[BioC] bioconductor 1.6, R 2.1.0a: "can't locate file for: -lcc_dynamic"

[Paul Shannon]

On Mac OS X 10.4.1, using a freshly installed R-2.1.0.dmg (with patch R-2.1.0a.dmg),
I ran 

  > source ("http://www.bioconductor.org/getBioC.R")
  > getBioC ("affy")

and then got the error message:

   /usr/bin/ld: can't locate file for: -lcc_dynamic

   installation of package 'affy' had non-zero exit status in:n
   install.packages(pkgs = "affy", repos = c("http://www.bioconductor.org/packages/bioc/stable",

while linking

    gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o \
       affy.so chipbackground.o getall_locations.o mas5calls.o qnorm.o \
       read_abatch.o rma2.o rma_background2.o rma_common.o -lz -lcc_dynamic \
       -framework R

The full session is included below.

Can anyone help?  Thanks!

 - Paul





R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.1.0  (2005-04-18), ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for a HTML browser interface to help.
Type 'q()' to quit R.

> source ("http://www.bioconductor.org/getBioC.r")
Error in file(file, "r", encoding = encoding) : 
      unable to open connection
In addition: Warning message:
cannot open: HTTP status was '404 Not Found' 
> source ("http://www.bioconductor.org/getBioC.R")
> getBioC ("affy")

Running getBioC version 0.2  with R version  2.1.0 
http://www.bioconductor.org/scripts/2.1/biocinstall.R
Running biocinstall version 0.9  with R version  2.1.0 
trying URL 'http://www.bioconductor.org/packages/bioc/stable/src/contrib/affy_1.6.7.tar.gz'
Content type 'application/x-gzip' length 1164993 bytes
opened URL
==================================================
downloaded 1137Kb

* Installing *source* package 'affy' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -DHAVE_ZLIB=1  -I/usr/local/include   -fno-common  -g -O2 -c chipbackground.c -o chipbackground.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -DHAVE_ZLIB=1  -I/usr/local/include   -fno-common  -g -O2 -c getall_locations.c -o getall_locations.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -DHAVE_ZLIB=1  -I/usr/local/include   -fno-common  -g -O2 -c mas5calls.c -o mas5calls.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -DHAVE_ZLIB=1  -I/usr/local/include   -fno-common  -g -O2 -c qnorm.c -o qnorm.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -DHAVE_ZLIB=1  -I/usr/local/include   -fno-common  -g -O2 -c read_abatch.c -o read_abatch.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -DHAVE_ZLIB=1  -I/usr/local/include   -fno-common  -g -O2 -c rma2.c -o rma2.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -DHAVE_ZLIB=1  -I/usr/local/include   -fno-common  -g -O2 -c rma_background2.c -o rma_background2.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -DHAVE_ZLIB=1  -I/usr/local/include   -fno-common  -g -O2 -c rma_common.c -o rma_common.o
gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o affy.so chipbackground.o getall_locations.o mas5calls.o qnorm.o read_abatch.o rma2.o rma_background2.o rma_common.o -lz  -lcc_dynamic -framework R
** Removing '/Users/paulshannon/Library/R/library/affy'
** Restoring previous '/Users/paulshannon/Library/R/library/affy'
/usr/bin/ld: can't locate file for: -lcc_dynamic
collect2: ld returned 1 exit status
make: *** [affy.so] Error 1
ERROR: compilation failed for package 'affy'

The downloaded packages are in
    /private/tmp/Rtmp5sLDRX/downloaded_packages
Warning message:
installation of package 'affy' had non-zero exit status in: install.packages(pkgs = "affy", repos = c("http://www.bioconductor.org/packages/bioc/stable",