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

buhard Ceph buhard at cephb.fr
Wed Mar 19 17:10:23 MET 2003

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.

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 ?

Any help greatly appreciated

thanks in advance.

BUHARD Olivier
27 rue Juliette DODU
75010 PARIS

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