Are R packages supposed to be "relocatable"? (avoiding BioConductor scripts...)

[PaulJohnson32gmail]

I've asked a question in the BioConductor list about package
management. My solution depends on your answer to the following
question.

Are installed R packages "relocatable"?

I mean relocatable in the same sense that files in a RedHat RPM file
might be "relocatable" after compiling
(http://www.rpm.org/max-rpm/ch-rpm-reloc.html).  This allows one to
build a package as the ordinary user and then the root user can take
the result and put it wherever it fits well in the path (say,
/usr/local/lib/R/library).

Here is why I asked.  I manage packages in our cluster and some users
have asked me to install some BioConductor packages.  BioConductor
install documents expect me to run a script as root that does a bunch
of changes, and I'm just unwilling to do that.  If I have to do
something as root, it has to be something more focused like running a
particular R command (install.packages(), for example).  It seems
insane to me that they expect (http://www.bioconductor.org/install) a
root user to run

source("http://bioconductor.org/biocLite.R")
biocLite("limma")

If I could do the installs as me with their script, and then copy the
install folder into the system, then it would be OK, if the packages
would work.

Or perhaps post-processing is required to fiddle some paths inside
package files?

pj
--
Paul E. Johnson
Professor, Political Science    Assoc. Director
1541 Lilac Lane, Room 504     Center for Research Methods
University of Kansas               University of Kansas
http://pj.freefaculty.org            http://quant.ku.edu

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[Simon Urbanek]

On Jul 19, 2012, at 12:13 PM, Paul Johnson wrote:

> I've asked a question in the BioConductor list about package
> management. My solution depends on your answer to the following
> question.
>
> Are installed R packages "relocatable"?
>

It depends on the platform and what you want to relocate (R or just the packages) and on the package itself. For example on OS X absolute paths are included in dylibs, so you can move packages that allow it and don't link to other packages but you can't relocate R or packages that link to other packages directly or libraries within the package (that should be rare, though). Whether a package allows relocation depends whether it hard-codes any paths it uses - typical packages use facilities like system.file to locate files so those are relocatable, but if a package determines paths at configure time it may not be relocatable.

Since you didn't even specify the platform you're interested in, this is only a generic answer ...

> I mean relocatable in the same sense that files in a RedHat RPM file
> might be "relocatable" after compiling
> (http://www.rpm.org/max-rpm/ch-rpm-reloc.html).  This allows one to
> build a package as the ordinary user and then the root user can take
> the result and put it wherever it fits well in the path (say,
> /usr/local/lib/R/library).
>
> Here is why I asked.  I manage packages in our cluster and some users
> have asked me to install some BioConductor packages.  BioConductor
> install documents expect me to run a script as root that does a bunch
> of changes, and I'm just unwilling to do that.  If I have to do
> something as root, it has to be something more focused like running a
> particular R command (install.packages(), for example).  It seems
> insane to me that they expect (http://www.bioconductor.org/install) a
> root user to run
>

You can install BioC packages simply with install.packages() - there is no black magic involved, it's a regular repository just like CRAN ...

Cheers,
Simon

> source("http://bioconductor.org/biocLite.R")
> biocLite("limma")
>
> If I could do the installs as me with their script, and then copy the
> install folder into the system, then it would be OK, if the packages
> would work.
>
> Or perhaps post-processing is required to fiddle some paths inside
> package files?
>
> pj
> --
> Paul E. Johnson
> Professor, Political Science    Assoc. Director
> 1541 Lilac Lane, Room 504     Center for Research Methods
> University of Kansas               University of Kansas
> http://pj.freefaculty.org            http://quant.ku.edu
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>

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[Prof Brian Ripley]

Short answer:

setRepositories() # chose what you want from BioC
install.packages()

works and always has. 'Smoke and mirrors' are not actually needed.

As for relocatability:

I am guessing you are talking about a Linux cluster ... but the details
do matter.

The distribution of Windows binaries relies on installed packages being
relocatable, so most packages are written to be.  There are a very few
exceptions: the one most frequently encountered is packages linked to
Rcpp, which on Linux put the path to Rcpp in their DSOs.  So you can
relocate the package, but not the Rcpp installation it is linked to.
(Not a problem on other OSes as it statically links elsewhere.)

A question you did not ask is if you can use differently located R: in
most cases yes (I regularly run different versions of R with the same
library trees).

We've relocated complete CRAN/BioC installations on Linux several times.

On 19/07/2012 17:13, Paul Johnson wrote:

> I've asked a question in the BioConductor list about package
> management. My solution depends on your answer to the following
> question.
>
> Are installed R packages "relocatable"?
>
> I mean relocatable in the same sense that files in a RedHat RPM file
> might be "relocatable" after compiling
> (http://www.rpm.org/max-rpm/ch-rpm-reloc.html).  This allows one to
> build a package as the ordinary user and then the root user can take
> the result and put it wherever it fits well in the path (say,
> /usr/local/lib/R/library).
>
> Here is why I asked.  I manage packages in our cluster and some users
> have asked me to install some BioConductor packages.  BioConductor
> install documents expect me to run a script as root that does a bunch
> of changes, and I'm just unwilling to do that.  If I have to do
> something as root, it has to be something more focused like running a
> particular R command (install.packages(), for example).  It seems
> insane to me that they expect (http://www.bioconductor.org/install) a
> root user to run
>
> source("http://bioconductor.org/biocLite.R")
> biocLite("limma")
>
> If I could do the installs as me with their script, and then copy the
> install folder into the system, then it would be OK, if the packages
> would work.
>
> Or perhaps post-processing is required to fiddle some paths inside
> package files?
>
> pj
>

--
Brian D. Ripley,                  [hidden email]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  [phone] (self)
1 South Parks Road,                     [phone] (PA)
Oxford OX1 3TG, UK                Fax:  [phone]

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[Martin Morgan]

On 07/19/2012 09:13 AM, Paul Johnson wrote:

> I've asked a question in the BioConductor list about package
> management. My solution depends on your answer to the following
> question.
>
> Are installed R packages "relocatable"?
>
> I mean relocatable in the same sense that files in a RedHat RPM file
> might be "relocatable" after compiling
> (http://www.rpm.org/max-rpm/ch-rpm-reloc.html).  This allows one to
> build a package as the ordinary user and then the root user can take
> the result and put it wherever it fits well in the path (say,
> /usr/local/lib/R/library).
>
> Here is why I asked.  I manage packages in our cluster and some users
> have asked me to install some BioConductor packages.  BioConductor
> install documents expect me to run a script as root that does a bunch
> of changes, and I'm just unwilling to do that.  If I have to do
> something as root, it has to be something more focused like running a
> particular R command (install.packages(), for example).  It seems
> insane to me that they expect (http://www.bioconductor.org/install) a
> root user to run
>
> source("http://bioconductor.org/biocLite.R")
> biocLite("limma")

For the record, this does four things.

(1) The 'source' command installs the BiocInstaller package appropriate
for your (recent) version of R or, if this package is already installed,
attaches it.

All remaining steps are executed by scripts in the BiocInstaller
package, so after an initial invocation the 'source()' statement can be
replaced by library(BiocInstaller).

(2) biocLite() invokes BiocInstaller::biocLite, which checks whether
BiocInstaller is current and, if not, updates it. Disable this behaviour
with the option suppressAutoUpdate=TRUE.

(3) The limma package and needed dependencies are installed, using
install.packages() and the repositories appropriate for your version of
R (paying attention to utils::setRepositories() and
utils::chooseBioCmirror()). The 'lib' argument to biocLite is passed to
install.packages() so the user has control over the directory in which
packages will be installed.

(4) biocLite checks whether any packages are out-of-date relative to the
version in the repository, and offers to update those that are out of
date. Packages that are in directories that cannot be written are
reported, via a warning and hence when biocLite finishes, as "installed
directory not writeable, cannot update packages '...'" (this message
apparently confused you; we will try for a better wording). Use
suppressUpdates=TRUE to suppress this step, ask=FALSE to have old
packages (in writeable directories) updated without being prompted; a
lib.loc argument can be used to restrict the locations where
old.packages() searches.

The arguments to biocLite are documented on its help page in the
BiocInstaller package, ?biocLite.


For step (3), Prof Ripley & Dr Urbanek (and me in my response to your
Bioconductor post,
https://stat.ethz.ch/pipermail/bioconductor/2012-July/046999.html) are
correct in stating that this can be done with a direct call to
install.packages().

Step (4) arises because Bioconductor packages (a) follow a semi-annual
release cycle, with a 'release' and 'devel' branch, and (b) generally
have greater dependencies amongst one another. In the past, two very
common scenarios leading to problems were that user installations mix
packages from different releases of Bioconductor, and users report bugs
that have already been addressed via bug fixes to the current release.
So step (4) is trying to be pro-active, and based on traffic to the
mailing list this has generally been successful. This synchronization is
more important, and difficult for the user to manage directly, now that
R has moved to an annual release cycle.

Steps (1) and (2) are needed to bootstrap the process. The relatively
recent introduction of the BiocInstaller package allows us to document
biocLite in a standard way, as well as provide the code in a more
familiar fashion. Step (1) is partly a legacy (BiocInstaller is not in
all releases of Bioconductor), and partly a simplification to avoid
confusion (avoiding 'first time users should do A, return users should
do B').


As a 'normal' user it is safe and appropriate to use biocLite to manage
Bioconductor (and CRAN) packages. One takes a more cautious approach as
'root', but I personally would be comfortable administering a widely
used R / Bioconductor installation with biocLite.

Martin Morgan
Bioconductor


> If I could do the installs as me with their script, and then copy the
> install folder into the system, then it would be OK, if the packages
> would work.
>
> Or perhaps post-processing is required to fiddle some paths inside
> package files?
>
> pj
>


--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: [phone]

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