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

[Seth Falcon]

Hi Paul,

Paul Shannon <pshannon at systemsbiology.org> writes:

> 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

We don't yet have OS X 10.4 installed on any of our systems, but we
will soon.  

Building R packages from source, as your system is attempting,
requires a number of tools and libraries.  Have you configured your
system for building source packages?  If so, then I'm afraid I don't
have any suggestions at the moment.  If not, then you should take a
look at the R for OSX FAQ.

Best,

+ seth