipe for target 'RMySQL.so' failed
make: *** [RMySQL.so] Error 1
ERROR: compilation failed for package ‘RMySQL’
* removing ‘/home/xps13/R/x86_64-redhat-linux-gnu-library/3.3/RMySQL’
* restoring previous ‘/home/xps13/R/x86_64-redhat-linux-gnu-library/3.3/RMySQL’

The downloaded source packages are in
	‘/tmp/Rtmp2EKM8n/downloaded_packages’
Warning message:
In install.packages("RMySQL") :
  installation of package ‘RMySQL’ had non-zero exit status
>  install.packages("RMySQL")
Installing package into ‘/home/xps13/R/x86_64-redhat-linux-gnu-library/3.3’
(as ‘lib’ is unspecified)
trying URL 'http://cran.univ-paris1.fr/src/contrib/RMySQL_0.10.11.tar.gz'
Content type 'application/x-gzip' length 54186 bytes (52 KB)
==================================================
downloaded 52 KB

* installing *source* package ‘RMySQL’ ...
** package ‘RMySQL’ successfully unpacked and MD5 sums checked
Found mysql_config cflags and libs!
Using PKG_CFLAGS=-I/usr/include/mysql -I/usr/include/mysql/mysql
Using PKG_LIBS=-L/usr/lib64/ -lmariadb -lpthread -ldl -lm -lssl -lcrypto
** libs
gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/include/mysql -I/usr/include/mysql/mysql -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c RMySQL-init.c -o RMySQL-init.o
gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/include/mysql -I/usr/include/mysql/mysql -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c connection.c -o connection.o
gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/include/mysql -I/usr/include/mysql/mysql -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c db-apply.c -o db-apply.o
gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/include/mysql -I/usr/include/mysql/mysql -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c driver.c -o driver.o
gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/include/mysql -I/usr/include/mysql/mysql -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c exception.c -o exception.o
gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/include/mysql -I/usr/include/mysql/mysql -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c fields.c -o fields.o
gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/include/mysql -I/usr/include/mysql/mysql -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c result.c -o result.o
gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/include/mysql -I/usr/include/mysql/mysql -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c utils.c -o utils.o
utils.c: In function ‘RS_DBI_newEntry’:
utils.c:131:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
   for(i = 0; i < length; i++)
   ^~~
utils.c:136:5: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘for’
     return indx;
     ^~~~~~
gcc -m64 -shared -L/usr/lib64/R/lib -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o RMySQL.so RMySQL-init.o connection.o db-apply.o driver.o exception.o fields.o result.o utils.o -L/usr/lib64/ -lmariadb -lpthread -ldl -lm -lssl -lcrypto -L/usr/lib64/R/lib -lR
/usr/bin/ld: cannot find -lmariadb
collect2: error: ld returned 1 exit status
/usr/share/R/make/shlib.mk:6: recipe for target 'RMySQL.so' failed
make: *** [RMySQL.so] Error 1
ERROR: compilation failed for package ‘RMySQL’
* removing ‘/home/xps13/R/x86_64-redhat-linux-gnu-library/3.3/RMySQL’
* restoring previous ‘/home/xps13/R/x86_64-redhat-linux-gnu-library/3.3/RMySQL’

The downloaded source packages are in
	‘/tmp/Rtmp2EKM8n/downloaded_packages’
Warning message:
In install.packages("RMySQL") :
  installation of package ‘RMySQL’ had non-zero exit status

[jeroen]

I think this is a bug in that custom mariadb repo. Their packag MariaDB-devel-10.2.6-1.fc25.x86_64 only contains a library named:

/usr/lib64/libmariadbclient.a

However their pkg-config yiels another name:

> pkg-config --libs mariadb
    -lmariadb

You best raise this at the maintainers of that repo. A workaround is to symlink libmariadbclient.a to libmariadb.a:

sudo ln -s /usr/lib64/libmariadbclient.a /usr/lib64/libmariadb.a

That fixes the installation.