在 SUSE Tumbleweed 上安装 RMySQL 的新错误

Posted 2023-03-23

【中文标题】在 SUSE Tumbleweed 上安装 RMySQL 的新错误

【英文标题】：New Error installing RMySQL on SUSE Tumbleweed

【发布时间】：2021-09-05 08:23:51

【问题描述】：

我在 SUSE Tumbleweed 20210618 上安装 Rmysql 时遇到了一个“新”问题。我以前使用过 RMySQL，但在项目之间，RMySQL 神秘地从 R 中消失了。

现在，当我运行“install.packages”时 - 它错误地读取了我的 mysql_config 参数（如下所示）。从 mysql_config 信息（也如下所示）可以看出，两者不匹配。

有没有办法“纠正” PKG_CFLAGS 和 PKG_LIBS 的设置方式 - 以便它们指向正确的位置？或者，是否还有其他问题导致这种情况持续存在？

谢谢...

这是我的“install.packages”运行：

Installing package into ‘/home/craig/R/x86_64-suse-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/RMySQL_0.10.21.tar.gz'
Content type 'application/x-gzip' length 53075 bytes (51 KB)
==================================================
downloaded 51 KB

* installing *source* package ‘RMySQL’ ...
** package ‘RMySQL’ successfully unpacked and MD5 sums checked
** using staged installation
Found mysql_config cflags and libs!
Using PKG_CFLAGS=-I/usr//usr/include/mysql -I/usr//usr/include/mysql/mysql
Using PKG_LIBS=-L/usr//usr/lib64/ -lmariadb
-----------------------------[ ANTICONF ]-----------------------------
Configure could not find suitable mysql/mariadb client library. Try installing:
 * deb: libmariadbclient-dev | libmariadb-client-lgpl-dev (Debian, Ubuntu)
 * rpm: mariadb-connector-c-devel | mariadb-devel | mysql-devel (Fedora, CentOS, RHEL)
 * csw: mysql56_dev (Solaris)
 * brew: mariadb-connector-c (OSX)
If you already have a mysql client library installed, verify that either
mariadb_config or mysql_config is on your PATH. If these are unavailable
you can also set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------[ ERROR MESSAGE ]----------------------------
<stdin>:1:10: fatal error: mysql.h: No such file or directory
compilation terminated.
-----------------------------------------------------------------------
ERROR: configuration failed for package ‘RMySQL’
* removing ‘/home/craig/R/x86_64-suse-linux-gnu-library/4.1/RMySQL’
Warning in install.packages :
  installation of package ‘RMySQL’ had non-zero exit status

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

我来自 mysql_config 的信息是：

Copyright 2011-2020 MariaDB Corporation AB
Get compiler flags for using the MariaDB Connector/C.
Usage: mysql_config [OPTIONS]
Compiler: GNU 11.1.1
  --cflags        [-I//usr/include/mysql -I//usr/include/mysql/mysql]
  --include       [-I//usr/include/mysql -I//usr/include/mysql/mysql]
  --libs          [-L//usr/lib64/ -lmariadb]
  --libs_r        [-L//usr/lib64/ -lmariadb]
  --libs_sys      [-lz -ldl -lm -lpthread -lssl -lcrypto]
  --version       [10.5.5]
  --cc_version    [3.1.12]
  --socket        [/run/mysql/mysql.sock]
  --port          [3306]
  --plugindir     [-L/usr/lib64 -lmariadbprivate -lz -ldl -lm -lpthread -lssl -lcrypto]
  --tlsinfo       [//usr/lib64/mysql/plugin/]
  --variable=OpenSSL 1.1.1k
      pkgincludedir  [//usr/include/mysql]
      pkglibdir      [//usr/lib64]
      pkgplugindir   [//usr/lib64/mysql/plugin/]
  --privatelibs   [VAR  VAR is one of:]

请注意，来自 install.packages 命令的 PKG_CFLAGS 读取配置文件不正确（例如，将其转换为 -I/usr//usr/include... 而不是 -I//usr/include... )。

【参考方案1】：

我尝试了很多排列，但通过下载适当的 RMySQL...tar.gz 文件然后执行以下命令找到了解决方案：

> R CMD INSTALL --configure-vars='INCLUDE_DIR=/usr/include/mysql/mysql INCLUDE_DIR=/usr/include/mysql  LIB_DIR=/usr/lib64/ LIB=mariadb' RMySQL_0.10.21.tar.gz 

这导致：

* installing to library ‘/home/craig/R/x86_64-suse-linux-gnu-library/4.1’
* installing *source* package ‘RMySQL’ ...
** package ‘RMySQL’ successfully unpacked and MD5 sums checked
** using staged installation
Found INCLUDE_DIR and/or LIB_DIR!
Using PKG_CFLAGS=-I/usr/include/mysql 
Using PKG_LIBS=-L/usr/lib64/ -lmysqlclient
** libs
rm -f RMySQL.so RMySQL-init.o connection.o db-apply.o driver.o exception.o fields.o result.o utils.o
gcc -I"/usr/lib64/R/include" -DNDEBUG -I/usr/include/mysql   -I/usr/local/include   -fpic  -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-***-protection -Werror=return-type -flto=auto  -c RMySQL-init.c -o RMySQL-init.o
gcc -I"/usr/lib64/R/include" -DNDEBUG -I/usr/include/mysql   -I/usr/local/include   -fpic  -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-***-protection -Werror=return-type -flto=auto  -c connection.c -o connection.o
gcc -I"/usr/lib64/R/include" -DNDEBUG -I/usr/include/mysql   -I/usr/local/include   -fpic  -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-***-protection -Werror=return-type -flto=auto  -c db-apply.c -o db-apply.o
gcc -I"/usr/lib64/R/include" -DNDEBUG -I/usr/include/mysql   -I/usr/local/include   -fpic  -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-***-protection -Werror=return-type -flto=auto  -c driver.c -o driver.o
gcc -I"/usr/lib64/R/include" -DNDEBUG -I/usr/include/mysql   -I/usr/local/include   -fpic  -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-***-protection -Werror=return-type -flto=auto  -c exception.c -o exception.o
gcc -I"/usr/lib64/R/include" -DNDEBUG -I/usr/include/mysql   -I/usr/local/include   -fpic  -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-***-protection -Werror=return-type -flto=auto  -c fields.c -o fields.o
gcc -I"/usr/lib64/R/include" -DNDEBUG -I/usr/include/mysql   -I/usr/local/include   -fpic  -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-***-protection -Werror=return-type -flto=auto  -c result.c -o result.o
gcc -I"/usr/lib64/R/include" -DNDEBUG -I/usr/include/mysql   -I/usr/local/include   -fpic  -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-***-protection -Werror=return-type -flto=auto  -c utils.c -o utils.o
utils.c: In function ‘RS_DBI_newEntry’:
utils.c:132:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  132 |   for(i = 0; i < length; i++)
      |   ^~~
utils.c:137:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  137 |     return indx;
      |     ^~~~~~
gcc -shared -L/usr/lib64/R/lib -flto=auto -o RMySQL.so RMySQL-init.o connection.o db-apply.o driver.o exception.o fields.o result.o utils.o -L/usr/lib64/ -lmysqlclient -L/usr/lib64/R/lib -lR
installing to /home/craig/R/x86_64-suse-linux-gnu-library/4.1/00LOCK-RMySQL/00new/RMySQL/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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RMySQL)