让 ROracle 在 ubuntu 上运行

Question

我已经从 Oracle 下载了 ROracle 1.3-1.tar.gz 和 Oracle 即时客户端 12.2 基本和开发 rpm。

如this post 中所述，我执行了这些命令：

export ORACLE_HOME=/usr/lib/oracle/12.2/client64
sudo mkdir $ORACLE_HOME/rdbms
sudo mkdir $ORACLE_HOME/rdbms/public
sudo cp /usr/include/oracle/12.2/client64/* $ORACLE_HOME/rdbms/public

我尝试使用

安装 ROracle

R CMD INSTALL --configure-args='--with-oci-lib=/usr/lib/oracle/12.2/client64/lib --with-oci-inc=/usr/include/oracle/12.2/client64'  ROracle_1.3-1.tar.gz

然后输出显示

* installing to library ‘/home/s9970/R/x86_64-pc-linux-gnu-library/3.4’
* installing *source* package ‘ROracle’ ...
** package ‘ROracle’ successfully unpacked and MD5 sums checked
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/oracle/12.2/client64     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rodbi.c -o rodbi.o
In file included from rodbi.c:182:0:
rodbi.c: In function ‘rodbiResBind’:
rodbi.h:43:20: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 3 has type ‘sb8 {aka long int}’ [-Wformat=]
 # define _(String) (String)
                    ^
rodbi.c:200:36: note: in expansion of macro ‘_’
 #define RODBI_ERR_BIND_VAL_TOOBIG  _("bind value is too big(%lld), exceeds 2GB")
                                    ^
rodbi.c:2432:26: note: in expansion of macro ‘RODBI_ERR_BIND_VAL_TOOBIG’
         sprintf(err_buf, RODBI_ERR_BIND_VAL_TOOBIG, bndsz);
                          ^
rodbi.h:43:20: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 3 has type ‘sb8 {aka long int}’ [-Wformat=]
 # define _(String) (String)
                    ^
rodbi.c:200:36: note: in expansion of macro ‘_’
 #define RODBI_ERR_BIND_VAL_TOOBIG  _("bind value is too big(%lld), exceeds 2GB")
                                    ^
rodbi.c:2469:26: note: in expansion of macro ‘RODBI_ERR_BIND_VAL_TOOBIG’
         sprintf(err_buf, RODBI_ERR_BIND_VAL_TOOBIG, bndsz);
                          ^
rodbi.c: In function ‘rodbiPlsqlResBind’:
rodbi.h:43:20: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 3 has type ‘sb8 {aka long int}’ [-Wformat=]
 # define _(String) (String)
                    ^
rodbi.c:200:36: note: in expansion of macro ‘_’
 #define RODBI_ERR_BIND_VAL_TOOBIG  _("bind value is too big(%lld), exceeds 2GB")
                                    ^
rodbi.c:2816:28: note: in expansion of macro ‘RODBI_ERR_BIND_VAL_TOOBIG’
           sprintf(err_buf, RODBI_ERR_BIND_VAL_TOOBIG, bndsz);
                            ^
rodbi.h:43:20: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 3 has type ‘sb8 {aka long int}’ [-Wformat=]
 # define _(String) (String)
                    ^
rodbi.c:200:36: note: in expansion of macro ‘_’
 #define RODBI_ERR_BIND_VAL_TOOBIG  _("bind value is too big(%lld), exceeds 2GB")
                                    ^
rodbi.c:2861:28: note: in expansion of macro ‘RODBI_ERR_BIND_VAL_TOOBIG’
           sprintf(err_buf, RODBI_ERR_BIND_VAL_TOOBIG, bndsz);
                            ^
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/oracle/12.2/client64     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rooci.c -o rooci.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o ROracle.so rodbi.o rooci.o -L/usr/lib/oracle/12.2/client64/lib -lclntsh -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -lclntsh
collect2: error: ld returned 1 exit status
/usr/share/R/share/make/shlib.mk:6: recipe for target 'ROracle.so' failed
make: *** [ROracle.so] Error 1
ERROR: compilation failed for package ‘ROracle’
* removing ‘/home/s9970/R/x86_64-pc-linux-gnu-library/3.4/ROracle’

我尝试导出这些环境变量，然后运行不带参数的命令，但我得到了同样的错误。

export LD_LIBRARY_PATH=/usr/lib/oracle/12.2/client64/lib:$LD_LIBRARY_PATH    
export ORACLE_HOME=/usr/lib/oracle/12.2/client64
export OCI_LIB=/usr/lib/oracle/12.2/client64/lib
export LD_LIBRARY_PATH_64=/usr/lib/oracle/11.2/client6/lib:$LD_LIBRARY_PATH_64
R CMD INSTALL ROracle_1.3-1.tar.gz

我还将LD_LIBRARY_PATH 写入conf 文件，如here 所述，通过

echo "/usr/lib/oracle/12.2/client64/lib" | sudo tee /etc/ld.so.conf.d/oracle.conf

当我尝试从 Rstudio 加载 ROracle 时，仍然出现以下错误：

> library(ROracle)
Loading required package: DBI
Error: package or namespace load failed for ‘ROracle’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/usr/local/lib/R/site-library/ROracle/libs/ROracle.so':
  libclntsh.so.11.1: cannot open shared object file: No such file or directory

我在 /usr/lib/oracle/12.2/client64/lib/ 处设置了从 libclntsh.so.12.1 到 libclntsh.so.11.1 的合成链接，但在我看来，RStudio 正在错误的位置寻找我的 R - 即 /usr/local/... 而不是 usr/...。 我该如何解决这个问题？

我也试过设置

export RSTUDIO_WHICH_R=/usr/bin/R

但它也没有帮助。

Answer 1

根据 ROracle INSTALL 文档，您应该使用

export LD_LIBRARY_PATH=/usr/lib/oracle/12.2/client64/lib:$LD_LIBRARY_PATH

注意缺少的$LD_LIBRARY_PATH。

安装后，您可能希望看到下面的加载包：

1. ROracle not working in R studio
2. failing to load ROracle: unable to load shared object ROracle.so: libclntsh.so.11.1 No such file or directory

Answer 2

安装 ROracle 真的很痛苦。我发现效果很好的不是在每个安装命令前面加上sudo，而是使用sudo su 切换到超级用户，然后以超级用户身份执行整个安装。我不是 Linux 专家，所以我不能告诉你为什么这是一种更稳定的方式。但它对我们有用。

我们还添加了一个 bash 文件 oracle.sh 到 /etc/profile.d/

oracle.sh

LD_LIBRARY_PATH="/usr/lib/oracle/12.1/client64/lib:${LD_LIBRARY_PATH}"
export LD_LIBRARY_PATH

Answer 3

sudo sh -c "echo /usr/lib/oracle/12.2/client64/lib > /etc/ld.so.conf.d/oracle-
instantclient.conf" sudo ldconfig

描述于

https://github.com/oracle/node-oracledb/issues/453

为我工作。

我用过

dyn.load('/usr/lib/oracle/12.1/client64/lib/libclntsh.so.12.1')

在 R 中检查。在执行上述命令之前，它返回错误。

我想知道前面提到的oracle.conf（check here）和oracle-instantclient.conf之间有什么区别（如果有的话）

Answer 4

这解决了我的问题：

R CMD INSTALL --configure-args='--with-oci-lib=/usr/lib/oracle/19.3/client64/lib --with-oci-inc=/usr/include/oracle/19.3/client64' ../ROracle_1.3-1.tar.gz