[BioC] Problem installing 'affy' with R-2.8.0

Martin Morgan mtmorgan at fhcrc.org
Mon Oct 27 15:22:56 CET 2008


"Mizanur Khondoker" <Mizanur.Khondoker at ed.ac.uk> writes:

> I am having problem installing affy package from source on my Debian system
> with R-2.8.0. The earlier version (from bioc2.2) works fine with R-2.7.0 on
> the same system.
> Any idea of what is going wrong with the new version?

I think you're installing over an existing installation, and you have
an outdated version of the 'preprocessCore' package that needs to be
updated. In a NEW R session, follow the 'Update installed
Bioconductor packages' directions at

http://bioconductor.org/docs/install/

No need to cross-post.

Martin

>
> ###################################################################
>> sessionInfo()
> R version 2.8.0 (2008-10-20)
> i686-pc-linux-gnu
>
> locale:
> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] tools_2.8.0
>
> ##################################################################
>> source("http://bioconductor.org/biocLite.R")
>> biocLite("affy")
>
> .............................
>
> * 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 -std=gnu99 -I/usr/local/lib/R/include -DHAVE_ZLIB=1
> -I/usr/local/include -I"/usr/local/lib/R/library/preprocessCore/include"
> -fpic  -g -O2 -c chipbackground.c -o chipbackground.o
> gcc -std=gnu99 -I/usr/local/lib/R/include -DHAVE_ZLIB=1
> -I/usr/local/include -I"/usr/local/lib/R/library/preprocessCore/include"
> -fpic  -g -O2 -c getall_locations.c -o getall_locations.o
> gcc -std=gnu99 -I/usr/local/lib/R/include -DHAVE_ZLIB=1
> -I/usr/local/include -I"/usr/local/lib/R/library/preprocessCore/include"
> -fpic  -g -O2 -c mas5calls.c -o mas5calls.o
> gcc -std=gnu99 -I/usr/local/lib/R/include -DHAVE_ZLIB=1
> -I/usr/local/include -I"/usr/local/lib/R/library/preprocessCore/include"
> -fpic  -g -O2 -c rma2.c -o rma2.o
> rma2.c:108:29: error: rma_background4.h: No such file or directory
> rma2.c:119:45: error: preprocessCore_background_stubs.c: No such file or
> directory
> rma2.c:123:31: error: R_subColSummarize.h: No such file or directory
> rma2.c:124:37: error: R_subColSummarize_stubs.c: No such file or directory
> rma2.c: In function 'do_RMA2':
> rma2.c:133: warning: implicit declaration of function
> 'R_subColSummarize_medianpolish_log'
> rma2.c:133: warning: assignment makes pointer from integer without a cast
> rma2.c: In function 'rma_c_complete':
> rma2.c:248: warning: implicit declaration of function 'rma_bg_correct'
> make: *** [rma2.o] Error 1
> chmod: cannot access `/usr/local/lib/R/site-library/affy/libs/*': No such
> file or directory
> ERROR: compilation failed for package 'affy'
> ** Removing '/usr/local/lib/R/site-library/affy'
> ** Restoring previous '/usr/local/lib/R/site-library/affy'
>
> The downloaded packages are in
>         /tmp/RtmprdJr3r/downloaded_packages
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>   installation of package 'affy' had non-zero exit status
>
>
>
>
> -- 
> Mizanur Khondoker
> Division of Pathway Medicine (DPM)
> The University of Edinburgh Medical School
> The Chancellor's Building
> 49 Little France Crescent
> Edinburgh EH16 4SB
> United Kingdom
>
> Tel:  +44 (0) 131 242 6287
> Fax: +44 (0) 131 242 6244
> http://www.pathwaymedicine.ed.ac.uk/
>
> 	[[alternative HTML version deleted]]
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793



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