I'm glad I didn't see those comments -- ;-)
Prof. Ripley also pointed out they weren't supposed to be macros.
The -bexpall (actuall -Wl,-bexpall) produced an effect: now it complains
about finding fortran libraries. gfortran was compiled with static libs
on this system. It is complaining as well about lapack-like names dger_,
dgemv_. This failure is happening around grDevices:
make[4]: Leaving directory
`/geno4/watplatt/R/R-2.4.0/src/library/grDevices/src'
Error in solve.default(rgb) : lapack routines cannot be loaded
In addition: Warning message:
unable to load shared library
'/geno4/watplatt/R/R-2.4.0/modules//lapack.so':
rtld: 0712-001 Symbol _gfortran_pow_r8_i4 was referenced
from module /geno4/watplatt/R/R-2.4.0/lib/libRlapack.so(), but a
runtime definition
of the symbol was not found.
rtld: 0712-001 Symbol _gfortran_compare_string was referenced
from module /geno4/watplatt/R/R-2.4.0/lib/libRlapack.so(), but a
runtime definition
of the symbol was not found.
rtld: 0712-001 Symbol _gfortran_copy_string was referenced
from module /geno4/watplatt/R/R-2.4.0/lib/libRlapack.so(), but a
runtime definition
of the symbol was not found.
rtld: 0712-001 Symbol dger_ was referenced
from module /geno4/watplatt/R/R-2.4.0/lib/libRlapack.so(), but a
runtime definition
of the symbol was not found.
rtld: 0712-001 Symbol dgemv_ was referenced
from module /geno4/watplatt/R/R-2.4.0/lib/libRlapack.so(), but a
runtime definition
of the symbol was not found.
rtld: 0712-001 Symbol _gfortr
Error: unable to load R code in package 'grDevices'
Execution halted
The directory path to lapack.so appears to be correct, not in a path
connected to other builds or versions, etc. The file lapack.so is sitting
in the directory as spec'd in the complaint.
Daniel E. Platt
Bioinformatics and Pattern Discovery
IBM T. J. Watson Research Center
Yorktown Hgts, NY 10598
(914)945-1388
Peter Dalgaard <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
10/16/2006 04:29 PM
To
Daniel Platt/Watson/[EMAIL PROTECTED]
cc
r-devel@stat.math.ethz.ch, [EMAIL PROTECTED]
Subject
Re: [Rd] PR#9295
[EMAIL PROTECTED] writes:
> I asked a question that might help me track down what changed between
> 2.3.1 that did build and the 2.4.0 version that will not build. Some of
> the undefined names the linker was complaining about looked like #define
> symbols that were not picked up by configure. The first thing I was
> hoping for was to find out if this problem looked familiar? Whether or
> not, I'm willing to try to work on it, but hope I can get reasonable
> answers to honest questions
Well, you should have seen the snide remarks that I decided to keep to
myself (Along the lines of "please tell us the fix in time for the
_next_ release")
Anyways, AFAIK those entry points are not supposed to be macros. They
are also undefined symbols in tools.so on Fedora, so your issue would
seem to be with the linker. The culprit is likely changes to the
symbol registration mechanism, or an unforeseen complication of this:
o configure now defaults to 'run-time linking' on AIX
(and AIX < 4.2 is no longer allowed), using -bexpall rather
than export/import files. If this works, it allows R to be
built in the same way as other Unix-alikes, including with R
as a shared library and with a shared BLAS.
Also, of course, check that you are doing a clean build and that the
previous build is not somehow interfering.
> Dan
>
> Saw:
>
> IBM employee is unable to make AIX work: so why does he expect us to?
>
> in response to:
>
> From: [EMAIL PROTECTED]
> To: [EMAIL PROTECTED]
> Subject: Unable to build
> Date: Fri, 13 Oct 2006 21:42:37 +0200 (CEST)
>
> Full_Name: Daniel E. Platt
> Version: 2.4.0
> OS: AIX 5.3
> Submission from: (NULL) (129.34.20.23)
>
>
> Did a new build of gcc c,c++,gfortran v4.1.1, (re)built R 2.3.1 using
> config.site as spec'd in R-admin.pdf in sec C.9 as described by Jagat
> Sheth,
> with addition of FC=gfortran (configure tried using f95, which is
present
> on the
> system, but won't bind with gcc's obj files).
>
>
> Applying the same to 4.1.1 produces the following:
>
> make[4]: Leaving directory
> `/geno4/watplatt/R/R-2.4.0/src/library/tools/src'
> Error in dyn.load(x, as.logical(local), as.logical(now)) :
> unable to load shared library
> '/geno4/watplatt/R/R-2.4.0/library/tools/libs/tools.so':
> rtld: 0712-001 Symbol TYPEOF was referenced
> from module
/geno4/watplatt/R/R-2.4.0/library/tools/libs/tools.so(),
> but a
> runtime definition
> of the symbol was not found.
> rtld: 0712-001 Symbol Rf_error was referenced
> from modul
