[Bioc-devel] installation errors with selected Bioconductor packages on Linux

[Richard Wang]

> sessionInfo()
R version 2.1.1, 2005-6-20, i686-redhat-linux-gnu

attached base packages:
[1] "methods"   "stats"     "graphics"   "grDevices" "utils"
"datasets"
[7] "base"

other attached packages:
  limma
"2.0.8"

_____________________________
Richard Wang
Biostatistician
UCSF - Immune Tolerance Network
4800 Montgomery Lane, Suite 300
Bethesda, MD 20814
(240) 235-6177
(240) 497-0351 fax
rwang at immunetolerance.org
 
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-----Original Message-----
From: Ting-Yuan Liu (FHCRC) [mailto:tliu at fhcrc.org] 
Sent: Wednesday, September 21, 2005 2:36 PM
To: Richard Wang
Cc: bioc-devel at stat.math.ethz.ch
Subject: Re: [Bioc-devel] installation errors with selected Bioconductor
packages on Linux


Hi Richard,

Could you provide the information from sessionInfo()?  It will help us 
understand your system more so that we can have a better idea about what

happened.  

Thanks,
Ting-Yaun

On Wed, 21 Sep 2005, Richard Wang wrote:

> Hello all-
> 
>  
> 
> I am currently trying to install Bioconductor on a Linux workstation.
> Using either the biocLite or getBioC installation commands, most
> packages install with no trouble (I've made use of limma already), but
> 11 packages have failed to install repeatedly.  I've appended an
example
> of the error message I'm getting, in this case for the affy package.
> Any advice or insights would be greatly appreciated.
> 
>  
> 
> > biocLite("affy")
> 
>  
> 
> Running bioCLite version 0.1  with R version  2.1.1
> 
>  
> 
> Running biocinstall version 1.2  with R version  2.1.1
> 
> 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 -I/usr/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include   -fPIC
> -O2 -g -pipe -m32 -march=i686 -mtune=pentium4 -c chipbackground.c -o
> chipbackground.o
> 
> gcc -I/usr/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include   -fPIC
> -O2 -g -pipe -m32 -march=i686 -mtune=pentium4 -c getall_locations.c -o
> getall_locations.o
> 
> gcc -I/usr/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include   -fPIC
> -O2 -g -pipe -m32 -march=i686 -mtune=pentium4 -c mas5calls.c -o
> mas5calls.o
> 
> gcc -I/usr/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include   -fPIC
> -O2 -g -pipe -m32 -march=i686 -mtune=pentium4 -c qnorm.c -o qnorm.o
> 
> gcc -I/usr/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include   -fPIC
> -O2 -g -pipe -m32 -march=i686 -mtune=pentium4 -c read_abatch.c -o
> read_abatch.o
> 
> gcc -I/usr/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include   -fPIC
> -O2 -g -pipe -m32 -march=i686 -mtune=pentium4 -c rma2.c -o rma2.o
> 
> gcc -I/usr/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include   -fPIC
> -O2 -g -pipe -m32 -march=i686 -mtune=pentium4 -c rma_background2.c -o
> rma_background2.o
> 
> gcc -I/usr/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include   -fPIC
> -O2 -g -pipe -m32 -march=i686 -mtune=pentium4 -c rma_common.c -o
> rma_common.o
> 
> gcc -shared -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   -L/usr/lib/R/lib -lR
> 
> gcc -shared -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   -L/usr/lib/R/lib -lR
> 
> /usr/bin/ld: skipping incompatible /usr/lib/R/lib/libR.so when
searching
> for -lR/usr/bin/ld: cannot find -lR
> 
> collect2: ld returned 1 exit status
> 
> make: *** [affy.so] Error 1
> 
> ERROR: compilation failed for package 'affy'
> 
> ** Removing '/usr/lib/R/library/affy'
> 
> ** Restoring previous '/usr/lib/R/library/affy'
> 
>  
> 
>  
> 
> _____________________________
> 
> Richard Wang
> 
> Biostatistician
> 
> UCSF - Immune Tolerance Network
> 
> 4800 Montgomery Lane, Suite 300
> 
> Bethesda, MD 20814
> 
> (240) 235-6177
> 
> (240) 497-0351 fax
> 
> rwang at immunetolerance.org
> 
>  
> 
> CONFIDENTIAL AND PROPRIETARY:  This email communication may contain
> confidential and proprietary information intended only for the use of
> the intended recipients identified above. If you are not the intended
> recipient of this communication, you are hereby notified that any
> unauthorized review, use, dissemination, distribution, downloading, or
> copying of this communication is strictly prohibited. If you are not
the
> intended recipient and have received this communication in error,
please
> immediately notify us by reply email, delete the communication and
> destroy all copies.
> 
>  
> 
> 
> 	[[alternative HTML version deleted]]
> 
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