Re: [R-SIG-Mac] packages failed to load - Now fixed
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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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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Re: [R-SIG-Mac] packages failed to load - Now fixed
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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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]]
___
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--
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
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 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
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]]
___
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--
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
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--
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
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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--
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
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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
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]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] packages failed to load
Just wanted to mention that I saw the same behavior with a package or two, and found the same workaround (copying libs to the 2.12 tree). Carl quote Message: 4 Date: Tue, 24 May 2011 16:32:41 +1000 From: Ian Reeve ire...@une.edu.au To: r-sig-mac@r-project.org r-sig-mac@r-project.org Subject: [R-SIG-Mac] Packages deldir, class and gpclib fail to load in R 2.13.0 Message-ID: 23292b0b-0329-454c-9a17-5bb1ccb45...@une.edu.au Content-Type: text/plain; charset=us-ascii Hi, I've been running rgdal, RColorBrewer, maptools, classInt, spdep, gpclib, raster, zoo, cluster and lattice in R2.12 on Mac OSX 10.6.7 for the last 6 months with no problems. Today I installed R 2.13.0, and downloaded the latest versions of the above packages. Most of them load without problems, but class (a depend of classInt), and deldir (a depend of spdep) failed to load. The error message is of the form: --- Loading required package: class Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/class/libs/x86_64/class.so': dlopen(/Library/Frameworks/R.framework/Versions/2.13/Resources/library/class/libs/x86_64/class.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libR.dylib Referenced from: /Library/Frameworks/R.framework/Versions/2.13/Resources/library/class/libs/x86_64/class.so Reason: image not found Error: package 'class' could not be loaded --- The problem seems to be either the package is looking in the wrong place (a subdirectory of 2.12 instead of a subdirectory of 2.13) for the file libR.dylib, or the install of R failed to put the files that package class needs in the 2.12 directory. In the case of deldir, the errant file is libgfortran.2.dylib. I can get package class to load without error by taking a copy of libR.dylib from the subdirectory of 2.13 and putting it in the subdirectory of 2.12 where class expects it to be. I'm concerned this might be a stupid short-term fix, as calls to the functions in class might also fail due to other files not being in the expected places. Can anyone suggest any leads to other approaches I could take to get these previously trouble-free packages to behave themselves in R 2.13? Thank you. Ian Reeve Institute for Rural Futures University of New England Armidale, NSW 2351 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] packages failed to load
Ian, I agree with Brian. I checked the CRAN binaries of class and deldir and they are correctly linking to 2.13, so I suspect you have old packages in your tree. I don't think this can happen with stock R binary, it seems that at some point you moved packages or there is/was a symlink between some libraries of 2.12 and 2.13. If the latter is true, to avoid future issues I would suggest sudo rm -rf /Library/Frameworks/R.framework and re-installing R. Cheers, Simon On May 24, 2011, at 9:48 AM, Prof Brian Ripley wrote: On Tue, 24 May 2011, Carl Witthoft wrote: Just wanted to mention that I saw the same behavior with a package or two, and found the same workaround (copying libs to the 2.12 tree). Maybe, but this is about the recommended package 'class'. In the CRAN distribution oF R 2.13.0 tystie% otool -L /Library/Frameworks/R.framework/Versions/2.13/Resources/library/class/libs/x86_64/class.so /Library/Frameworks/R.framework/Versions/2.13/Resources/library/class/libs/x86_64/class.so: class.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libR.dylib (compatibility version 2.13.0, current version 2.13.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 476.19.0) /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 111.1.5) So class.so is linked to the correct libR.dylib. Something odd has happened on Ian Reeve's system, and I suspect that a binary copy of 'class' built for R 2.12.x has been installed into 2.13.0. I suggest at a minimum running update.packages(checkBuilt=TRUE) and if the problems persist a complete clear out and re-install. Carl quote Message: 4 Date: Tue, 24 May 2011 16:32:41 +1000 From: Ian Reeve ire...@une.edu.au To: r-sig-mac@r-project.org r-sig-mac@r-project.org Subject: [R-SIG-Mac] Packages deldir,class and gpclib fail to load in R 2.13.0 Message-ID: 23292b0b-0329-454c-9a17-5bb1ccb45...@une.edu.au Content-Type: text/plain; charset=us-ascii Hi, I've been running rgdal, RColorBrewer, maptools, classInt, spdep, gpclib, raster, zoo, cluster and lattice in R2.12 on Mac OSX 10.6.7 for the last 6 months with no problems. Today I installed R 2.13.0, and downloaded the latest versions of the above packages. Most of them load without problems, but class (a depend of classInt), and deldir (a depend of spdep) failed to load. The error message is of the form: --- Loading required package: class Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/class/libs/x86_64/class.so': dlopen(/Library/Frameworks/R.framework/Versions/2.13/Resources/library/class/libs/x86_64/class.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libR.dylib Referenced from: /Library/Frameworks/R.framework/Versions/2.13/Resources/library/class/libs/x86_64/class.so Reason: image not found Error: package 'class' could not be loaded --- The problem seems to be either the package is looking in the wrong place (a subdirectory of 2.12 instead of a subdirectory of 2.13) for the file libR.dylib, or the install of R failed to put the files that package class needs in the 2.12 directory. In the case of deldir, the errant file is libgfortran.2.dylib. I can get package class to load without error by taking a copy of libR.dylib from the subdirectory of 2.13 and putting it in the subdirectory of 2.12 where class expects it to be. I'm concerned this might be a stupid short-term fix, as calls to the functions in class might also fail due to other files not being in the expected places. Can anyone suggest any leads to other approaches I could take to get these previously trouble-free packages to behave themselves in R 2.13? Thank you. Ian Reeve Institute for Rural Futures University of New England Armidale, NSW 2351 ___ 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 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org
Re: [R-SIG-Mac] packages failed to load - Now fixed
Thanks Brian and Simon for the suggestions. update.packages(checkBuilt=TRUE) fixed the load problem and all the functions I was using in R 2.12 are running identically in R 2.13.0. For future reference, when I update to a new version of R, is it good practice to: sudo rm -rf /Library/Frameworks/R.framework and then download and install the contributed packages one needs? Otherwise, does the installing process for the base R package look at what is already there in R.framework tree and retain the contributed packages that were installed under the previous version? Thanks Brian, Carl and Simon for your prompt assistance - it's very much appreciated. Regards Ian On 24/05/2011, at 11:48 PM, Prof Brian Ripley wrote: On Tue, 24 May 2011, Carl Witthoft wrote: Just wanted to mention that I saw the same behavior with a package or two, and found the same workaround (copying libs to the 2.12 tree). Maybe, but this is about the recommended package 'class'. In the CRAN distribution oF R 2.13.0 tystie% otool -L /Library/Frameworks/R.framework/Versions/2.13/Resources/library/class/libs/x86_64/class.so /Library/Frameworks/R.framework/Versions/2.13/Resources/library/class/libs/x86_64/class.so: class.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libR.dylib (compatibility version 2.13.0, current version 2.13.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 476.19.0) /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 111.1.5) So class.so is linked to the correct libR.dylib. Something odd has happened on Ian Reeve's system, and I suspect that a binary copy of 'class' built for R 2.12.x has been installed into 2.13.0. I suggest at a minimum running update.packages(checkBuilt=TRUE) and if the problems persist a complete clear out and re-install. Carl quote Message: 4 Date: Tue, 24 May 2011 16:32:41 +1000 From: Ian Reeve ire...@une.edu.au To: r-sig-mac@r-project.org r-sig-mac@r-project.org Subject: [R-SIG-Mac] Packages deldir,class and gpclib fail to load in R 2.13.0 Message-ID: 23292b0b-0329-454c-9a17-5bb1ccb45...@une.edu.au Content-Type: text/plain; charset=us-ascii Hi, I've been running rgdal, RColorBrewer, maptools, classInt, spdep, gpclib, raster, zoo, cluster and lattice in R2.12 on Mac OSX 10.6.7 for the last 6 months with no problems. Today I installed R 2.13.0, and downloaded the latest versions of the above packages. Most of them load without problems, but class (a depend of classInt), and deldir (a depend of spdep) failed to load. The error message is of the form: --- Loading required package: class Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/class/libs/x86_64/class.so': dlopen(/Library/Frameworks/R.framework/Versions/2.13/Resources/library/class/libs/x86_64/class.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libR.dylib Referenced from: /Library/Frameworks/R.framework/Versions/2.13/Resources/library/class/libs/x86_64/class.so Reason: image not found Error: package 'class' could not be loaded --- The problem seems to be either the package is looking in the wrong place (a subdirectory of 2.12 instead of a subdirectory of 2.13) for the file libR.dylib, or the install of R failed to put the files that package class needs in the 2.12 directory. In the case of deldir, the errant file is libgfortran.2.dylib. I can get package class to load without error by taking a copy of libR.dylib from the subdirectory of 2.13 and putting it in the subdirectory of 2.12 where class expects it to be. I'm concerned this might be a stupid short-term fix, as calls to the functions in class might also fail due to other files not being in the expected places. Can anyone suggest any leads to other approaches I could take to get these previously trouble-free packages to behave themselves in R 2.13? Thank you. Ian Reeve Institute for Rural Futures University of New England Armidale, NSW 2351 ___ 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 Ian Reeve Institute for Rural Futures University of New
Re: [R-SIG-Mac] packages failed to load - Now fixed
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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