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 <thern...@mayo.edu> >> To: Dirk Eddelbuettel <e...@debian.org> >> Cc: c...@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. >> | >> | >> > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
