[BioC] Install problem of some BioConductor packages under linux R session

[Laurent Gautier]

On Wed, Mar 19, 2003 at 05:10:23PM +0100, buhard Ceph wrote:
> Hi all,
> 
> 
> 
> I encounter some problems while trying to install BioConductor packages under R for Linux (perhaps as a new Bioconductor user, and not a linux expert !).
> 
> I've downloaded the tar.gz file sources of Bioconductor and successfully installed a part of the bundle... but installation stops at 'hexbin', with an error indicating '-lreadline' is nof found, as reported here :
> 
> 
> 
> After R CMD INSTALL treated 'graph' package, I get the following messages :
> 
> * Installing *source* package 'hexbin' ...
> ** libs
> g77 -mieee-fp  -O3 -fomit-frame-pointer -pipe -mcpu=pentiumpro -march=i586 -fno-fast-math -fno-strength-reduce  -O3 -fomit-frame-pointer -pipe -mcpu=pentiumpro -march=i586 -fno-fast-math -fno-strength-reduce -c hbin.f -o hbin.o
> g77 -mieee-fp  -O3 -fomit-frame-pointer -pipe -mcpu=pentiumpro -march=i586 -fno-fast-math -fno-strength-reduce  -O3 -fomit-frame-pointer -pipe -mcpu=pentiumpro -march=i586 -fno-fast-math -fno-strength-reduce -c hcell.f -o hcell.o
> g77 -mieee-fp  -O3 -fomit-frame-pointer -pipe -mcpu=pentiumpro -march=i586 -fno-fast-math -fno-strength-reduce  -O3 -fomit-frame-pointer -pipe -mcpu=pentiumpro -march=i586 -fno-fast-math -fno-strength-reduce -c herode.f -o herode.o
> g77 -mieee-fp  -O3 -fomit-frame-pointer -pipe -mcpu=pentiumpro -march=i586 -fno-fast-math -fno-strength-reduce  -O3 -fomit-frame-pointer -pipe -mcpu=pentiumpro -march=i586 -fno-fast-math -fno-strength-reduce -c hsm.f -o hsm.o
> g77 -mieee-fp  -O3 -fomit-frame-pointer -pipe -mcpu=pentiumpro -march=i586 -fno-fast-math -fno-strength-reduce  -O3 -fomit-frame-pointer -pipe -mcpu=pentiumpro -march=i586 -fno-fast-math -fno-strength-reduce -c htst.f -o htst.o
> gcc -shared -L/usr/local/lib -o hexbin.so hbin.o hcell.o herode.o hsm.o htst.o  -L/usr/local/lib -L/usr/lib/gcc-lib/i586-mandrake-linux-gnu/3.2 -L/usr/lib/gcc-lib/i586-mandrake-linux-gnu/3.2/../../.. -lreadline -ldl -lncurses -lfrtbegin -lg2c -lm -lgcc_s -L/usr/lib/R/bin -lR
> /usr/bin/ld: cannot find -lreadline
> collect2: ld returned 1 exit status
> make: *** [hexbin.so] Erreur 1
> ERROR: compilation failed for package 'hexbin'
> [root at localhost root]#
> 
> 
> 
> None of all subsequent packages is installed then.

As far as I remember, few packages (if any) depend on hexbin. You should
be able to install the others one by one.

The install script available is an option you should consider too..

> 
> Maybe there's something missing on my OS (mdk 9, kernel 2.4.19-24) ? Or a library with a bad (or missing) path declaration ? what else ?

If you did a vanilla install of Mandrake, I think you still need to install
the rpm 'readline-devel'.


Hopin' it helps,




Laurent





> 
> Any help greatly appreciated
> 
> thanks in advance.
> 
> 
> 
> BUHARD Olivier
> INSERM U434/CEPH
> 27 rue Juliette DODU
> 75010 PARIS
> 
> 
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> 
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Laurent Gautier			CBS, Building 208, DTU
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