Discussion:
[R-SIG-Mac] Update underlying SQLite for RSQLite
Merton Lister
2015-09-27 00:02:15 UTC
Permalink
Hello,

I've just installed R on my mac and installed some packages, but I have a
couple of questions regarding updating a package.

I've found some instructions on how to update version of SQLite here:
https://github.com/rstats-db/RSQLite#update-version-of-sqlite.

However, it is unclear to me how this will actually update the underlying
SQLite engine used by RSQLite. If I execute the listed commands in R
console, it seems that all they do is to download the a version of SQLite
source code, and extract the files into 'src/' minus the 'shell.c' file.

I have two questions: 1. where exactly is this 'src/' directory? (is it
specifically for RSQLite only?) 2. After extracting the source files, don't
we need to compile them into RSQLite?

Best,
Merton

[[alternative HTML version deleted]]
David Winsemius
2015-09-27 07:00:25 UTC
Permalink
Post by Merton Lister
Hello,
I've just installed R on my mac and installed some packages, but I have a
couple of questions regarding updating a package.
https://github.com/rstats-db/RSQLite#update-version-of-sqlite.
However, it is unclear to me how this will actually update the underlying
SQLite engine used by RSQLite. If I execute the listed commands in R
console, it seems that all they do is to download the a version of SQLite
source code, and extract the files into 'src/' minus the 'shell.c' file.
I have two questions: 1. where exactly is this 'src/' directory?
I have no idea. These directions may be Linux specific.
Post by Merton Lister
(is it
specifically for RSQLite only?) 2. After extracting the source files, don't
we need to compile them into RSQLite?
I would have thought so, too. This is the top of the description file for RSQLite
------------------
Version 1.0.0

Title SQLite Interface for R

Package ‘RSQLite’

February 19, 2015

Description This package embeds the SQLite database engine in R and provides an interface compliant with the DBI package.
The source for the SQLite engine (version 3.8.6) is included.
-----------------

So that is (only?) 5 minor versions behind the current one: 3.8.11.1.

There are precompiled versions for each of the three "standard" platforms at the SQLite website. I agree that unzipping a source version seems unlikely to change the compiled engine. If I were trying to be bleeding edgy, which I generally try to avoid, I would have installed the appropriate binary:

http://www.sqlite.org/2015/sqlite-shell-osx-x86-3081101.zip
Post by Merton Lister
Best,
Merton
[[alternative HTML version deleted]]
_______________________________________________
R-SIG-Mac mailing list
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
David Winsemius
Alameda, CA, USA
Prof Brian Ripley
2015-09-27 09:26:27 UTC
Permalink
Those instructions are for updating the source package. As RSQLite
always uses the version of SQLite included in its sources, installing
another version will not help! You need to update the source package
and then install it (which inter alia involves compiling the SQLite it
contains).

The current sources are

http://www.sqlite.org/2015/sqlite-amalgamation-3081101.zip

and those instructions are not right, as that needs to be extracted to
RSQLite/src/sqlite, not RSQLite/src .

You can use something like

curl -O http://www.sqlite.org/2015/sqlite-amalgamation-3081101.zip
tar xvf .../RSQLite_1.0.0.tar.gz
pushd RSQLite/src/sqlite
unzip -j ../../../sqlite-amalgamation-3081101.zip
rm shell.c
popd
R CMD INSTALL RSQLite

Works for me ....
Post by David Winsemius
Post by Merton Lister
Hello,
I've just installed R on my mac and installed some packages, but I have a
couple of questions regarding updating a package.
https://github.com/rstats-db/RSQLite#update-version-of-sqlite.
However, it is unclear to me how this will actually update the underlying
SQLite engine used by RSQLite. If I execute the listed commands in R
console, it seems that all they do is to download the a version of SQLite
source code, and extract the files into 'src/' minus the 'shell.c' file.
I have two questions: 1. where exactly is this 'src/' directory?
I have no idea. These directions may be Linux specific.
Post by Merton Lister
(is it
specifically for RSQLite only?) 2. After extracting the source files, don't
we need to compile them into RSQLite?
I would have thought so, too. This is the top of the description file for RSQLite
------------------
Version 1.0.0
Title SQLite Interface for R
Package ‘RSQLite’
February 19, 2015
Description This package embeds the SQLite database engine in R and provides an interface compliant with the DBI package.
The source for the SQLite engine (version 3.8.6) is included.
-----------------
So that is (only?) 5 minor versions behind the current one: 3.8.11.1.
http://www.sqlite.org/2015/sqlite-shell-osx-x86-3081101.zip
Post by Merton Lister
Best,
Merton
[[alternative HTML version deleted]]
_______________________________________________
R-SIG-Mac mailing list
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
David Winsemius
Alameda, CA, USA
_______________________________________________
R-SIG-Mac mailing list
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
--
Brian D. Ripley, ***@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
1 South Parks Road, Oxford OX1 3TG, UK
Merton Lister
2015-09-28 00:20:14 UTC
Permalink
Thank you for pointing out the error in the doc, Prof. Ripley.

I have built and installed RSQLite as per your instructions. Any way to
double-check the version of SQLite engine actually used by RSQLite? Perhaps
some attribute we can print out in the console?

Best,
Merton
Those instructions are for updating the source package. As RSQLite always
uses the version of SQLite included in its sources, installing another
version will not help! You need to update the source package and then
install it (which inter alia involves compiling the SQLite it contains).
The current sources are
http://www.sqlite.org/2015/sqlite-amalgamation-3081101.zip
and those instructions are not right, as that needs to be extracted to
RSQLite/src/sqlite, not RSQLite/src .
You can use something like
curl -O http://www.sqlite.org/2015/sqlite-amalgamation-3081101.zip
tar xvf .../RSQLite_1.0.0.tar.gz
pushd RSQLite/src/sqlite
unzip -j ../../../sqlite-amalgamation-3081101.zip
rm shell.c
popd
R CMD INSTALL RSQLite
Works for me ....
Post by Merton Lister
Hello,
Post by Merton Lister
I've just installed R on my mac and installed some packages, but I have a
couple of questions regarding updating a package.
https://github.com/rstats-db/RSQLite#update-version-of-sqlite.
However, it is unclear to me how this will actually update the underlying
SQLite engine used by RSQLite. If I execute the listed commands in R
console, it seems that all they do is to download the a version of SQLite
source code, and extract the files into 'src/' minus the 'shell.c' file.
I have two questions: 1. where exactly is this 'src/' directory?
I have no idea. These directions may be Linux specific.
(is it
Post by Merton Lister
specifically for RSQLite only?) 2. After extracting the source files, don't
we need to compile them into RSQLite?
I would have thought so, too. This is the top of the description file for RSQLite
------------------
Version 1.0.0
Title SQLite Interface for R
Package ‘RSQLite’
February 19, 2015
Description This package embeds the SQLite database engine in R and
provides an interface compliant with the DBI package.
The source for the SQLite engine (version 3.8.6) is included.
-----------------
So that is (only?) 5 minor versions behind the current one: 3.8.11.1.
There are precompiled versions for each of the three "standard"
platforms at the SQLite website. I agree that unzipping a source version
seems unlikely to change the compiled engine. If I were trying to be
bleeding edgy, which I generally try to avoid, I would have installed the
http://www.sqlite.org/2015/sqlite-shell-osx-x86-3081101.zip
Best,
Post by Merton Lister
Merton
[[alternative HTML version deleted]]
_______________________________________________
R-SIG-Mac mailing list
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
David Winsemius
Alameda, CA, USA
_______________________________________________
R-SIG-Mac mailing list
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
--
Emeritus Professor of Applied Statistics, University of Oxford
1 South Parks Road, Oxford OX1 3TG, UK
[[alternative HTML version deleted]]
Dan Tenenbaum
2015-09-28 01:19:43 UTC
Permalink
----- Original Message -----
Sent: Sunday, September 27, 2015 5:20:14 PM
Subject: Re: [R-SIG-Mac] Update underlying SQLite for RSQLite
Thank you for pointing out the error in the doc, Prof. Ripley.
I have built and installed RSQLite as per your instructions. Any way
to
double-check the version of SQLite engine actually used by RSQLite?
Perhaps
some attribute we can print out in the console?
library(RSQLite)
db = dbConnect(SQLite(), dbname="")
dbGetQuery(conn=db, "SELECT sqlite_version() AS 'SQLite Version'")
SQLite Version
1 3.8.6

Dan
Best,
Merton
On Sun, Sep 27, 2015 at 2:26 AM, Prof Brian Ripley
Post by Prof Brian Ripley
Those instructions are for updating the source package. As RSQLite
always
uses the version of SQLite included in its sources, installing
another
version will not help! You need to update the source package and
then
install it (which inter alia involves compiling the SQLite it
contains).
The current sources are
http://www.sqlite.org/2015/sqlite-amalgamation-3081101.zip
and those instructions are not right, as that needs to be extracted
to
RSQLite/src/sqlite, not RSQLite/src .
You can use something like
curl -O http://www.sqlite.org/2015/sqlite-amalgamation-3081101.zip
tar xvf .../RSQLite_1.0.0.tar.gz
pushd RSQLite/src/sqlite
unzip -j ../../../sqlite-amalgamation-3081101.zip
rm shell.c
popd
R CMD INSTALL RSQLite
Works for me ....
Post by Merton Lister
Hello,
Post by Merton Lister
I've just installed R on my mac and installed some packages, but
I have a
couple of questions regarding updating a package.
I've found some instructions on how to update version of SQLite
https://github.com/rstats-db/RSQLite#update-version-of-sqlite.
However, it is unclear to me how this will actually update the
underlying
SQLite engine used by RSQLite. If I execute the listed commands
in R
console, it seems that all they do is to download the a version
of SQLite
source code, and extract the files into 'src/' minus the
'shell.c' file.
I have two questions: 1. where exactly is this 'src/' directory?
I have no idea. These directions may be Linux specific.
(is it
Post by Merton Lister
specifically for RSQLite only?) 2. After extracting the source
files,
don't
we need to compile them into RSQLite?
I would have thought so, too. This is the top of the description
file for
RSQLite
------------------
Version 1.0.0
Title SQLite Interface for R
Package ‘RSQLite’
February 19, 2015
Description This package embeds the SQLite database engine in R
and
provides an interface compliant with the DBI package.
The source for the SQLite engine (version 3.8.6) is included.
-----------------
3.8.11.1.
There are precompiled versions for each of the three "standard"
platforms at the SQLite website. I agree that unzipping a source
version
seems unlikely to change the compiled engine. If I were trying to
be
bleeding edgy, which I generally try to avoid, I would have
installed the
http://www.sqlite.org/2015/sqlite-shell-osx-x86-3081101.zip
Best,
Post by Merton Lister
Merton
[[alternative HTML version deleted]]
_______________________________________________
R-SIG-Mac mailing list
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
David Winsemius
Alameda, CA, USA
_______________________________________________
R-SIG-Mac mailing list
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
--
Emeritus Professor of Applied Statistics, University of Oxford
1 South Parks Road, Oxford OX1 3TG, UK
[[alternative HTML version deleted]]
_______________________________________________
R-SIG-Mac mailing list
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Merton Lister
2015-09-28 03:26:52 UTC
Permalink
Perfect. Thanks!
Post by Dan Tenenbaum
----- Original Message -----
Sent: Sunday, September 27, 2015 5:20:14 PM
Subject: Re: [R-SIG-Mac] Update underlying SQLite for RSQLite
Thank you for pointing out the error in the doc, Prof. Ripley.
I have built and installed RSQLite as per your instructions. Any way to
double-check the version of SQLite engine actually used by RSQLite? Perhaps
some attribute we can print out in the console?
library(RSQLite)
db = dbConnect(SQLite(), dbname="")
dbGetQuery(conn=db, "SELECT sqlite_version() AS 'SQLite Version'")
SQLite Version
1 3.8.6
Dan
Best,
Merton
On Sun, Sep 27, 2015 at 2:26 AM, Prof Brian Ripley
Those instructions are for updating the source package. As RSQLite always
uses the version of SQLite included in its sources, installing another
version will not help! You need to update the source package and then
install it (which inter alia involves compiling the SQLite it contains).
The current sources are
http://www.sqlite.org/2015/sqlite-amalgamation-3081101.zip
and those instructions are not right, as that needs to be extracted to
RSQLite/src/sqlite, not RSQLite/src .
You can use something like
curl -O http://www.sqlite.org/2015/sqlite-amalgamation-3081101.zip
tar xvf .../RSQLite_1.0.0.tar.gz
pushd RSQLite/src/sqlite
unzip -j ../../../sqlite-amalgamation-3081101.zip
rm shell.c
popd
R CMD INSTALL RSQLite
Works for me ....
Post by Merton Lister
Hello,
Post by Merton Lister
I've just installed R on my mac and installed some packages, but I have a
couple of questions regarding updating a package.
https://github.com/rstats-db/RSQLite#update-version-of-sqlite.
However, it is unclear to me how this will actually update the underlying
SQLite engine used by RSQLite. If I execute the listed commands in R
console, it seems that all they do is to download the a version of SQLite
source code, and extract the files into 'src/' minus the
'shell.c' file.
I have two questions: 1. where exactly is this 'src/' directory?
I have no idea. These directions may be Linux specific.
(is it
Post by Merton Lister
specifically for RSQLite only?) 2. After extracting the source
files,
don't
we need to compile them into RSQLite?
I would have thought so, too. This is the top of the description
file for
RSQLite
------------------
Version 1.0.0
Title SQLite Interface for R
Package ‘RSQLite’
February 19, 2015
Description This package embeds the SQLite database engine in R and
provides an interface compliant with the DBI package.
The source for the SQLite engine (version 3.8.6) is included.
-----------------
So that is (only?) 5 minor versions behind the current one: 3.8.11.1.
There are precompiled versions for each of the three "standard"
platforms at the SQLite website. I agree that unzipping a source version
seems unlikely to change the compiled engine. If I were trying to be
bleeding edgy, which I generally try to avoid, I would have installed the
http://www.sqlite.org/2015/sqlite-shell-osx-x86-3081101.zip
Best,
Post by Merton Lister
Merton
[[alternative HTML version deleted]]
_______________________________________________
R-SIG-Mac mailing list
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
David Winsemius
Alameda, CA, USA
_______________________________________________
R-SIG-Mac mailing list
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
--
Emeritus Professor of Applied Statistics, University of Oxford
1 South Parks Road, Oxford OX1 3TG, UK
[[alternative HTML version deleted]]
_______________________________________________
R-SIG-Mac mailing list
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[[alternative HTML version deleted]]

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