Fwd: RPostgreSQL on OS X 10.9

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NISHIYAMA Tomoaki

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Oct 27, 2013, 7:58:30 AM10/27/13

to rpostgr...@googlegroups.com, Neil Tiffin, NISHIYAMA Tomoaki

Hi Neil,

I got the message that RPostgreSQL doesn't compile on OS X 10.9.

Thereafter, I updated the only machine running 10.8 to 10.9 and

made it work on 10.9 (r353). Thus, I cannot test whether this still

works on 10.8.

Can you check the r253 on OS X systems?

Kind regards,

Tomoaki NISHIYAMA

Advanced Science Research Center,

Kanazawa University,

13-1 Takara-machi,

Kanazawa, 920-0934, Japan

Begin forwarded message:

From: Prof Brian Ripley <rip...@stats.ox.ac.uk>
To: Tomoaki Nishiyama <tomo...@staff.kanazawa-u.ac.jp>
Cc: CRAN <CR...@r-project.org>
Subject: RPostgreSQL on OS X 10.9

On 10.9 (but not 10.8) this fails with

clang -mtune=native -I/Users/ripley/R/R-devel/include -DNDEBUG -I -I/usr/local/include    -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -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' file not found
#    include "libpq-fe.h"
            ^
1 error generated.

The problem is the '-I', which is generated by your configure script: you need to set PG_INCDIR=libpq before you start searching so the local copy can be used.

In 10.8, there is a /usr/include/libpq-fe.h, but system headers are located in SDK-specific directories in 10.9.

Please submit a corrected update.

--
Brian D. Ripley,                  rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel: +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax: +44 1865 272595

Neil Tiffin

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Oct 27, 2013, 10:44:53 AM10/27/13

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Yes I will, but I am really busy at the moment so I'm not sure when that will be this week.

Neil

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Neil Tiffin

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Oct 27, 2013, 11:27:08 AM10/27/13

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Decided to give it a quick test anyway.

Here is the output:

MBP:rpostgresql nt$ ./check_with_vars_neil.sh

-------------- Creating and starting postgresql.

-------------- make 64 bit version ----------------------

* installing to library '/Library/Frameworks/R.framework/Versions/3.0/Resources/library'

* installing *source* package 'RPostgreSQL' ...

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-apple-darwin12.5.0

checking host system type... x86_64-apple-darwin12.5.0

checking target system type... x86_64-apple-darwin12.5.0

checking for pg_config... /Library/PostgreSQL/bin/pg_config

checking for "/Library/PostgreSQL/Versions/9.2.2/include/libpq-fe.h"... yes

configure: creating ./config.status

config.status: creating src/Makevars

** libs

llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Library/PostgreSQL/Versions/9.2.2/include -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c RS-DBI.c -o RS-DBI.o

llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -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/Library/PostgreSQL/Versions/9.2.2/lib -lpq -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation

installing to /Library/Frameworks/R.framework/Versions/3.0/Resources/library/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'

** help

*** installing help indices

** building package indices

** installing vignettes

** testing if installed package can be loaded

* DONE (RPostgreSQL)

-------------- version info ----------------------

ProductName: Mac OS X

ProductVersion: 10.8.5

BuildVersion: 12F45

Machine Processor Architecture: i386

version

----------------------------------------------------------------------------------------------------------------------------------------------

PostgreSQL 9.2.2 on x86_64-apple-darwin10.8.0, compiled by i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3), 64-bit

(1 row)

R version 3.0.2 (2013-09-25)

Platform: x86_64-apple-darwin10.8.0 (64-bit)

RPostgreSQL svn version: 253

Package: RPostgreSQL

Version: 0.5

Packaged: NA

Built: R 3.0.2; x86_64-apple-darwin10.8.0; 2013-10-27 15:20:49 UTC;

-------------- start checks ----------------------

==== 'R --slave RPostgreSQL/tests/connectWithNull.R'

Loading required package: RPostgreSQL

Loading required package: DBI

<PostgreSQLConnection:(11398,0)>

[1] TRUE

==== 'R --slave RPostgreSQL/tests/createTableMixedCaseTest.R'

Loading required package: RPostgreSQL

Loading required package: DBI

Test should create foo1 and Foo2 tables

Pass - Foo1 Table does not exist.

Pass - foo1 Table exists.

Pass - Foo2 Table exists.

Pass - foo2 Table does not exist.

Pass - "Foo2" Table does not exist.

Pass - "foo2" Table does not exist.

[1] TRUE

==== 'R --slave RPostgreSQL/tests/dataTypeTests.R'

Loading required package: RPostgreSQL

Loading required package: DBI

Read Numeric values

GOOD -- all numeric types are as expected

GOOD -- all numeric values are as expected

Read Logical values

GOOD -- all logical types are as expected

GOOD -- all logical values are as expected

Read Character values

GOOD -- all character types are as expected

GOOD -- all character values are as expected

DONE

==== 'R --slave RPostgreSQL/tests/dateTZ.R'

Loading required package: RPostgreSQL

Loading required package: DBI

[1] "2008-07-01 14:15:16 UTC" "2000-01-02 03:04:05 UTC"

testing UTC

**** Trying with timestamp

inserted string 1: 2008-07-01 14:15:16.123+00

inserted string 2: 2000-01-02 03:04:05.678+00

[1] "2008-07-01 14:15:16 UTC" "2000-01-02 03:04:05 UTC"

PASS

**** Trying with timestamp with time zone

inserted string 1: 2008-07-01 14:15:16.123+00

inserted string 2: 2000-01-02 03:04:05.678+00

[1] "2008-07-01 14:15:16 UTC" "2000-01-02 03:04:05 UTC"

PASS

testing Asia/Tokyo

**** Trying with timestamp

inserted string 1: 2008-07-01 14:15:16.123+00

inserted string 2: 2000-01-02 03:04:05.678+00

[1] "2008-07-01 14:15:16 UTC" "2000-01-02 03:04:05 UTC"

PASS

**** Trying with timestamp with time zone

inserted string 1: 2008-07-01 14:15:16.123+00

inserted string 2: 2000-01-02 03:04:05.678+00

[1] "2008-07-01 14:15:16 UTC" "2000-01-02 03:04:05 UTC"

PASS

testing Australlia/South

**** Trying with timestamp

inserted string 1: 2008-07-01 14:15:16.123+00

inserted string 2: 2000-01-02 03:04:05.678+00

[1] "2008-07-01 14:15:16 UTC" "2000-01-02 03:04:05 UTC"

PASS

**** Trying with timestamp with time zone

inserted string 1: 2008-07-01 14:15:16.123+00

inserted string 2: 2000-01-02 03:04:05.678+00

[1] "2008-07-01 14:15:16 UTC" "2000-01-02 03:04:05 UTC"

PASS

testing America/New_York

**** Trying with timestamp

inserted string 1: 2008-07-01 14:15:16.123+00

inserted string 2: 2000-01-02 03:04:05.678+00

[1] "2008-07-01 14:15:16 UTC" "2000-01-02 03:04:05 UTC"

PASS

**** Trying with timestamp with time zone

inserted string 1: 2008-07-01 14:15:16.123+00

inserted string 2: 2000-01-02 03:04:05.678+00

[1] "2008-07-01 14:15:16 UTC" "2000-01-02 03:04:05 UTC"

PASS

[1] TRUE

==== 'R --slave RPostgreSQL/tests/datetimeTests.R'

Loading required package: RPostgreSQL

Loading required package: DBI

**** Trying with timestamp

tt zz

1 2008-07-01 14:15:16 1

2 2000-01-02 03:04:05 2

name Sclass type len precision scale nullOK

1 tt POSIXct TIMESTAMP 8 -1 -1 TRUE

[1] "2008-07-01 14:15:16 UTC" "2000-01-02 03:04:05 UTC"

[1] "POSIXct" "POSIXt"

Time difference of -3103.466 days

**** Trying with timestamp with time zone

tt zz

1 2008-07-01 19:15:16 1

2 2000-01-02 09:04:05 2

name Sclass type len precision scale nullOK

1 tt POSIXct TIMESTAMPTZOID 8 -1 -1 TRUE

[1] "2008-07-01 19:15:16 UTC" "2000-01-02 09:04:05 UTC"

[1] "POSIXct" "POSIXt"

Time difference of -3103.424 days

**** Trying with date

tt zz

1 2008-07-01 1

2 2000-01-02 2

name Sclass type len precision scale nullOK

1 tt Date DATE 4 -1 -1 TRUE

[1] "2008-07-01" "2000-01-02"

[1] "Date"

Time difference of -3103 days

[1] TRUE

==== 'R --slave RPostgreSQL/tests/datetimestampwrite.R'

Loading required package: RPostgreSQL

Loading required package: DBI

Read Date and TIMESTAMP values

PASS -- Date type is as expected

PASS -- TIMESTAMP is received as POSIXct

Check that read after write gets the same data types

PASS -- Date type is as expected

PASS -- TIMESTAMP is received as POSIXct

DONE

==== 'R --slave RPostgreSQL/tests/dbColumnInfo.R'

Loading required package: RPostgreSQL

Loading required package: DBI

NOTICE: CREATE TABLE / PRIMARY KEY will create implicit index "aa_pkey" for table "aa"

dbColumnInfo

name Sclass type len precision scale nullOK

1 pk integer INTEGER 4 -1 -1 FALSE

2 v1 double FLOAT8 8 -1 -1 FALSE

3 v2 double FLOAT8 8 -1 -1 TRUE

4 ?column? double FLOAT8 8 -1 -1 NA

name Sclass type len precision scale nullOK

1 pk integer INTEGER 4 -1 -1 FALSE

2 v1 double FLOAT8 8 -1 -1 FALSE

3 v2 double FLOAT8 8 -1 -1 TRUE

4 ?column? double FLOAT8 8 -1 -1 NA

SELECT result

pk v1 v2 ?column?

1 3 2 NA NA

Removing "AA"

[1] TRUE

==== 'R --slave RPostgreSQL/tests/dbExistsIssue.R'

Loading required package: RPostgreSQL

Loading required package: DBI

Does rockdata exist? [1] TRUE

Does public.rockdata exist? [1] FALSE

[1] "Removing rockdata\n"

[1] TRUE

==== 'R --slave RPostgreSQL/tests/dbExistsq.R'

Loading required package: RPostgreSQL

Loading required package: DBI

Write rock'data

Does rock'data exist? [1] TRUE

Does "public.rock'data" exist? [1] FALSE

Removing rock'data

[1] TRUE

==== 'R --slave RPostgreSQL/tests/dbExistsqc.R'

Loading required package: RPostgreSQL

Loading required package: DBI

Does rock.data exist?

PASS: true

create schema testschema and change the search_path

Does rock.data exist?

PASS: false as the search_path changed

Does testschema."rock.data" exist?

PASS: false as the testschema specified

Does public."rock.data" exist?

PASS: true despite search_path change

write in current schema

Does rock.data exist?

PASS: true

[1] TRUE

==== 'R --slave RPostgreSQL/tests/dbGetQueryParams.R'

Loading required package: RPostgreSQL

Loading required package: DBI

row.names area peri shape perm

1 6 7979 4010.15 0.167045 17.1

2 7 9333 4345.75 0.189651 17.1

3 8 8209 4344.75 0.164127 17.1

4 11 9364 4480.05 0.150944 119.0

5 13 10651 4036.54 0.228595 82.4

6 17 10962 4608.66 0.204314 58.6

7 18 10743 4787.62 0.262727 58.6

8 19 11878 4864.22 0.200071 58.6

9 20 9867 4479.41 0.144810 58.6

10 22 11876 4353.14 0.291029 142.0

row.names area peri shape perm

1 6 7979 4010.15 0.167045 17.1

2 7 9333 4345.75 0.189651 17.1

3 8 8209 4344.75 0.164127 17.1

4 11 9364 4480.05 0.150944 119.0

5 20 9867 4479.41 0.144810 58.6

[1] "Removing rockdata\n"

[1] TRUE

==== 'R --slave RPostgreSQL/tests/dbListFields.R'

Loading required package: RPostgreSQL

Loading required package: DBI

[1] "pk" "v1" "v2"

PASS: 3 fields returned

[1] "pid" "name"

PASS: 2 fields returned

Removing "AA"

[1] TRUE

==== 'R --slave RPostgreSQL/tests/dbTransactionTests.R'

Loading required package: RPostgreSQL

Loading required package: DBI

begin transaction in con1

create table rockdata in con1

PASS rockdata is visible through con1

PASS rockdata is invisible through con2

commit in con1

PASS rockdata is visible through con2

remove the table from con1

PASS rockdata is invisible through con2

begin transaction in con1

create table rockdata in con1

PASS rockdata is visible through con1

RollBack con1

PASS rockdata is invisible through con1

[1] TRUE

==== 'R --slave RPostgreSQL/tests/dbWriteTableFailTest.R'

Loading required package: RPostgreSQL

Loading required package: DBI

create incompatible table rockdata

write table to rockdata with append=TRUE

Error in postgresqlpqExec(new.con, sql4) :

RS-DBI driver: (could not Retrieve the result : ERROR: column "row.names" of relation "rockdata" does not exist

)

write table to rockdata

[1] FALSE

PASS as the return value is false

data frame with 0 columns and 0 rows

[1] "Removing rockdata\n"

[1] TRUE

Warning message:

In postgresqlWriteTable(conn, name, value, ...) :

table rockdata exists in database: aborting assignTable

==== 'R --slave RPostgreSQL/tests/dbWriteTableSchema.R'

Loading required package: RPostgreSQL

Loading required package: DBI

row.names area peri shape perm

1 1 4990 2791.90 0.0903296 6.3

2 2 7002 3892.60 0.1486220 6.3

3 3 7558 3930.66 0.1833120 6.3

4 4 7352 3869.32 0.1170630 6.3

5 5 7943 3948.54 0.1224170 17.1

6 6 7979 4010.15 0.1670450 17.1

7 7 9333 4345.75 0.1896510 17.1

8 8 8209 4344.75 0.1641270 17.1

9 9 8393 3682.04 0.2036540 119.0

10 10 6425 3098.65 0.1623940 119.0

[1] "Removing rockdata\n"

[1] TRUE

==== 'R --slave RPostgreSQL/tests/dbWriteTableTest.R'

Loading required package: RPostgreSQL

Loading required package: DBI

row.names area peri shape perm

1 1 4990 2791.90 0.0903296 6.3

2 2 7002 3892.60 0.1486220 6.3

3 3 7558 3930.66 0.1833120 6.3

4 4 7352 3869.32 0.1170630 6.3

5 5 7943 3948.54 0.1224170 17.1

row.names area peri shape perm

1 1 4990 2791.90 0.0903296 6.3

2 2 7002 3892.60 0.1486220 6.3

3 3 7558 3930.66 0.1833120 6.3

4 4 7352 3869.32 0.1170630 6.3

5 5 7943 3948.54 0.1224170 17.1

6 6 7979 4010.15 0.1670450 17.1

7 7 9333 4345.75 0.1896510 17.1

8 8 8209 4344.75 0.1641270 17.1

9 9 8393 3682.04 0.2036540 119.0

10 10 6425 3098.65 0.1623940 119.0

[1] "Removing rockdata\n"

[1] TRUE

==== 'R --slave RPostgreSQL/tests/dbWriteTabletypes.R'

Loading required package: RPostgreSQL

Loading required package: DBI

row.names strings

1 1 normal

2 2 t\tab

3 3 v\vertical tab

4 4 n\newline

5 5 r carriage \retern

6 6 back \\ slash

7 7 f\form feed

[1] "Removing rockdata\n"

1 normal

2 müß

[1] "Removing rockdata\n"

PASS: could write small umlaut u and ligature sz

1 normal

2 kanji漢字

[1] "Removing rockdata\n"

PASS: could write kanji

Read Numeric values

PASS -- all integer is as expected

PASS integer value is preservedGOOD -- all numeric values are as expected

Read Logical values

GOOD -- all logical types are as expected

GOOD -- all logical values are as expected

Read Character values

GOOD -- all character types are as expected

GOOD -- all character values are as expected

Check that read after write gets the same data types

PASS -- Date type is as expected

PASS -- TIMESTAMP is received as POSIXct

DONE

==== 'R --slave RPostgreSQL/tests/dbtemptable.R'

Loading required package: RPostgreSQL

Loading required package: DBI

name

1 bar

PASS -- ended without segmentation fault

==== 'R --slave RPostgreSQL/tests/escape.R'

Loading required package: RPostgreSQL

Loading required package: DBI

[1] "aaa"

[1] "aa''a"

[1] TRUE

==== 'R --slave RPostgreSQL/tests/loadDriverAndConnect.R'

Loading required package: RPostgreSQL

Loading required package: DBI

datname encoding datallowconn

1 template0 6 FALSE

2 template1 6 TRUE

[1] TRUE

==== 'R --slave RPostgreSQL/tests/openSendQuery.R'

Loading required package: RPostgreSQL

Loading required package: DBI

create temp table tmptest with dbGetQuery

data frame with 0 columns and 0 rows

create temp table tmptest with dbSendQuery

data frame with 0 columns and 0 rows

PASS tmptest disappeared after disconnection

[1] TRUE

==== 'R --slave RPostgreSQL/tests/selectWhereZero.R'

Loading required package: RPostgreSQL

Loading required package: DBI

Error in postgresqlExecStatement(conn, statement, ...) :

RS-DBI driver: (could not Retrieve the result : ERROR: operator does not exist: text = integer

LINE 1: select * from tmpirisdata where "Species"=0

HINT: No operator matches the given name and argument type(s). You might need to add explicit type casts.

)

NULL

[1] "Removing tmpirisdata\n"

PASS: reached to the end of the test code without segmentation fault

Warning message:

In postgresqlQuickSQL(conn, statement, ...) :

Could not create executeselect * from tmpirisdata where "Species"=0

==== 'R --slave RPostgreSQL/tests/selectWithAlias.R'

Loading required package: RPostgreSQL

Loading required package: DBI

ar pe sh pr

1 4990 2791.90 0.0903296 6.3

2 7002 3892.60 0.1486220 6.3

3 7558 3930.66 0.1833120 6.3

4 7352 3869.32 0.1170630 6.3

5 7943 3948.54 0.1224170 17.1

6 7979 4010.15 0.1670450 17.1

7 9333 4345.75 0.1896510 17.1

8 8209 4344.75 0.1641270 17.1

9 8393 3682.04 0.2036540 119.0

10 6425 3098.65 0.1623940 119.0

[1] "Removing rockdata\n"

[1] TRUE

==== 'R --slave RPostgreSQL/tests/unknowntype.R'

Loading required package: RPostgreSQL

Loading required package: DBI

<PostgreSQLResult:(11485,0,4)>

name Sclass type len precision scale nullOK

1 ra character UNKNOWN -1 -1 -1 TRUE

data frame with 0 columns and 0 rows

[1] "Removing tmpirisdata\n"

PASS: reached to the end of the test code without segmentation fault

Warning message:

In postgresqlDescribeFields(res, ...) :

RS-DBI driver warning: (unknown (1021))

Done

MBP:rpostgresql nt$

On Oct 27, 2013, at 6:58 AM, NISHIYAMA Tomoaki <tomo...@staff.kanazawa-u.ac.jp> wrote:

Jose Luis Velasco

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Jun 3, 2014, 8:55:46 AM6/3/14

to rpostgr...@googlegroups.com, ne...@neiltiffin.com, tomo...@staff.kanazawa-u.ac.jp

Hello, I am trying to compile RPostgreSQL in Mavericks 10.9.3 and PostgreSQL 9.3 (Installed through EDB Enterprise) and I try a similar message: ./RS-PostgreSQL.h:23:14: fatal error: 'libpq-fe.h' file not found

# include "libpq-fe.h"

Thanks in advance and regards,

José Luis

NISHIYAMA Tomoaki

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Jun 3, 2014, 9:29:57 AM6/3/14

to rpostgr...@googlegroups.com, NISHIYAMA Tomoaki, ne...@neiltiffin.com

Hi,

Which version of RPostgreSQL did you try?
The one from svn should work.
% svn checkout http://rpostgresql.googlecode.com/svn/trunk/ rpostgresql-read-only
% cd rpostgresql-read-only
% R CMD INSTALL RPostgreSQL

Please let me know if this give you any error.

kind regards,

Tomoaki

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Jose Luis Velasco

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Jun 3, 2014, 11:04:50 AM6/3/14

to rpostgr...@googlegroups.com, ne...@neiltiffin.com, tomo...@staff.kanazawa-u.ac.jp

Hello again,

Problem solved. I have installed the Postgres application and I have included in .bash_profile the following line: export PATH=$PATH:/Applications/Postgres.app/Contents/Versions/9.3/bin

Regards,

José Luis

On Sunday, October 27, 2013 12:58:30 PM UTC+1, Tomoaki wrote:

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