RPostgres appears to require Homebrew installation on OS X

[r-dbi]

RPostgres appears to require Homebrew installation on OS X

[hadley]

Can you please show the output of running system("pg_config")?

(Most of these compilation problems will go away once the package is on CRAN, but we would like to make the configuration a bit more robust)

[iangow]

Sure. I’m using a “Mavericks” build of R from CRAN and PostgreSQL from MacPorts.

Last login: Sun Mar 15 21:40:31 2015 from 192.168.2.3
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system("pg_config")
BINDIR = /opt/local/lib/postgresql94/bin
DOCDIR = /opt/local/share/doc/postgresql
HTMLDIR = /opt/local/share/doc/postgresql
INCLUDEDIR = /opt/local/include/postgresql94
PKGINCLUDEDIR = /opt/local/include/postgresql94
INCLUDEDIR-SERVER = /opt/local/include/postgresql94/server
LIBDIR = /opt/local/lib/postgresql94
PKGLIBDIR = /opt/local/lib/postgresql94
LOCALEDIR = /opt/local/share/locale
MANDIR = /opt/local/share/man
SHAREDIR = /opt/local/share/postgresql94
SYSCONFDIR = /opt/local/etc/postgresql94
PGXS = /opt/local/lib/postgresql94/pgxs/src/makefiles/pgxs.mk
CONFIGURE = '--prefix=/opt/local' '--sysconfdir=/opt/local/etc/postgresql94' '--bindir=/opt/local/lib/postgresql94/bin' '--libdir=/opt/local/lib/postgresql94' '--includedir=/opt/local/include/postgresql94' '--datadir=/opt/local/share/postgresql94' '--mandir=/opt/local/share/man' '--with-includes=/opt/local/include' '--with-libraries=/opt/local/lib' '--with-openssl' '--with-bonjour' '--with-readline' '--with-zlib' '--with-libxml' '--with-libxslt' '--with-gssapi' '--enable-thread-safety' '--with-uuid=e2fs' '--with-python' '--with-perl' 'CC=/usr/bin/clang' 'CFLAGS=-pipe -Os -arch x86_64' 'LDFLAGS=-L/opt/local/lib -Wl,-headerpad_max_install_names -headerpad_max_install_names -arch x86_64' 'CPPFLAGS=-I/opt/local/include'
CC = /usr/bin/clang
CPPFLAGS = -I/opt/local/include -I/opt/local/include/libxml2 -I/opt/local/include
CFLAGS = -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -pipe -Os -arch x86_64
CFLAGS_SL =
LDFLAGS = -L../../../src/common -L/opt/local/lib -Wl,-headerpad_max_install_names -headerpad_max_install_names -arch x86_64 -L/opt/local/lib -L/opt/local/lib -Wl,-dead_strip_dylibs
LDFLAGS_EX =
LDFLAGS_SL =
LIBS = -lpgcommon -lpgport -lxslt -lxml2 -lssl -lcrypto -lgssapi_krb5 -lz -lreadline -lm
VERSION = PostgreSQL 9.4.1

On Mar 16, 2015, at 8:43 AM, Hadley Wickham [email protected] wrote:

Can you please show the output of running system("pg_config")?

(Most of these compilation problems will go away once the package is on CRAN, but we would like to make the configuration a bit more robust)

—
Reply to this email directly or view it on GitHub #22 (comment).

[krlmlr]

Does @mmuurr's pull request #81 work for you?

devtools::install_github("rstats-db/RPostgres#81")

[iangow]

Yes. This works on Mac OS X with a MacPorts installation of PostgreSQL 9.4 (also with another installation with PostgreSQL 9.5.1).

In one case I got an error that prevented installation (message contained namespace ‘DBI’ 0.3.1 is being loaded, but >= 0.3.1.9008 is required), but this was easily fixed with devtools::install_github("rstats-db/DBI") (does it make sense to handle this dependency automatically?).

> devtools::install_github("rstats-db/RPostgres#81")
Downloading GitHub repo mmuurr/RPostgres@Amazon-Linux-configure
Installing RPostgres
Skipping 1 packages ahead of CRAN: DBI
Installing 2 packages: BH, Rcpp
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore CMD INSTALL  \
  '/private/var/folders/0y/v7w1215j0ylb22zqgt9nsh1m0000gn/T/RtmpYOV6BG/devtools11a7e3bd9ec32/mmuurr-rstats-db.RPostgres-6e8fcab' --library='/Library/Frameworks/R.framework/Versions/3.2/Resources/library'  \
  --install-tests 

* installing *source* package ‘RPostgres’ ...
Found pg_config includedir!
Found pg_config libdir!
Using PKG_CFLAGS=-I/opt/local/include/postgresql94 
Using PKG_LIBS=-L/opt/local/lib/postgresql94 -lpq
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/local/include/postgresql94  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RPostgres-init.c -o RPostgres-init.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/local/include/postgresql94  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/local/include/postgresql94  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c connection.cpp -o connection.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/local/include/postgresql94  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c encode.cpp -o encode.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/local/include/postgresql94  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c encrypt.cpp -o encrypt.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/local/include/postgresql94  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c result.cpp -o result.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o RPostgres.so RPostgres-init.o RcppExports.o connection.o encode.o encrypt.o result.o -L/opt/local/lib/postgresql94 -lpq -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.2/Resources/library/RPostgres/libs
** R
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (RPostgres)
> library(RPostgres)
> pg <- RPostgres::dbConnect(RPostgres::Postgres())
> dbListTables(pg)
[lotsa tables]

[krlmlr]

Thanks for confirming it.

[cilindrox]

Confirming this works on Docker, too.

devtools::install_github("rstats-db/RPostgres") fails (no libpq binary found)

devtools::install_github("rstats-db/RPostgres#81") nets a successful installation.

[github-actions]

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