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

[stefano iacus]

On 23/mag/05, at 02:20, Paul Shannon wrote:

> 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
>

Hi Paul,
the binary distribution of R (R.app) has been configured on Panther so,  
in principle, to build packages from source, you should have the same  
setup.
Tiger has no cc_dynamic around and comes with gcc 4.0, but you can  
still build R from sources switching to gcc3.3 which is supported by  
panther as well. The same applies to the fortran compiler: you need g77  
for panther and not gfortran.
You should follow the instructions reported here
http://wiki.urbanek.info/index.cgi?TigeR

under the section "CRAN build and Tiger".

stefano
p.s. BTW, we currently build binary packages for Mac OS X and in a  
couple of days they'll be ready to be downloaded in binary form  
directly from inside R.app



> 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
>
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> Type 'demo()' for some demos, 'help()' for on-line help, or
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>
>> 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",
>
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