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

Sean Davis sdavis2 at mail.nih.gov
Wed May 25 15:57:59 CEST 2011 

On Wed, May 25, 2011 at 9:52 AM, Tom Hopper <tomhopper at gmail.com> wrote:
> On Wed, May 25, 2011 at 15:23, Simon Urbanek <simon.urbanek at r-project.org>wrote:
>
>>
>> On May 25, 2011, at 7:17 AM, Tom Hopper wrote:
>>
>> > On Wed, May 25, 2011 at 11:50, Prof Brian Ripley <ripley at 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-windows at r-project.org separately.
>> >>>
>> >>> - Tom
>> >>>
>> >>> On Wed, May 25, 2011 at 07:58, Prof Brian Ripley <
>> ripley at 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 at r-project.org
>> >>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> >>>>>
>> >>>>>
>> >>>>> --
>> >>>> Brian D. Ripley,                  ripley at stats.ox.ac.uk
>> >>>> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
>> >>>> University of Oxford,             Tel:  +44 1865 272861 (self)
>> >>>> 1 South Parks Road,                     +44 1865 272866 (PA)
>> >>>> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>> >>>>
>> >>>>
>> >>>       [[alternative HTML version deleted]]
>> >>>
>> >>> _______________________________________________
>> >>> R-SIG-Mac mailing list
>> >>> R-SIG-Mac at r-project.org
>> >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> >>>
>> >>>
>> >> --
>> >> Brian D. Ripley,                  ripley at stats.ox.ac.uk
>> >> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
>> >> University of Oxford,             Tel:  +44 1865 272861 (self)
>> >> 1 South Parks Road,                     +44 1865 272866 (PA)
>> >> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>> >>
>> >
>> >       [[alternative HTML version deleted]]
>> >
>> > _______________________________________________
>> > R-SIG-Mac mailing list
>> > R-SIG-Mac at r-project.org
>> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> >
>> >
>>
>>
>
>        [[alternative HTML version deleted]]
>
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