Problems installing RMariaDB on ubuntu 22

[vboyce]

I have installed libmariadb-dev and libssl-dev.

sudo apt-get install -y libmariadb-dev
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
libmariadb-dev is already the newest version (1:10.6.18-0ubuntu0.22.04.1).

sudo apt install libssl-dev
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
libssl-dev is already the newest version (3.0.2-0ubuntu1.17).

When I try to install RMariaDB using install.packages("RMariaDB"), I get the following error:

Error: package or namespace load failed for ‘RMariaDB’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-RMariaDB/00new/RMariaDB/libs/RMariaDB.so':
libmysqlclient.so.20: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted

This seems like it may be the same issue as #168.

The same issue occurs if I install libmysqlclient-dev instead of libmariadb-dev.

The same issue occurs if I install the dev version of RMariaDB from github.

In case it's relevant, it says that it's using "mysql_config" -- I don't know how to force it to use mariadb_config instead or whether this matters.

[krlmlr]

Thanks. Can you please post the complete log from install.packages() ?

[vboyce]

install.packages("RMariaDB")
Installing package into ‘/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/RMariaDB_1.3.2.tar.gz'
Content type 'application/x-gzip' length 909239 bytes (887 KB)
==================================================
downloaded 887 KB

• installing source package ‘RMariaDB’ ...
  ** package ‘RMariaDB’ successfully unpacked and MD5 sums checked
  ** using staged installation
  Using mysql_config
  RMariaDB 1.2.0 will default to use mariadb_config.
  Set the RMARIADB_FORCE_MYSQLCONFIG environment variable to a nonempty value to force mysql_config.
  Found mysql_config cflags and libs!
  Using PKG_CFLAGS=-I/home/vboyce/miniconda3/include/mysql
  Using PKG_LIBS=-L/home/vboyce/miniconda3/lib -lmysqlclient -lpthread -lm -lrt -latomic -lssl -lcrypto -ldl
  Using PKG_PLOGR=
  ** libs
  g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I/home/vboyce/miniconda3/include/mysql -Ivendor -DBOOST_NO_AUTO_PTR -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/cpp11/include' -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/plogr/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c DbConnection.cpp -o DbConnection.o
  g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I/home/vboyce/miniconda3/include/mysql -Ivendor -DBOOST_NO_AUTO_PTR -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/cpp11/include' -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/plogr/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c DbResult.cpp -o DbResult.o
  g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I/home/vboyce/miniconda3/include/mysql -Ivendor -DBOOST_NO_AUTO_PTR -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/cpp11/include' -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/plogr/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c MariaBinding.cpp -o MariaBinding.o
  g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I/home/vboyce/miniconda3/include/mysql -Ivendor -DBOOST_NO_AUTO_PTR -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/cpp11/include' -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/plogr/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c MariaResult.cpp -o MariaResult.o
  g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I/home/vboyce/miniconda3/include/mysql -Ivendor -DBOOST_NO_AUTO_PTR -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/cpp11/include' -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/plogr/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c MariaResultImpl.cpp -o MariaResultImpl.o
  g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I/home/vboyce/miniconda3/include/mysql -Ivendor -DBOOST_NO_AUTO_PTR -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/cpp11/include' -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/plogr/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c MariaResultPrep.cpp -o MariaResultPrep.o
  g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I/home/vboyce/miniconda3/include/mysql -Ivendor -DBOOST_NO_AUTO_PTR -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/cpp11/include' -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/plogr/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c MariaResultSimple.cpp -o MariaResultSimple.o
  g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I/home/vboyce/miniconda3/include/mysql -Ivendor -DBOOST_NO_AUTO_PTR -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/cpp11/include' -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/plogr/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c MariaRow.cpp -o MariaRow.o
  g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I/home/vboyce/miniconda3/include/mysql -Ivendor -DBOOST_NO_AUTO_PTR -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/cpp11/include' -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/plogr/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c MariaTypes.cpp -o MariaTypes.o
  g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I/home/vboyce/miniconda3/include/mysql -Ivendor -DBOOST_NO_AUTO_PTR -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/cpp11/include' -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/plogr/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c MariaUtils.cpp -o MariaUtils.o
  g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I/home/vboyce/miniconda3/include/mysql -Ivendor -DBOOST_NO_AUTO_PTR -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/cpp11/include' -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/plogr/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c connection.cpp -o connection.o
  g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I/home/vboyce/miniconda3/include/mysql -Ivendor -DBOOST_NO_AUTO_PTR -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/cpp11/include' -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/plogr/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cpp11.cpp -o cpp11.o
  g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I/home/vboyce/miniconda3/include/mysql -Ivendor -DBOOST_NO_AUTO_PTR -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/cpp11/include' -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/plogr/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c driver.cpp -o driver.o
  g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I/home/vboyce/miniconda3/include/mysql -Ivendor -DBOOST_NO_AUTO_PTR -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/cpp11/include' -I'/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/plogr/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c result.cpp -o result.o
  g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o RMariaDB.so DbConnection.o DbResult.o MariaBinding.o MariaResult.o MariaResultImpl.o MariaResultPrep.o MariaResultSimple.o MariaRow.o MariaTypes.o MariaUtils.o connection.o cpp11.o driver.o result.o -L/home/vboyce/miniconda3/lib -lmysqlclient -lpthread -lm -lrt -latomic -lssl -lcrypto -ldl -L/usr/lib/R/lib -lR
  installing to /home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-RMariaDB/00new/RMariaDB/libs
  ** R
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** testing if installed package can be loaded from temporary location
  Error: package or namespace load failed for ‘RMariaDB’ in dyn.load(file, DLLpath = DLLpath, ...):
  unable to load shared object '/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-RMariaDB/00new/RMariaDB/libs/RMariaDB.so':
  libmysqlclient.so.20: cannot open shared object file: No such file or directory
  Error: loading failed
  Execution halted
  ERROR: loading failed
• removing ‘/home/vboyce/R/x86_64-pc-linux-gnu-library/4.1/RMariaDB’
  Warning in install.packages :
  installation of package ‘RMariaDB’ had non-zero exit status

The downloaded source packages are in
‘/tmp/Rtmp6WBxMs/downloaded_packages’

[krlmlr]

For some reason, compilation seems to use libs from miniconda:

Found mysql_config cflags and libs!
Using PKG_CFLAGS=-I/home/vboyce/miniconda3/include/mysql
Using PKG_LIBS=-L/home/vboyce/miniconda3/lib -lmysqlclient -lpthread -lm -lrt -latomic -lssl -lcrypto -ldl

Is this intended? Is there a libmysqlclient.so.20 somewhere underneath the miniconda path?

[vboyce]

That was not my intention at least.

I did conda remove mysql and then restarted R and RMariaDB installed just fine. Thanks!