date:20110525

Simon,

That's a better way, indeed. I had missed your previous post, so thank you
for reposting. My original motivation for the script was to sync certain
core packages across multiple machines, but it works well for upgrades,
too. The script also provides a means of weeding out my library by not
automatically installing old, unused packages.

I find the Package Manager is great for installing individual packages, but
is error-prone for installing a lot of packages at once (as a user
interface...too many chances to, for instance, forget a package).

Thanks,

Tom

On Wed, May 25, 2011 at 06:35, Simon Urbanek simon.urba...@r-project.orgwrote:

 Well, that's a bit convoluted way (I really don't see the point of that
 script) - if you want to re-install packages across R versions (not the
 topic of this thread!) it is far easier than that and I posted it here just
 a few days ago:

 # for packages from user location:
 install.packages(row.names(installed.packages(~/Library/R/2.12/library)))

 # for packages from system location:

 install.packages(row.names(installed.packages(/Library/Frameworks/R.framework/Versions/2.12/Resources/library)))

 but as I said, the Package Manager gives you the latter without the need to
 type anything ...

 Cheers,
 Simon



 On May 24, 2011, at 11:07 PM, Tom Hopper wrote:

  There's a handy script to automate the update process that I came across
  some time ago at
 
 https://bridgewater.wordpress.com/2010/12/21/my-favorite-r-packages-installed-with-one-command/
 
  When you run the script, it will automatically install the libraries that
  you set up in the script. When you run it, it will install into the first
  location in .libPaths(). If you want packages installed in
 ~/Library/R...,
  then you need to check the Default Library Paths option in
  R--Preferences--Startup. Alternatively, you could supply the lib=
 argument
  to the install.packages() call. With a little extra code, you could even
  define the install location for each package individually.
 
  Here's a shortened version:
  # Essential R packages: 2011-01-02
  # Originally from: R packages I use commonly: 12/21/2010 twitter:
  drbridgewater
  # Jeff S. A. Bridgewater
  #
 
 https://bridgewater.wordpress.com/2010/12/21/my-favorite-r-packages-installed-with-one-command/
  #
 
  #list all packages currently installed
  p-c()
 
  #add essential packages:
  p-c(p,survival)
  p-c(p,Hmisc)
  # add more packages here
 
  # UPDATE the repository list to point to your local repositories
  repositories-c(http://mirrors.softliste.de/cran/,;
  http://mirrors.softliste.de/cran/;)
  install_package-function(pack,repositories)
  {
  if(!(pack %in% row.names(installed.packages(
  {
  update.packages(repos=repositories, ask=F)
  install.packages(pack, repos=repositories, dependencies=T)
  }
  require(pack,character.only=TRUE)
  }
 
  for( pack in p)
  {
  install_package(pack,repositories)
  }
 
[[alternative HTML version deleted]]
 
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[[alternative HTML version deleted]]

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Re: [R-SIG-Mac] packages failed to load - Now fixed

Well, that's a bit convoluted way (I really don't see the point of that 
script) - if you want to re-install packages across R versions (not the topic 
of this thread!) it is far easier than that and I posted it here just a few 
days ago:

# for packages from user location:
install.packages(row.names(installed.packages(~/Library/R/2.12/library)))

# for packages from system location:
install.packages(row.names(installed.packages(/Library/Frameworks/R.framework/Versions/2.12/Resources/library)))

but as I said, the Package Manager gives you the latter without the need to 
type anything ...

Cheers,
Simon



On May 24, 2011, at 11:07 PM, Tom Hopper wrote:

 There's a handy script to automate the update process that I came across
 some time ago at
 https://bridgewater.wordpress.com/2010/12/21/my-favorite-r-packages-installed-with-one-command/
 
 When you run the script, it will automatically install the libraries that
 you set up in the script. When you run it, it will install into the first
 location in .libPaths(). If you want packages installed in ~/Library/R...,
 then you need to check the Default Library Paths option in
 R--Preferences--Startup. Alternatively, you could supply the lib= argument
 to the install.packages() call. With a little extra code, you could even
 define the install location for each package individually.
 
 Here's a shortened version:
 # Essential R packages: 2011-01-02
 # Originally from: R packages I use commonly: 12/21/2010 twitter:
 drbridgewater
 # Jeff S. A. Bridgewater
 #
 https://bridgewater.wordpress.com/2010/12/21/my-favorite-r-packages-installed-with-one-command/
 #
 
 #list all packages currently installed
 p-c()
 
 #add essential packages:
 p-c(p,survival)
 p-c(p,Hmisc)
 # add more packages here
 
 # UPDATE the repository list to point to your local repositories
 repositories-c(http://mirrors.softliste.de/cran/,;
 http://mirrors.softliste.de/cran/;)
 install_package-function(pack,repositories)
 {
 if(!(pack %in% row.names(installed.packages(
 {
 update.packages(repos=repositories, ask=F)
 install.packages(pack, repos=repositories, dependencies=T)
 }
 require(pack,character.only=TRUE)
 }
 
 for( pack in p)
 {
 install_package(pack,repositories)
 }
 
   [[alternative HTML version deleted]]
 
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 R-SIG-Mac@r-project.org
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Re: [R-SIG-Mac] packages failed to load - Now fixed

Brian,

Since the problem was fixed by updating packages with checkBuilt=T, wouldn't
installing packages fresh using the script have avoided the problem?

Perhaps section 2.8 of the Windows FAQ should be incorporated into the Mac
FAQ? The checkBuilt trick is otherwise not brought to our attention.

The FAQ could also be clearer on whether recommended packages can be
replaced with older versions using this method; it's much easier to
copy-and-paste everything in the directory than to hunt-and-peck for only
the packages that aren't installed by default. I'll submit that suggestion
to r-wind...@r-project.org separately.

- Tom

On Wed, May 25, 2011 at 07:58, Prof Brian Ripley rip...@stats.ox.ac.ukwrote:

 It's really odd that people blog about their own inefficient scripts rather
 than read the R documentation.

 Because this scripts checks (very inefficiently) if a package is already
 installed, it would not solve the problem discussed in this thread.  And
 install.packages() takes a vector of packages, and 'survival' is a
 recommended package and should always be installed.

 Because people have differing needs there are different ways to do this.
  But the ideas of


 http://cran.r-project.org/bin/windows/base/rw-FAQ.html#What_0027s-the-best-way-to-upgrade_003f

 suit many.



 On Wed, 25 May 2011, Tom Hopper wrote:

  There's a handy script to automate the update process that I came across
 some time ago at

 https://bridgewater.wordpress.com/2010/12/21/my-favorite-r-packages-installed-with-one-command/

 When you run the script, it will automatically install the libraries that
 you set up in the script. When you run it, it will install into the first
 location in .libPaths(). If you want packages installed in ~/Library/R...,
 then you need to check the Default Library Paths option in
 R--Preferences--Startup. Alternatively, you could supply the lib=
 argument
 to the install.packages() call. With a little extra code, you could even
 define the install location for each package individually.

 Here's a shortened version:
 # Essential R packages: 2011-01-02
 # Originally from: R packages I use commonly: 12/21/2010 twitter:
 drbridgewater
 # Jeff S. A. Bridgewater
 #

 https://bridgewater.wordpress.com/2010/12/21/my-favorite-r-packages-installed-with-one-command/
 #

 #list all packages currently installed
 p-c()

 #add essential packages:
 p-c(p,survival)
 p-c(p,Hmisc)
 # add more packages here

 # UPDATE the repository list to point to your local repositories
 repositories-c(http://mirrors.softliste.de/cran/,;
 http://mirrors.softliste.de/cran/;)
 install_package-function(pack,repositories)
 {
 if(!(pack %in% row.names(installed.packages(
 {
 update.packages(repos=repositories, ask=F)
 install.packages(pack, repos=repositories, dependencies=T)
 }
 require(pack,character.only=TRUE)
 }

 for( pack in p)
 {
 install_package(pack,repositories)
 }

[[alternative HTML version deleted]]

 ___
 R-SIG-Mac mailing list
 R-SIG-Mac@r-project.org
 https://stat.ethz.ch/mailman/listinfo/r-sig-mac


 --
 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, UKFax:  +44 1865 272595


[[alternative HTML version deleted]]

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Re: [R-SIG-Mac] packages failed to load - Now fixed

2011-05-25 Thread Ian Reeve


On 25/05/2011, at 12:19 PM, Simon Urbanek wrote:

 Normally you just install new R and then use Package Manager to install 
 packages to match your previous version. If you blow away old R, you will 
 have no track of packages you installed before.


I've been in the habit of keeping all the .tgz files in a directory and using 
that as a guide for installing packages in the new R.  So I'm happy to trash 
the old R.

Thanks
Ian

Ian Reeve
Institute for Rural Futures
University of New England
Armidale, NSW 2351

02 67735145

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[R-SIG-Mac] install.packages: location of system-wide library tree

2011-05-25 Thread jochen laubrock

Dear expeRts,

On (my?) macs, .libPaths() contains two entries, with the first pointing to a 
user's library tree and the second to the system-wide library tree, as in

## begin code
v - getRversion()
userLib - Sys.glob(sprintf(~/Library/R/%s.%s/library, v$major, v$minor))
systemLib - 
sprintf(/Library/Frameworks/R.framework/Versions/%s.%s/Resources/library, 
v$major, v$minor)
userLib == .libPaths()[1]
systemLib == .libPaths()[2]
# both return TRUE (on my system)
## end code

When installing new packages, I would like to make them available to all users. 
However, the 'lib' parameter of 'install.packages' defaults to the first 
element of '.libPaths()'. How do I reliably specify the location of the system 
library: Is it always equal to '.libPaths()[-1]'? And why is '.Library.site' 
empty? 

Jochen


 sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)


Jochen Laubrock, Dept. of Psychology, University of Potsdam,
Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
phone: +49-331-977-2346, fax: +49-331-977-2793

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Re: [R-SIG-Mac] install.packages: location of system-wide library tree

2011-05-25 Thread Sean Davis

See help(.Library).

Sean

On Wed, May 25, 2011 at 6:35 AM, jochen laubrock
jochen.laubr...@gmail.com wrote:
 Dear expeRts,

 On (my?) macs, .libPaths() contains two entries, with the first pointing to a 
 user's library tree and the second to the system-wide library tree, as in

 ## begin code
 v - getRversion()
 userLib - Sys.glob(sprintf(~/Library/R/%s.%s/library, v$major, v$minor))
 systemLib - 
 sprintf(/Library/Frameworks/R.framework/Versions/%s.%s/Resources/library, 
 v$major, v$minor)
 userLib == .libPaths()[1]
 systemLib == .libPaths()[2]
 # both return TRUE (on my system)
 ## end code

 When installing new packages, I would like to make them available to all 
 users. However, the 'lib' parameter of 'install.packages' defaults to the 
 first element of '.libPaths()'. How do I reliably specify the location of the 
 system library: Is it always equal to '.libPaths()[-1]'? And why is 
 '.Library.site' empty?

 Jochen


 sessionInfo()
 R version 2.13.0 (2011-04-13)
 Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

 
 Jochen Laubrock, Dept. of Psychology, University of Potsdam,
 Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
 phone: +49-331-977-2346, fax: +49-331-977-2793

 ___
 R-SIG-Mac mailing list
 R-SIG-Mac@r-project.org
 https://stat.ethz.ch/mailman/listinfo/r-sig-mac


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Re: [R-SIG-Mac] packages failed to load - Now fixed

On Wed, May 25, 2011 at 11:50, Prof Brian Ripley rip...@stats.ox.ac.ukwrote:

 On Wed, 25 May 2011, Tom Hopper wrote:

  Brian,

 Since the problem was fixed by updating packages with checkBuilt=T,
 wouldn't
 installing packages fresh using the script have avoided the problem?


 No, because it checks if they are already installed *as I said*.


Sorry, my question was poorly structured. I understood your original
statement, and was following up with regards to the update process of R for
Mac and some of its inner workings. Since I don't have your knowledge of the
software, and am unlikely to develop such knowledge in the foreseeable
future, I (perhaps incorrectly) addressed my question to you.

I take it from your response that the problem that Ian Reeve encountered is
due to an unresolved bug in R and that there was nothing that could have
been done to get the packages to correctly install when moving from 2.12 to
2.13.0, short of including checkBuilt=T.

Thank you,

Tom



 Perhaps section 2.8 of the Windows FAQ should be incorporated into the Mac
 FAQ? The checkBuilt trick is otherwise not brought to our attention.

 The FAQ could also be clearer on whether recommended packages can be
 replaced with older versions using this method; it's much easier to
 copy-and-paste everything in the directory than to hunt-and-peck for only
 the packages that aren't installed by default. I'll submit that suggestion
 to r-wind...@r-project.org separately.

 - Tom

 On Wed, May 25, 2011 at 07:58, Prof Brian Ripley rip...@stats.ox.ac.uk
 wrote:

  It's really odd that people blog about their own inefficient scripts
 rather
 than read the R documentation.

 Because this scripts checks (very inefficiently) if a package is already
 installed, it would not solve the problem discussed in this thread.  And
 install.packages() takes a vector of packages, and 'survival' is a
 recommended package and should always be installed.

 Because people have differing needs there are different ways to do this.
  But the ideas of



 http://cran.r-project.org/bin/windows/base/rw-FAQ.html#What_0027s-the-best-way-to-upgrade_003f

 suit many.



 On Wed, 25 May 2011, Tom Hopper wrote:

  There's a handy script to automate the update process that I came across

 some time ago at


 https://bridgewater.wordpress.com/2010/12/21/my-favorite-r-packages-installed-with-one-command/

 When you run the script, it will automatically install the libraries
 that
 you set up in the script. When you run it, it will install into the
 first
 location in .libPaths(). If you want packages installed in
 ~/Library/R...,
 then you need to check the Default Library Paths option in
 R--Preferences--Startup. Alternatively, you could supply the lib=
 argument
 to the install.packages() call. With a little extra code, you could even
 define the install location for each package individually.

 Here's a shortened version:
 # Essential R packages: 2011-01-02
 # Originally from: R packages I use commonly: 12/21/2010 twitter:
 drbridgewater
 # Jeff S. A. Bridgewater
 #


 https://bridgewater.wordpress.com/2010/12/21/my-favorite-r-packages-installed-with-one-command/
 #

 #list all packages currently installed
 p-c()

 #add essential packages:
 p-c(p,survival)
 p-c(p,Hmisc)
 # add more packages here

 # UPDATE the repository list to point to your local repositories
 repositories-c(http://mirrors.softliste.de/cran/,;
 http://mirrors.softliste.de/cran/;)
 install_package-function(pack,repositories)
 {
 if(!(pack %in% row.names(installed.packages(
 {
 update.packages(repos=repositories, ask=F)
 install.packages(pack, repos=repositories, dependencies=T)
 }
 require(pack,character.only=TRUE)
 }

 for( pack in p)
 {
 install_package(pack,repositories)
 }

   [[alternative HTML version deleted]]

 ___
 R-SIG-Mac mailing list
 R-SIG-Mac@r-project.org
 https://stat.ethz.ch/mailman/listinfo/r-sig-mac


  --
 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, UKFax:  +44 1865 272595


[[alternative HTML version deleted]]

 ___
 R-SIG-Mac mailing list
 R-SIG-Mac@r-project.org
 https://stat.ethz.ch/mailman/listinfo/r-sig-mac


 --
 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, UKFax:  +44 1865 272595


[[alternative HTML version deleted]]

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Re: [R-SIG-Mac] install.packages: location of system-wide library tree

2011-05-25 Thread Kasper Daniel Hansen

.Library.site becomes not empty when you create a site library, for example by
  mkdir  {PATH to R}/R/lib64/site-library
(of course lib64 assumes a 64 bit architecture)

Kasper

On Wed, May 25, 2011 at 6:51 AM, Sean Davis sdav...@mail.nih.gov wrote:
 See help(.Library).

 Sean

 On Wed, May 25, 2011 at 6:35 AM, jochen laubrock
 jochen.laubr...@gmail.com wrote:
 Dear expeRts,

 On (my?) macs, .libPaths() contains two entries, with the first pointing to 
 a user's library tree and the second to the system-wide library tree, as in

 ## begin code
 v - getRversion()
 userLib - Sys.glob(sprintf(~/Library/R/%s.%s/library, v$major, v$minor))
 systemLib - 
 sprintf(/Library/Frameworks/R.framework/Versions/%s.%s/Resources/library, 
 v$major, v$minor)
 userLib == .libPaths()[1]
 systemLib == .libPaths()[2]
 # both return TRUE (on my system)
 ## end code

 When installing new packages, I would like to make them available to all 
 users. However, the 'lib' parameter of 'install.packages' defaults to the 
 first element of '.libPaths()'. How do I reliably specify the location of 
 the system library: Is it always equal to '.libPaths()[-1]'? And why is 
 '.Library.site' empty?

 Jochen


 sessionInfo()
 R version 2.13.0 (2011-04-13)
 Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

 
 Jochen Laubrock, Dept. of Psychology, University of Potsdam,
 Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
 phone: +49-331-977-2346, fax: +49-331-977-2793

 ___
 R-SIG-Mac mailing list
 R-SIG-Mac@r-project.org
 https://stat.ethz.ch/mailman/listinfo/r-sig-mac


 ___
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Re: [R-SIG-Mac] packages failed to load - Now fixed

On May 25, 2011, at 7:17 AM, Tom Hopper wrote:

On Wed, May 25, 2011 at 11:50, Prof Brian Ripley rip...@stats.ox.ac.ukwrote:

On Wed, 25 May 2011, Tom Hopper wrote:

Brian,

Since the problem was fixed by updating packages with checkBuilt=T,
wouldn't
installing packages fresh using the script have avoided the problem?

No, because it checks if they are already installed *as I said*.

Sorry, my question was poorly structured. I understood your original
statement, and was following up with regards to the update process of R for
Mac and some of its inner workings. Since I don't have your knowledge of the
software, and am unlikely to develop such knowledge in the foreseeable
future, I (perhaps incorrectly) addressed my question to you.

I take it from your response that the problem that Ian Reeve encountered is
due to an unresolved bug in R and that there was nothing that could have
been done to get the packages to correctly install when moving from 2.12 to
2.13.0, short of including checkBuilt=T.

No, you got it completely backwards! The script you referred to is useless in
that case (and I told you that you are entirely off topic with that!), it has
nothing to do with R. There is no bug in R mentioned anywhere in the thread,
so you are really inventing things here. Please *do* read the e-mails you are
receiving.

Thanks,
Simon

Perhaps section 2.8 of the Windows FAQ should be incorporated into the Mac
FAQ? The checkBuilt trick is otherwise not brought to our attention.

The FAQ could also be clearer on whether recommended packages can be
replaced with older versions using this method; it's much easier to
copy-and-paste everything in the directory than to hunt-and-peck for only
the packages that aren't installed by default. I'll submit that suggestion
to r-wind...@r-project.org separately.

- Tom

On Wed, May 25, 2011 at 07:58, Prof Brian Ripley rip...@stats.ox.ac.uk
wrote:

It's really odd that people blog about their own inefficient scripts
rather
than read the R documentation.

Because this scripts checks (very inefficiently) if a package is already
installed, it would not solve the problem discussed in this thread. And
install.packages() takes a vector of packages, and 'survival' is a
recommended package and should always be installed.

Because people have differing needs there are different ways to do this.
But the ideas of

http://cran.r-project.org/bin/windows/base/rw-FAQ.html#What_0027s-the-best-way-to-upgrade_003f

suit many.

On Wed, 25 May 2011, Tom Hopper wrote:

There's a handy script to automate the update process that I came across

some time ago at

https://bridgewater.wordpress.com/2010/12/21/my-favorite-r-packages-installed-with-one-command/

When you run the script, it will automatically install the libraries
that
you set up in the script. When you run it, it will install into the
first
location in .libPaths(). If you want packages installed in
~/Library/R...,
then you need to check the Default Library Paths option in
R--Preferences--Startup. Alternatively, you could supply the lib=
argument
to the install.packages() call. With a little extra code, you could even
define the install location for each package individually.

Here's a shortened version:
# Essential R packages: 2011-01-02
# Originally from: R packages I use commonly: 12/21/2010 twitter:
drbridgewater
# Jeff S. A. Bridgewater
#

https://bridgewater.wordpress.com/2010/12/21/my-favorite-r-packages-installed-with-one-command/
#

#list all packages currently installed
p-c()

#add essential packages:
p-c(p,survival)
p-c(p,Hmisc)
# add more packages here

# UPDATE the repository list to point to your local repositories
repositories-c(http://mirrors.softliste.de/cran/,;
http://mirrors.softliste.de/cran/;)
install_package-function(pack,repositories)
{
if(!(pack %in% row.names(installed.packages(
{
update.packages(repos=repositories, ask=F)
install.packages(pack, repos=repositories, dependencies=T)
}
require(pack,character.only=TRUE)
}

for( pack in p)
{
install_package(pack,repositories)
}

[[alternative HTML version deleted]]

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--
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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, UKFax: +44 1865 272595

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Professor of Applied Statistics,

Re: [R-SIG-Mac] packages failed to load - Now fixed

On Wed, May 25, 2011 at 15:23, Simon Urbanek simon.urba...@r-project.orgwrote:


 On May 25, 2011, at 7:17 AM, Tom Hopper wrote:

  On Wed, May 25, 2011 at 11:50, Prof Brian Ripley rip...@stats.ox.ac.uk
 wrote:
 
  On Wed, 25 May 2011, Tom Hopper wrote:
 
  Brian,
 
  Since the problem was fixed by updating packages with checkBuilt=T,
  wouldn't
  installing packages fresh using the script have avoided the problem?
 
 
  No, because it checks if they are already installed *as I said*.
 
 
  Sorry, my question was poorly structured. I understood your original
  statement, and was following up with regards to the update process of R
 for
  Mac and some of its inner workings. Since I don't have your knowledge of
 the
  software, and am unlikely to develop such knowledge in the foreseeable
  future, I (perhaps incorrectly) addressed my question to you.
 
  I take it from your response that the problem that Ian Reeve encountered
 is
  due to an unresolved bug in R and that there was nothing that could have
  been done to get the packages to correctly install when moving from 2.12
 to
  2.13.0, short of including checkBuilt=T.
 

 No, you got it completely backwards! The script you referred to is useless
 in that case (and I told you that you are entirely off topic with that!), it
 has nothing to do with R. There is no bug in R mentioned anywhere in the
 thread, so you are really inventing things here. Please *do* read the
 e-mails you are receiving.


Ignoring the personal attack, I'd like to get back to the thread, and my
question.

Having read through the thread a couple of times, my understanding is that
Ian Reeve updated R for Mac using the installer, then installed all of the
packages he wanted from CRAN. As I understand the thread, after this update,
an old package compiled under 2.12 was, inexplicably, located in his 2.13
library. That it was a package problem and not something else was confirmed
by resolving the problem with update.packages(checkBuilt=T), rather than the
other methods suggested. It seems to me that either the R installer did not
update correctly, perhaps by retaining a link to the 2.12 directory, or Ian
accidentally copied a package over rather than reinstalling everything fresh
from CRAN. I believe that you, Simon, suggested the latter as a possibility.
I refer to the former possibility as a bug, because, to the best of my
knowledge, it should happen and shouldn't be possible. Use other
terminology, if you like. Ian then asked if he should delete the old
directory before performing an upgrade, to which you responded that doing so
shouldn't be necessary, and we should just install new R and then use
Package Manager to install packages.

As I understood this, it means a file was accidentally copied over when it
shouldn't have been, so the fix is to install packages directly from CRAN
using the Package Manager, a script or some other method, just so long as
there's no copying. Alternatively, copying must be followed by
update.packages(checkBuilt=T).

Now, I'm sure that I have this wrong, someplace, and since I update multiple
computers on multiple platforms, without your expertise in R, I'm trying to
understand this well enough so that I can avoid similar problems. If I
install a new version of R and then, without doing anything else, either use
the Package Manager or a script to install the packages I want, would I
encounter the same problem?

Thank you,

Tom



 Thanks,
 Simon


 
 
 
  Perhaps section 2.8 of the Windows FAQ should be incorporated into the
 Mac
  FAQ? The checkBuilt trick is otherwise not brought to our attention.
 
  The FAQ could also be clearer on whether recommended packages can be
  replaced with older versions using this method; it's much easier to
  copy-and-paste everything in the directory than to hunt-and-peck for
 only
  the packages that aren't installed by default. I'll submit that
 suggestion
  to r-wind...@r-project.org separately.
 
  - Tom
 
  On Wed, May 25, 2011 at 07:58, Prof Brian Ripley 
 rip...@stats.ox.ac.uk
  wrote:
 
  It's really odd that people blog about their own inefficient scripts
  rather
  than read the R documentation.
 
  Because this scripts checks (very inefficiently) if a package is
 already
  installed, it would not solve the problem discussed in this thread.
  And
  install.packages() takes a vector of packages, and 'survival' is a
  recommended package and should always be installed.
 
  Because people have differing needs there are different ways to do
 this.
  But the ideas of
 
 
 
 
 http://cran.r-project.org/bin/windows/base/rw-FAQ.html#What_0027s-the-best-way-to-upgrade_003f
 
  suit many.
 
 
 
  On Wed, 25 May 2011, Tom Hopper wrote:
 
  There's a handy script to automate the update process that I came
 across
 
  some time ago at
 
 
 
 https://bridgewater.wordpress.com/2010/12/21/my-favorite-r-packages-installed-with-one-command/
 
  When you run the script, it will automatically install the libraries
  that
  you set

Re: [R-SIG-Mac] packages failed to load - Now fixed

2011-05-25 Thread Sean Davis

On Wed, May 25, 2011 at 9:52 AM, Tom Hopper tomhop...@gmail.com wrote:
 On Wed, May 25, 2011 at 15:23, Simon Urbanek 
 simon.urba...@r-project.orgwrote:


 On May 25, 2011, at 7:17 AM, Tom Hopper wrote:

  On Wed, May 25, 2011 at 11:50, Prof Brian Ripley rip...@stats.ox.ac.uk
 wrote:
 
  On Wed, 25 May 2011, Tom Hopper wrote:
 
  Brian,
 
  Since the problem was fixed by updating packages with checkBuilt=T,
  wouldn't
  installing packages fresh using the script have avoided the problem?
 
 
  No, because it checks if they are already installed *as I said*.
 
 
  Sorry, my question was poorly structured. I understood your original
  statement, and was following up with regards to the update process of R
 for
  Mac and some of its inner workings. Since I don't have your knowledge of
 the
  software, and am unlikely to develop such knowledge in the foreseeable
  future, I (perhaps incorrectly) addressed my question to you.
 
  I take it from your response that the problem that Ian Reeve encountered
 is
  due to an unresolved bug in R and that there was nothing that could have
  been done to get the packages to correctly install when moving from 2.12
 to
  2.13.0, short of including checkBuilt=T.
 

 No, you got it completely backwards! The script you referred to is useless
 in that case (and I told you that you are entirely off topic with that!), it
 has nothing to do with R. There is no bug in R mentioned anywhere in the
 thread, so you are really inventing things here. Please *do* read the
 e-mails you are receiving.


 Ignoring the personal attack, I'd like to get back to the thread, and my
 question.

 Having read through the thread a couple of times, my understanding is that
 Ian Reeve updated R for Mac using the installer, then installed all of the
 packages he wanted from CRAN. As I understand the thread, after this update,
 an old package compiled under 2.12 was, inexplicably, located in his 2.13
 library. That it was a package problem and not something else was confirmed
 by resolving the problem with update.packages(checkBuilt=T), rather than the
 other methods suggested. It seems to me that either the R installer did not
 update correctly, perhaps by retaining a link to the 2.12 directory, or Ian
 accidentally copied a package over rather than reinstalling everything fresh
 from CRAN. I believe that you, Simon, suggested the latter as a possibility.
 I refer to the former possibility as a bug, because, to the best of my
 knowledge, it should happen and shouldn't be possible. Use other
 terminology, if you like. Ian then asked if he should delete the old
 directory before performing an upgrade, to which you responded that doing so
 shouldn't be necessary, and we should just install new R and then use
 Package Manager to install packages.

 As I understood this, it means a file was accidentally copied over when it
 shouldn't have been, so the fix is to install packages directly from CRAN
 using the Package Manager, a script or some other method, just so long as
 there's no copying. Alternatively, copying must be followed by
 update.packages(checkBuilt=T).

 Now, I'm sure that I have this wrong, someplace, and since I update multiple
 computers on multiple platforms, without your expertise in R, I'm trying to
 understand this well enough so that I can avoid similar problems. If I
 install a new version of R and then, without doing anything else, either use
 the Package Manager or a script to install the packages I want, would I
 encounter the same problem?

You should not.

Sean


 Thanks,
 Simon


 
 
 
  Perhaps section 2.8 of the Windows FAQ should be incorporated into the
 Mac
  FAQ? The checkBuilt trick is otherwise not brought to our attention.
 
  The FAQ could also be clearer on whether recommended packages can be
  replaced with older versions using this method; it's much easier to
  copy-and-paste everything in the directory than to hunt-and-peck for
 only
  the packages that aren't installed by default. I'll submit that
 suggestion
  to r-wind...@r-project.org separately.
 
  - Tom
 
  On Wed, May 25, 2011 at 07:58, Prof Brian Ripley 
 rip...@stats.ox.ac.uk
  wrote:
 
  It's really odd that people blog about their own inefficient scripts
  rather
  than read the R documentation.
 
  Because this scripts checks (very inefficiently) if a package is
 already
  installed, it would not solve the problem discussed in this thread.
  And
  install.packages() takes a vector of packages, and 'survival' is a
  recommended package and should always be installed.
 
  Because people have differing needs there are different ways to do
 this.
  But the ideas of
 
 
 
 
 http://cran.r-project.org/bin/windows/base/rw-FAQ.html#What_0027s-the-best-way-to-upgrade_003f
 
  suit many.
 
 
 
  On Wed, 25 May 2011, Tom Hopper wrote:
 
  There's a handy script to automate the update process that I came
 across
 
  some time ago at

Re: [R-SIG-Mac] packages failed to load - Now fixed

On Wed, May 25, 2011 at 15:57, Sean Davis sdav...@mail.nih.gov wrote:

 On Wed, May 25, 2011 at 9:52 AM, Tom Hopper tomhop...@gmail.com wrote:

 snip

  understand this well enough so that I can avoid similar problems. If I
  install a new version of R and then, without doing anything else, either
 use
  the Package Manager or a script to install the packages I want, would I
  encounter the same problem?

 You should not.


Thank you.

- Tom

[[alternative HTML version deleted]]

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[R-SIG-Mac] ? as a valid help request

Hi all,
I wonder if there could be a way to allow querys like the following to succeed 
by changes to the gui command line?

?
 Error: unexpected '' in ?”

?%*%
Error: unexpected SPECIAL in ?%*%

cheers,
tim

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Scotland, with registration number SC005336.

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Re: [R-SIG-Mac] ? as a valid help request

2011-05-25 Thread Marc Schwartz

On May 25, 2011, at 11:14 AM, Timothy Bates wrote:

 Hi all,
 I wonder if there could be a way to allow querys like the following to 
 succeed by changes to the gui command line?
 
 ?
 Error: unexpected '' in ?”
 
 ?%*%
 Error: unexpected SPECIAL in ?%*%
 
 cheers,
 tim


Just surround the topic with quotes:

?

and 

?%in%


This is covered in ?help:

Some topics need to be quoted (by backticks) or given as a character string. 
There include those which cannot syntactically appear on their own such as 
unary and binary operators, function and control-flow reserved words (including 
if, elsefor, in, repeat, while, break and next. The other reserved words can be 
used as if they were names, for example TRUE, NA and Inf.

HTH.

Marc Schwartz

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Re: [R-SIG-Mac] ? as a valid help request

 just do
 '?'
On 25 May 2011, at 5:20 PM, Marc Schwartz wrote:
 ?
 Error: unexpected '' in “?”


Thanks Mark and Ian,
Glad it’s a straightforward and memorable workaround. And this is easy in the 
new GUI (which adds quotes around a selection. Still wish that the error told 
me that was a likely cause: I just assumed it was impossible to search on.

Followup GUI query: Is there a was to go to the beginning of the command line 
directly? My method is to cmd-right select the line, then use right arrow to 
fall off the end of the selection leaving the cursor at the start (ready to 
type a ?)

This fails: The right arrow just does nothing…

As cmd-shift-? opens help, a lovely enhancement would be for cmd-cntrl-? to 
execute ?rGUISelection

Then help would be just a matter of select and keystroke, with no need to 
delete the? or pollute the history.

EnjoyR,
tim


-- 
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Scotland, with registration number SC005336.

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Re: [R-SIG-Mac] ? as a valid help request

2011-05-25 Thread David Winsemius



On May 25, 2011, at 12:32 PM, Timothy Bates wrote:


just do
'?'

On 25 May 2011, at 5:20 PM, Marc Schwartz wrote:

?
Error: unexpected '' in “?”



Thanks Mark and Ian,
Glad it’s a straightforward and memorable workaround. And this is  
easy in the new GUI (which adds quotes around a selection. Still  
wish that the error told me that was a likely cause: I just assumed  
it was impossible to search on.


Followup GUI query: Is there a was to go to the beginning of the  
command line directly? My method is to cmd-right select the line,  
then use right arrow to fall off the end of the selection leaving  
the cursor at the start (ready to type a ?)


cntrl-a works for me on the GUI and I suspect on a terminal console  
session as well, since I have been told that it is a UNIX convention.


--

David Winsemius, MD
West Hartford, CT

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Re: [R-SIG-Mac] ? as a valid help request

2011-05-25 Thread Berend Hasselman


On 25-05-2011, at 18:32, Timothy Bates wrote:

 just do
 '?'
 On 25 May 2011, at 5:20 PM, Marc Schwartz wrote:
 ?
 Error: unexpected '' in “?”
 
 
 Thanks Mark and Ian,
 Glad it’s a straightforward and memorable workaround. And this is easy in the 
 new GUI (which adds quotes around a selection. Still wish that the error told 
 me that was a likely cause: I just assumed it was impossible to search on.
 
 Followup GUI query: Is there a was to go to the beginning of the command line 
 directly? My method is to cmd-right select the line, then use right arrow to 
 fall off the end of the selection leaving the cursor at the start (ready to 
 type a ?)
 
 This fails: The right arrow just does nothing…

Command-left arrow
Ctrl-A

And you can create a DefaultKeyBinding.dict in the directory 
~/Library/Keybindings with  a mapping of the Home to the Cocoa cursor command 
moveToBeginningOfLine:.
See http://www.hcs.harvard.edu/~jrus/site/cocoa-text.html

For example, if you have a DefaultKeyBinding.dict file containing

{
/* home  Shift+home*/
\UF729  = moveToBeginningOfLine:;
$\UF729 = moveToBeginningOfLineAndModifySelection:;

/* end  Shift+end*/
\UF72B  = moveToEndOfLine:;
$\UF72B = moveToEndOfLineAndModifySelection:;
}

Home will move the cursor to the start of a line
End  will move the cursor to the end of a line

Combined with a  shift key, these will select from the current cursor position 
to the start/end of line.


Berend
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[R-SIG-Mac] left-arrow doesn't unselect and move left (was ? as a valid help request)

On 25 May 2011, at 5:50 PM, Berend Hasselman wrote:
 The left arrow just does nothing when a selection has been made (whereas the 
 right arrow undoes the selection, leaving the cursor to its right)
 Command-left arrow
 Ctrl-A
 …


Again, thanks for the help: I think it is a bug that left-arrow does not 
deselect the selection and leave the cursor immediately to the left of the old 
selection. having hte left-arrow move left is completely standard on mac 
applications., where as control-A is Unix only.

thanks again for the replies,
t

 Home will move the cursor to the start of a line
 End  will move the cursor to the end of a line
PS: not keys I have unfortunately :-(


-- 
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Re: [R-SIG-Mac] ? as a valid help request

2011-05-25 Thread David Winsemius



On May 25, 2011, at 12:50 PM, Berend Hasselman wrote:




Home will move the cursor to the start of a line
End  will move the cursor to the end of a line


Not on my machine in the GUI. Goes to top or bottom of the console  
window.


--

David Winsemius, MD
West Hartford, CT

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Re: [R-SIG-Mac] ? as a valid help request

2011-05-25 Thread Berend Hasselman


On 25-05-2011, at 19:10, David Winsemius wrote:

 
 On May 25, 2011, at 12:50 PM, Berend Hasselman wrote:
 
 
 
 Home will move the cursor to the start of a line
 End  will move the cursor to the end of a line
 
 Not on my machine in the GUI. Goes to top or bottom of the console window.


To get the behaviour I described you have to have a DefaultKeyBinding.dict with 
the appropriate key definitions.
Otherwise indeed Home/End go to top/end of text/window.

Berend
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Re: [R-SIG-Mac] ? as a valid help request

2011-05-25 Thread Hans-Jörg Bibiko

On 25 May 2011, at 18:14, Timothy Bates wrote:

 I wonder if there could be a way to allow querys like the following to 
 succeed by changes to the gui command line?
 
 ?
 Error: unexpected '' in ?”
 

Hi Tim,

did you try to simply select the pattern (here  ) and press CTRL+H or 
right-click for content menu and select Show Help for current Function?

Cheers,
--Hans
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[R-SIG-Mac] Key bindings in the GUI [Was: ? as a valid help request]


On May 25, 2011, at 1:10 PM, David Winsemius wrote:

 
 On May 25, 2011, at 12:50 PM, Berend Hasselman wrote:
 
 
 
 Home will move the cursor to the start of a line
 End  will move the cursor to the end of a line
 
 Not on my machine in the GUI. Goes to top or bottom of the console window.
 

What Berend meant is that if you want to re-define the behavior to be 
non-standard with the modifications he listed (which you cut out), you can have 
it behave that way. It is not the default or intended behavior, though. 
(Windows users may be more used to it which is presumably why he mentioned it).

Just to re-iterate, the standard Mac way to go to the beginning of the line is 
CmdLeft. The standard Mac way to move up a paragraph is AltUp (which is 
equivalent to going to the beginning of a paragraph except when you are already 
there). There is an emacs equivalent CtrlA which goes to the beginning of 
the paragraph.

Now, in fact he GUI behaves slightly differently, but no one noticed ;). Due to 
the special treatment of the prompt, the commands concerning the beginnings of 
things have special work-arounds, so for example beginning of the line equals 
beginning of the paragraph in the GUI. However, this is what people most 
commonly want, so I'm not sure it's abad thing. I'll see if I can make the 
behavior consistent, though.

Cheers,
Simon

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Re: [R-SIG-Mac] ? as a valid help request


Hans said:
 did you try to simply select the function and press CTRL+H or right-click for 
 content menu and select Show Help for current Function”?

fantastic Hans!
PS: I looked in the help menu and saw nothing like “help on selection cntrl-H” 
…. that would help with newbie discovery (like me :-) )

Simon said:
 the GUI behaves slightly differently, but no one noticed ;). Due to the 
 special treatment of the prompt, the commands concerning the beginnings of 
 things have special work-arounds, so for example beginning of the line equals 
 beginning of the paragraph in the GUI. However, this is what people most 
 commonly want, so I'm not sure it's abad thing. I'll see if I can make the 
 behavior consistent, though.

Would be great: it is unusual not to be able to left-arrow out of a selection. 
Maybe I can get used to Cmd–left-arrow to go to beginning of line: I think I 
use the shift key to highlight so I can attend the new location of the cursor 
more easily.

t


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Re: [R-SIG-Mac] ? as a valid help request