Unable to install in R

[xiw588]

I am trying to install the package in r but kept receiving the following error messages and was unable to install.

trying URL 'https://mirrors.nics.utk.edu/cran/src/contrib/RPostgreSQL_0.7-3.tar.gz'
Content type 'application/x-gzip' length 580771 bytes (567 KB)

downloaded 567 KB

• installing source package ‘RPostgreSQL’ ...
  ** package ‘RPostgreSQL’ successfully unpacked and MD5 sums checked
  checking for gcc... gcc
  checking whether the C compiler works... yes
  checking for C compiler default output file name... a.out
  checking for suffix of executables...
  checking whether we are cross compiling... no
  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-pc-linux-gnu
  checking host system type... x86_64-pc-linux-gnu
  checking target system type... x86_64-pc-linux-gnu
  checking for pg_config... no
  configure: checking for PostgreSQL header files
  configure: Checking include /usr/include.
  configure: Checking include /usr/include/postgresql.
  configure: Checking include /usr/local/include.
  configure: Checking include /usr/local/include/postgresql.
  configure: Checking include /usr/local/pgsql/include.
  configure: Checking include /usr/local/postgresql/include.
  configure: Checking lib /usr/lib.
  configure: Checking lib /usr/lib/postgresql.
  configure: Checking lib /usr/local/lib.
  configure: Checking lib /usr/local/lib/postgresql.
  configure: Checking lib /usr/local/postgresql/lib.
  gcc -g -O2 -I -L conftest.c -lpq -o pqconftest
  conftest.c:1:22: fatal error: libpq-fe.h: No such file or directory
  #include <libpq-fe.h>
  ^
  compilation terminated.
  ./pqconftest
  ./configure: line 2852: ./pqconftest: No such file or directory
  system -lpq don't appear to work; use internal
  checking for "/libpq-fe.h"... no
  configure: creating ./config.status
  config.status: creating src/Makevars
  ** libs
  gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -I"/n/helmod/apps/centos7/Core/R_core/3.5.1-fasrc01/lib64/R/include" -DNDEBUG -I -I/usr/local/include -fpic -g -O2 -c RS-DBI.c -o RS-DBI.o
  gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -I"/n/helmod/apps/centos7/Core/R_core/3.5.1-fasrc01/lib64/R/include" -DNDEBUG -I -I/usr/local/include -fpic -g -O2 -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’

[benz0li]

See Issue #116

[tomoakin]

Have you installed a postgresql-devel package with
sudo yum install postgresql-devel
or
sudo yum install postgresql[appropriate version no]-devel
?

[xiw588]

@tomoakin no..I was trying to install on cluster, not allowed to sudo

[xiw588]

@benz0li I tried install.packages("RPostgreSQL", configure.args = c(PG_INCDIR = "/usr/pgsql-11/include")) but same error

[tomoakin]

The first thing you should do is to find pg_config and put it in your PATH.
If there isn't on the system, I do not understand what is your idea to use PostgreSQL at all (where is the server running and are they accessible?)
Regardless of sudo privilege, you can compile and install the whole PostgreSQL under your home directory if you have sufficient capacity. Then you can direct the PATH to include them.
However, the PostgreSQL server normally requires to occupy certain resource (port etc.) for operation and belongs to the superuser control. You can use some non-default port, though.

[tomoakin]

The lesson of #116 is to ask the IT staff for necessary information.
If your include files aren't in /usr/pgsql-11/include,
install.packages("RPostgreSQL", configure.args = c(PG_INCDIR = "/usr/pgsql-11/include"))
will not help.

[philiporlando]

I'm seeing a similar issue on a Windows server:

> install.packages("RPostgreSQL")
# Downloading packages -------------------------------------------------------
- Downloading RPostgreSQL from CRAN ...       OK [file is up to date]
Successfully downloaded 1 package in 67 milliseconds.

The following package(s) will be installed:
- RPostgreSQL [0.7-8]
These packages will be installed into "F:/Projects/Production/my-project/renv/library/R-4.1/x86_64-w64-mingw32".

Do you want to proceed? [Y/n]: y

# Installing packages --------------------------------------------------------
- Installing RPostgreSQL ...                    FAILED
Error: Error installing package 'RPostgreSQL':
=======================================

* installing *source* package 'RPostgreSQL' ...
** package 'RPostgreSQL' successfully unpacked and MD5 sums checked
** using staged installation
** libs
/mingw64/bin/gcc  -I"F:/R/R-4.1.3/include" -DNDEBUG     -I"C:\Users\MyUsername\AppData\Local/R/cache/R/renv/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c RS-DBI.c -o RS-DBI.o
/mingw64/bin/gcc  -I"F:/R/R-4.1.3/include" -DNDEBUG     -I"C:\Users\MyUsername\AppData\Local/R/cache/R/renv/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c RS-PQescape.c -o RS-PQescape.o
In file included from RS-PQescape.c:7:
RS-PostgreSQL.h:23:14: fatal error: libpq-fe.h: No such file or directory
 #    include "libpq-fe.h"
              ^~~~~~~~~~~~
compilation terminated.
make: *** [F:/R/R-4.1.3/etc/x64/Makeconf:238: RS-PQescape.o] Error 1
ERROR: compilation failed for package 'RPostgreSQL'
* removing 'F:/Projects/Production/my-project/renv/staging/1/RPostgreSQL'
install of package 'RPostgreSQL' failed [error code 1]
Traceback (most recent calls last):
15: install.packages("RPostgreSQL")
14: eval(call, envir = parent.frame())
13: eval(call, envir = parent.frame())
12: renv::install("RPostgreSQL")
11: renv_install_impl(records)
10: renv_install_staged(records)
 9: renv_install_default(records)
 8: handler(package, renv_install_package(record))
 7: renv_install_package(record)
 6: withCallingHandlers(renv_install_package_impl(record), error = function(e) writef("FAILED"))
 5: renv_install_package_impl(record)
 4: r_cmd_install(package, path)
 3: r_exec_error(package, output, "install", status)
 2: abort(all)
 1: stop(fallback)

I've already added pg_config to my PATH. Setting PG_INCDIR did not resolve this either:

> install.packages("RPostgreSQL", configure.args = c(PG_INCDIR = "F:/PostgreSQL/12/include"))
Installing package into ‘F:/Projects/Production/my-project/renv/library/R-4.1/x86_64-w64-mingw32’
(as ‘lib’ is unspecified)
Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘RPostgreSQL’
installing the source package ‘RPostgreSQL’
trying URL 'https://posit-package-prod.appl.org/newprod-cran/__linux__/centos8/latest/src/contrib/RPostgreSQL_0.7-8.tar.gz'
Content type 'application/x-gzip' length 567106 bytes (553 KB)
downloaded 553 KB

* installing *source* package 'RPostgreSQL' ...
** package 'RPostgreSQL' successfully unpacked and MD5 sums checked
** using staged installation
** libs
/mingw64/bin/gcc  -I"F:/R/R-4.1.3/include" -DNDEBUG     -I"C:\Users\MyUsername\AppData\Local/R/cache/R/renv/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c RS-DBI.c -o RS-DBI.o
/mingw64/bin/gcc  -I"F:/R/R-4.1.3/include" -DNDEBUG     -I"C:\Users\MyUsername\AppData\Local/R/cache/R/renv/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c RS-PQescape.c -o RS-PQescape.o
In file included from RS-PQescape.c:7:
RS-PostgreSQL.h:23:14: fatal error: libpq-fe.h: No such file or directory
 #    include "libpq-fe.h"
              ^~~~~~~~~~~~
compilation terminated.
make: *** [F:/R/R-4.1.3/etc/x64/Makeconf:238: RS-PQescape.o] Error 1
ERROR: compilation failed for package 'RPostgreSQL'
* removing 'F:/Projects/Production/my-project/renv/library/R-4.1/x86_64-w64-mingw32/RPostgreSQL'

Any troubleshooting help is appreciated!

Edit: Downgrading to 0.7-4 avoids this issue!

> renv::install("RPostgreSQL@0.7-4", configure.args = c(PG_INCDIR = "F:/PostgreSQL/12/include"))
# Downloading packages -------------------------------------------------------
- Downloading RPostgreSQL from P3M ...          OK [603.2 Kb in 1.5s]
Successfully downloaded 1 package in 2.5 seconds.

The following package(s) will be installed:
- RPostgreSQL [0.7-4]
These packages will be installed into "F:/Projects/Production/my-project/renv/library/R-4.1/x86_64-w64-mingw32".