无法在CentOS 7上的R Studio中安装RPostgreSQL包

w8biq8rn  于 2022-11-07  发布在  PostgreSQL
关注(0)|答案(3)|浏览(131)

我安装了PostgreSQL 9.6与PostGIS 2.3使用企业数据库的一个点击安装程序在这里我的CentOS 7（x64）Linux为基础的机器上。现在我试图连接R Studio到Postgres。为此，我试图安装RPostgreSQL包在R Studio中，但我得到以下错误：

> install.packages("RPostgreSQL")
Installing package into ‘/home/jk/R/x86_64-redhat-linux-gnu-library/3.3’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/RPostgreSQL_0.4-1.tar.gz'
Content type 'unknown' length 476204 bytes (465 KB)
==================================================
downloaded 465 KB

* installing *source* package ‘RPostgreSQL’ ...
**package ‘RPostgreSQL’ successfully unpacked and MD5 sums checked

checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
checking for pg_config... no
configure: checking for PostgreSQL header files
configure: Checking include /usr/include.
configure: Checking include /usr/include/pgsql.
configure: Checking include /usr/include/postgresql.
configure: Checking include /usr/local/include.
configure: Checking include /usr/local/include/pgsql.
configure: Checking include /usr/local/include/postgresql.
configure: Checking include /usr/local/pgsql/include.
configure: Checking include /usr/local/postgresql/include.
configure: Checking include /opt/include.
configure: Checking include /opt/include/pgsql.
configure: Checking include /opt/include/postgresql.
configure: Checking include /opt/local/include.
configure: Checking include /opt/local/include/postgresql.
configure: Checking include /opt/local/include/postgresql84.
configure: Checking include /sw/opt/postgresql-8.4/include.
configure: Checking include /Library/PostgresPlus/8.4SS/include.
configure: Checking include /sw/include/postgresql.
configure: Checking lib /usr/lib.
configure: Checking lib /usr/lib/pgsql.
configure: Checking lib /usr/lib/postgresql.
configure: Checking lib /usr/local/lib.
configure: Checking lib /usr/local/lib/pgsql.
configure: Checking lib /usr/local/lib/postgresql.
configure: Checking lib /usr/local/pgsql/lib.
configure: Checking lib /usr/local/postgresql/lib.
configure: Checking lib /opt/lib.
configure: Checking lib /opt/lib/pgsql.
configure: Checking lib /opt/lib/postgresql.
configure: Checking lib /opt/local/lib.
configure: Checking lib /opt/local/lib/postgresql.
configure: Checking lib /opt/local/lib/postgresql84.
configure: Checking lib /sw/opt/postgresql-8.4/lib.
configure: Checking lib /Library/PostgresPlus/8.4SS/lib.
configure: Checking lib /sw/lib.
checking for "/libpq-fe.h"... no
configure: creating ./config.status
config.status: creating src/Makevars

**libs

gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c RS-DBI.c -o RS-DBI.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c RS-PQescape.c -o RS-PQescape.o
In file included from RS-PQescape.c:7:0:
RS-PostgreSQL.h:23:26: fatal error: libpq-fe.h: No such file or directory

# include "libpq-fe.h"

                      ^
compilation terminated.
make:***[RS-PQescape.o] Error 1
ERROR: compilation failed for package ‘RPostgreSQL’

* removing ‘/home/jk/R/x86_64-redhat-linux-gnu-library/3.3/RPostgreSQL’

Warning in install.packages :
installation of package ‘RPostgreSQL’ had non-zero exit status

PostgreSQL 9.6的安装目录是/opt/PostgreSQL/9.6/bin，这似乎不在上面的错误中。有人能帮助我解决这个错误吗？
编辑1：
感谢@lavajumper的建议，我摆脱了上面的错误。但现在得到这个错误，它显示了一些丢失的html链接。

> install.packages("RPostgreSQL")
Installing package into ‘/home/jk/R/x86_64-redhat-linux-gnu-library/3.3’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/RPostgreSQL_0.4-1.tar.gz'
Content type 'unknown' length 476204 bytes (465 KB)
==================================================
downloaded 465 KB

* installing *source* package ‘RPostgreSQL’ ...
**package ‘RPostgreSQL’ successfully unpacked and MD5 sums checked

checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
checking for pg_config... no
configure: checking for PostgreSQL header files
configure: Checking include /usr/include.
configure: Checking lib /usr/lib.
configure: Checking lib /usr/lib/pgsql.
configure: Checking lib /usr/lib/postgresql.
configure: Checking lib /usr/local/lib.
configure: Checking lib /usr/local/lib/pgsql.
configure: Checking lib /usr/local/lib/postgresql.
configure: Checking lib /usr/local/pgsql/lib.
configure: Checking lib /usr/local/postgresql/lib.
configure: Checking lib /opt/lib.
configure: Checking lib /opt/lib/pgsql.
configure: Checking lib /opt/lib/postgresql.
configure: Checking lib /opt/local/lib.
configure: Checking lib /opt/local/lib/postgresql.
configure: Checking lib /opt/local/lib/postgresql84.
configure: Checking lib /sw/opt/postgresql-8.4/lib.
configure: Checking lib /Library/PostgresPlus/8.4SS/lib.
configure: Checking lib /sw/lib.
checking for "/usr/include/libpq-fe.h"... yes
configure: creating ./config.status
config.status: creating src/Makevars

**libs

gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/include -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c RS-DBI.c -o RS-DBI.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/include -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c RS-PQescape.c -o RS-PQescape.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/include -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c RS-PostgreSQL.c -o RS-PostgreSQL.o
RS-PostgreSQL.c: In function ‘RS_PostgreSQL_createDataMappings’:
RS-PostgreSQL.c:446:5: warning: passing argument 1 of ‘Rf_protect’ from   incompatible pointer type [enabled by default]
 PROTECT(flds = RS_DBI_allocFields(num_fields));
 ^
In file included from /usr/include/R/Rdefines.h:36:0,
             from S4R.h:64,
             from RS-DBI.h:29,
             from RS-PostgreSQL.h:25,
             from RS-PostgreSQL.c:17:
/usr/include/R/Rinternals.h:1348:6: note: expected ‘SEXP’ but
argument is of type ‘struct RS_DBI_fields *’
SEXP Rf_protect(SEXP);
     ^
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/include -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c RS-pgsql-copy.c -o RS-pgsql-copy.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/include -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c RS-pgsql-getResult.c -o RS-pgsql-getResult.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/include -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c RS-pgsql-pqexec.c -o RS-pgsql-pqexec.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/include -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c RS-pgsql-pqexecparams.c -o RS-pgsql-pqexecparams.o
gcc -m64 -std=gnu99 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o RPostgreSQL.so RS-DBI.o RS-PQescape.o RS-PostgreSQL.o RS-pgsql-copy.o RS-pgsql-getResult.o RS-pgsql-pqexec.o RS-pgsql-pqexecparams.o -L -lpq -L/usr/lib64/R/lib -lR
installing to /home/jk/R/x86_64-redhat-linux-gnu-library/3.3/RPostgreSQL/libs

**R
**inst
**preparing package for lazy loading

Creating a generic function for ‘format’ from package ‘base’ in package   ‘RPostgreSQL’
Creating a generic function for ‘print’ from package ‘base’ in package ‘RPostgreSQL’
Creating a generic function for ‘summary’ from package ‘base’ in package ‘RPostgreSQL’

**help
***installing help indices

converting help for package ‘RPostgreSQL’
finding HTML links ... done
PostgreSQL                              html  
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL /man/PostgreSQL.Rd:26: missing file link ‘fetch’
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/PostgreSQL.Rd:76: missing file link ‘dbUnloadDriver’
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/PostgreSQL.Rd:84: missing file link ‘fetch’
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/PostgreSQL.Rd:89: missing file link ‘dbCommit’
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/PostgreSQL.Rd:90: missing file link ‘dbRollback’
PostgreSQLConnection-class              html  
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/PostgreSQLConnection-class.Rd:20: missing file link ‘dbCommit’
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/PostgreSQLConnection-class.Rd:32: missing file link ‘dbRollback’
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/PostgreSQLConnection-class.Rd:34: missing file link ‘dbWriteTable’
PostgreSQLDriver-class                  html  
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/PostgreSQLDriver-class.Rd:25: missing file link ‘dbUnloadDriver’
PostgreSQLObject-class                  html  
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/PostgreSQLObject-class.Rd:20: missing file link ‘isSQLKeyword’
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/PostgreSQLObject-class.Rd:22: missing file link ‘SQLKeywords’
  PostgreSQLResult-class                  html  
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/PostgreSQLResult-class.Rd:31: missing file link ‘fetch’
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/PostgreSQLResult-class.Rd:32: missing file link ‘fetch’
S4R                                     html  
dbApply-methods                         html  
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/dbApply-methods.Rd:27: missing file link ‘fetch’
dbApply                                 html  
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/dbApply.Rd:37: missing file link ‘fetch’
dbCallProc-methods                      html  
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/dbCallProc-methods.Rd:31: missing file link ‘fetch’
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/dbCallProc-methods.Rd:32: missing file link ‘dbCommit’
dbCommit-methods                        html  
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/dbCommit-methods.Rd:36: missing file link ‘fetch’
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/dbCommit-methods.Rd:37: missing file link ‘dbCommit’
dbConnect-methods                       html  
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/dbConnect-methods.Rd:58: missing file link ‘fetch’
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/dbConnect-methods.Rd:59: missing file link ‘dbCommit’
dbDataType-methods                      html  
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/dbDataType-methods.Rd:33: missing file link ‘isSQLKeyword’
dbDriver-methods                        html  
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/dbDriver-methods.Rd:26: missing file link ‘fetch’
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/dbDriver-methods.Rd:44: missing file link ‘fetch’
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/dbDriver-methods.Rd:45: missing file link ‘dbCommit’
dbGetInfo-methods                       html  
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/dbGetInfo-methods.Rd:47: missing file link ‘fetch’
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/dbGetInfo-methods.Rd:48: missing file link ‘dbCommit’
dbListTables-methods                    html  
dbObjectId-class                        html  
dbReadTable-methods                     html  
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/dbReadTable-methods.Rd:119: missing file link ‘isSQLKeyword’
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/dbReadTable-methods.Rd:124: missing file link ‘fetch’
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/dbReadTable-methods.Rd:125: missing file link ‘dbCommit’
dbSendQuery-methods                     html  
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/dbSendQuery-methods.Rd:40: missing file link ‘fetch’
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/dbSendQuery-methods.Rd:41: missing file link ‘dbCommit’
dbSetDataMappings-methods               html  
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/dbSetDataMappings-methods.Rd:33: missing file link ‘fetch’
fetch-methods                           html  
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/fetch-methods.Rd:46: missing file link ‘dbCommit’
isPostgresqlIdCurrent                   html  
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/isPostgresqlIdCurrent.Rd:34: missing file link ‘fetch’
make.db.names-methods                   html  
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/make.db.names-methods.Rd:69: missing file link ‘dbWriteTable’
postgresqlBuildTableDefinition          html  
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/postgresqlBuildTableDefinition.Rd:41: missing file link ‘fetch’
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/postgresqlBuildTableDefinition.Rd:42: missing file link ‘dbCommit’
postgresqlDBApply                       html  
Rd warning: /tmp/Rtmp15353Q/R.INSTALL161911b14876/RPostgreSQL/man/postgresqlDBApply.Rd:75: missing file link ‘fetch’
 postgresqlSupport                       html  
 summary-methods                         html  

**building package indices
**testing if installed package can be loaded

 Error in dyn.load(file, DLLpath = DLLpath, ...) : 
 unable to load shared object '/home/jk/R/x86_64-redhat-linux-gnu-library /3.3/RPostgreSQL/libs/RPostgreSQL.so':
 /home/jk/R/x86_64-redhat-linux-gnu-library/3.3/RPostgreSQL/libs/RPostgreSQL.so: undefined symbol: PQfmod
 Error: loading failed
 Execution halted
 ERROR: loading failed
 * removing ‘/home/jk/R/x86_64-redhat-linux-gnu-library/3.3/RPostgreSQL’
 Warning in install.packages :
 installation of package ‘RPostgreSQL’ had non-zero exit status
centos

3条答案

按热度按时间
c2e8gylq

c2e8gylq1#

好的，我自己解决了这个问题。@Manoj在this链接处给出的答案帮助我解决了第二个错误。根据上面提到的链接，RPostgreSQL只检查这些目录中的库：

/usr/lib 
/usr/lib/pgsql 
/usr/lib/postgresql 
/usr/local/lib 
/usr/local/lib/pgsql 
/usr/local/lib/postgresql 
/usr/local/pgsql/lib 
/usr/local/postgresql/lib 
/opt/lib 
/opt/lib/pgsql 
/opt/lib/postgresql 
/opt/local/lib 
/opt/local/lib/postgresql 
/opt/local/lib/postgresql84 
/sw/opt/postgresql-8.4/lib 
/Library/PostgresPlus/8.4SS/lib 
/sw/lib

因此，作为超级用户，我将库文件从Postgres安装目录复制到/usr/lib，并在R Studio中再次运行该命令，如下所示：

install.packages('RPostgreSQL', dependencies=TRUE, repos='http://cran.rstudio.com/')

而且成功了！：）

赞(0）分享  回复(0）举报  2022-11-07
bn31dyow

bn31dyow2#

我也遇到过类似的问题（但是对于RPostgres，您可以考虑切换到该包），通过Docker构建容器以供API用途：RPostgres已安装，但库无法加载libpq.so.5“，无法加载共享对象”/usr/local/lib/R/站点库/RPostgres/libs/RPostgres.so“：\n libpq.so.5：无法打开共享对象文件：没有这样的文件或目录””。因为我已经在我的机器上安装了Postgres，我想这个问题已经解决了，所以我在本地没有这样的消息;但我是这样在我的dockerfile中解决这个问题的（多亏了this post），在没有安装任何与R相关的东西的机器上100%验证（Centos，服务器）：
RUN apt-get update && apt-get install libpq5 -y。因此，在您的终端上执行apt-get update && apt-get install libpq5 -y应该就可以了。轻巧而高效。

赞(0）分享  回复(0）举报  2022-11-07
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