"Frank" == Frank E Harrell <[EMAIL PROTECTED]> on Tue, 01 Jun 2004 07:48:17 +0200 writes:
Frank> Martin Maechler wrote:
>>>>>>> "Frank" == Frank E Harrell <[EMAIL PROTECTED]>
>>>>>>> on Mon, 31 May 2004 18:44:55 +0200 writes:
>> >> Frank> I am having difficulty running R CMD check using the
Frank> 30May04 version of R-devel and a new version of the
Frank> Hmisc package:
>> Frank> * checking S3 generic/method consistency ... WARNING
Frank> Error in .tryQuietly({ : Error in library(package, lib.loc = lib.loc, Frank> character.only = TRUE, verbose = FALSE) :
Frank> .First.lib failed
Frank> Execution halted
>> Frank> See section 'Generic functions and methods' of the
Frank> 'Writing R Extensions' manual.
>> >> I'm not sure, but I'd guess it's simply the last line of your
>> .First.lib. that fails, i.e.,
>> library.dynam("Hmisc", pkg, lib)
>> which fails loading the C/Fortran code.
>> I've had similar experiences. The 'R CMD check' error message
>> is definitely ``sub optimal''.
>> >> Simply try (in R-devel)
>> >> library(Hmisc, lib.loc="~/R/Hmisc.Rcheck")
>> >> This should give a much better error message.
>> Let us know if this helped.
>> >> Regards, Martin
Frank> Thanks Martin. Here's what I get:
>> library(Hmisc,lib.loc="~/R/Hmisc.Rcheck") Frank> Hmisc library by Frank E Harrell Jr
Frank> Type library(help='Hmisc'), ?Overview, or ?Hmisc.Overview') Frank> to see overall documentation.
Frank> Hmisc redefines [.factor to drop unused levels of factor variables Frank> when subscripting. To prevent this behaviour, issue the command Frank> options(drop.unused.levels=F).
Frank> Error in dyn.load(x, as.logical(local), as.logical(now)) :
Frank> unable to load shared library Frank> "/home/harrelfe/R/Hmisc.Rcheck/Hmisc/libs/Hmisc.so":
Frank> libR.so: cannot open shared object file: No such file or directory
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
this probably is the clue : Hmisc.so expects an libR.so which is what you get when you do ......./configure --enable-shared and make for building R itself.
It looks like your version of R-devel hasn't successfully been built with the ..shared option. But when using it to build packages, it *does* assume the 'shared R' (libR.so in unix) to be available.
[or Hmisc.so itself or its underlying *.o files were built with a non-shared (i.e. default) version of R ?]
If it the former (and incomplete shared installation) I'd consider wiping that out and rebuild R afresh -- shared or not -- test R ("make check" or even "make check-all") and when successful, rebuild Hmisc {removing at least Hmisc/src/*o beforehand!} with that version of R.
Martin
Thanks very much Martin. I think you've hit on it. The problem seems to have to do with the order in which I install Hmisc using regular (non-shared) R (installed the usual Debian way) with regard to when I run CMD check under R-devel. I configured R-devel using --enable-shared (if this matters) and ran R-devel CMD check "fresh" and all seems to be well. Thanks for your insight. In the future I think I'll just remove the *.o files from regular R before running CMD check. I am surprised that R-devel and R 1.9 are inconsistent on this point. -Frank
Frank> Error in library(Hmisc, lib.loc = "~/R/Hmisc.Rcheck") : Frank> .First.lib failed
Frank> Since Hmisc.so is in the right place:
Frank> ~/R/Hmisc.Rcheck/Hmisc/libs harrelfe:ls -la Frank> total 48 Frank> drwxr-xr-x 2 harrelfe harrelfe 4096 May 31 18:31 . Frank> drwxr-xr-x 10 harrelfe harrelfe 4096 May 31 18:34 .. Frank> -rwxr-xr-x 1 harrelfe harrelfe 37524 May 31 18:31 Hmisc.so
Frank> I don't understand the problem. The same Hmisc.so (under Frank> /usr/local/lib/R/site-library) loads fine under R 1.9.
Frank> Frank
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University______________________________________________ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
