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....
Dan
Saw:
IBM employee is unable to make AIX work: so why does he expect us to?
in response to:
From: watplatt at us.ibm.com
To: R-bugs at biostat.ku.dk
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 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_asLogical 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 LENGTH 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 STRING_ELT was referenced
from module /geno4/watplatt/R/R-2.4.0/library/tools/libs/tools.so(),
bu
Execution halted
make[3]: *** [all] Error 1
make[3]: Leaving directory `/geno4/watplatt/R/R-2.4.0/src/library/tools'
make[2]: *** [R] Error 1
make[2]: Leaving directory `/geno4/watplatt/R/R-2.4.0/src/library'
make[1]: *** [R] Error 1
make[1]: Leaving directory `/geno4/watplatt/R/R-2.4.0/src'
make: *** [R] Error 1
Are there undefined #define's leaking in as code?
Dan
Daniel E. Platt
Bioinformatics and Pattern Discovery
IBM T. J. Watson Research Center
Yorktown Hgts, NY 10598
(914)945-1388
[[alternative HTML version deleted]]
On 10/16/2006 3:47 PM, watplatt at us.ibm.com wrote:> 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.Actually, I think your message came through as a bug report, suggesting you were expecting someone else to fix it. Perhaps now that it's clear that you are asking a question, someone will be able to help: but surely you have access to better AIX tech support than most people on this list? Duncan Murdoch 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.... > > Dan > > Saw: > > IBM employee is unable to make AIX work: so why does he expect us to? > > in response to: > > From: watplatt at us.ibm.com > To: R-bugs at biostat.ku.dk > 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 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_asLogical 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 LENGTH 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 STRING_ELT was referenced > from module /geno4/watplatt/R/R-2.4.0/library/tools/libs/tools.so(), > bu > Execution halted > make[3]: *** [all] Error 1 > make[3]: Leaving directory `/geno4/watplatt/R/R-2.4.0/src/library/tools' > make[2]: *** [R] Error 1 > make[2]: Leaving directory `/geno4/watplatt/R/R-2.4.0/src/library' > make[1]: *** [R] Error 1 > make[1]: Leaving directory `/geno4/watplatt/R/R-2.4.0/src' > make: *** [R] Error 1 > > Are there undefined #define's leaking in as code? > > Dan > > > > > Daniel E. Platt > Bioinformatics and Pattern Discovery > IBM T. J. Watson Research Center > Yorktown Hgts, NY 10598 > (914)945-1388 > [[alternative HTML version deleted]] > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel
watplatt at us.ibm.com 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: watplatt at us.ibm.com > To: R-bugs at biostat.ku.dk > 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 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_asLogical 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 LENGTH 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 STRING_ELT was referenced > from module /geno4/watplatt/R/R-2.4.0/library/tools/libs/tools.so(), > bu > Execution halted > make[3]: *** [all] Error 1 > make[3]: Leaving directory `/geno4/watplatt/R/R-2.4.0/src/library/tools' > make[2]: *** [R] Error 1 > make[2]: Leaving directory `/geno4/watplatt/R/R-2.4.0/src/library' > make[1]: *** [R] Error 1 > make[1]: Leaving directory `/geno4/watplatt/R/R-2.4.0/src' > make: *** [R] Error 1 > > Are there undefined #define's leaking in as code? > > Dan > > > > > Daniel E. Platt > Bioinformatics and Pattern Discovery > IBM T. J. Watson Research Center > Yorktown Hgts, NY 10598 > (914)945-1388 > [[alternative HTML version deleted]] > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >-- O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907