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我使用企业数据库的一键式安装程序安装了 PostgreSQL 9.6 和 PostGIS 2.3 here在我的基于 CentOS 7 (x64) Linux 的机器上。现在我正在尝试将 R Studio 连接到 Postgres。为此,我尝试在 R Studio 中安装 RPostgreSQL
包,但出现以下错误:
> 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
好像不是上面的错误。有人可以帮我解决这个错误吗?
编辑 1:
感谢@lavajumper 的建议,我摆脱了上述错误。但现在出现此错误,显示缺少一些 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
最佳答案
好吧,我自己解决了这个问题。 @Manoj 在 this 给出的答案链接帮助我解决了第二个错误。根据提到的链接,RPostgreSQL 仅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 super 用户,我将库文件从 Postgres 安装目录复制到 /usr/lib
并在 R Studio 中像这样再次运行命令:
install.packages('RPostgreSQL', dependencies=TRUE, repos='http://cran.rstudio.com/')
成功了! :)
关于r - 无法在 CentOS 7 上的 R Studio 中安装 RPostgreSQL 包,我们在Stack Overflow上找到一个类似的问题: https://stackoverflow.com/questions/40307386/
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