Problem with dyn.load in R 2.13.0 -- the real problem

On Apr 13, 2011, at 4:47 PM, Terry Therneau wrote:

On Wed, 2011-04-13 at 15:32 -0500, Dirk Eddelbuettel wrote:

Terry,

You replied to

?From: Terry Therneau <therneau at mayo.edu>
?To: Dirk Eddelbuettel <edd at debian.org>
?Cc: cran at r-project.org
?Subject: Re: [Rd] Problem with dyn.load in R 2.13.0 -- the real problem

but dropped r-devel. On purpose?

No, not on purpose. ?Corrected.

This still looks like a local config issue about local libraries to me.

Dirk

I fail to see how. ?Running the newest release of R 2.13, if I issue a library() command for something installed earlier in R_LIBS_USER, something I expect lots of people to do, and that library has a .so file with reference to the now-nonexistent Rlib.so file, an error ensues.

This depends on the OS - on Linux the path to libR is not embedded in the package's .so, so R will happily try to load whatever libR is current - regardless whether that breaks or not. Again, this is entirely OS-dependent. Also in your case you have an entirely different build of R so your issue is independent of R version - you'd get exactly the same issue if both R builds were 2.12.2.

This is easy to test elsewhere.
?I don't anticipate that every user will erase all libraries and
reinstall with each new R release.

Well, then they are entirely on their own. Major releases are not guaranteed to be binary compatible and often they are not. Depending on the subset of the features a package may use it may or may not work, but it is never guaranteed. The first thing any user should do after R upgrade is to run update.packages. But, again, this is not really related to your problem ;). I suppose your admin has forgotten to use --enable-R-shlib when building 2.13.0.

Cheers,
Simon

At work particularly, the default R
release changes without user intervention; the system admin is not going
to go looking for all local downloads. ?(A lot of people use
R_LIBS_USER, as they don't have permission to put things elsewhere --
this includes me.)
?The error message for logspline is great as it tells them what to do.
I'm only looking for a better one in the case I found.

On 13 April 2011 at 15:01, Terry Therneau wrote:
| Dirk's comment made it clearer:
|
| On Wed, 2011-04-13 at 13:34 -0500, Dirk Eddelbuettel wrote:
| > What does 'ldd /path/to/your/survial.so' say? ?Does the system find
| > libR.so?
| >
|
| tmt1077% pwd
| /people/biostat2/therneau/research/surv/Rtest
| tmt1078% ldd survival.so
| ? ? ? ? libR.so => not found
| ? ? ? ? libc.so.6 => /lib64/libc.so.6 (0x00002aede2d94000)
| ? ? ? ? /lib64/ld-linux-x86-64.so.2 (0x00000033cd800000)
|
| However, this is a survival.so file created by R12, and that version has
| a libR.so in RHOME/lib. ?Version R2.13 has no such file. ?If I remake
| the .so file using R 2.13: then I get
|
| tmt1084% ldd survival.so
| ? ? ? ? libc.so.6 => /lib64/libc.so.6 (0x00002b656a2f1000)
| ? ? ? ? /lib64/ld-linux-x86-64.so.2 (0x00000033cd800000)
|
| And R
|
| --------------
|
| So, the real problem is a misleading error message. ?I have several
| pacakges loaded into my own ~/Rlib. ?When I access one of these from
| version 2.13 I get variable errors, or success.
|
| tmt1087% R13 --vanilla
|
| R version 2.13.0 RC (2011-04-11 r55409)
| Copyright (C) 2011 The R Foundation for Statistical Computing
| ISBN 3-900051-07-0
| Platform: x86_64-unknown-linux-gnu (64-bit)
| ...
|
| > library(logspline)
| Error: package 'logspline' was built before R 2.10.0: please re-install
| it
|
| > library(quadprog)
| Error in dyn.load(file, DLLpath = DLLpath, ...) :
| ? unable to load shared object
| '/people/biostat2/therneau/Rlib/quadprog/libs/quadprog.so':
| ? libR.so: cannot open shared object file: No such file or directory
| Error: package/namespace load failed for 'quadprog'
|
| > library(xtable)
| >
|
| My problem is solved, but is this a "user confuser" issue that should be
| addressed in the release?
|
| Terry T.
|
|