[BioC] Re: Bioconductor Digest, Vol 1, Issue 270

[Nicholas Lewin-Koh]

Hi,
I don't think this is a g77 error, this is a linker error. I use redhat
linux myself so
I don't know much about the mandrake distribution. I would suggest first
following Laurent's advice and make sure that the readline libs are
installed on your system. As Laurent also comments nothing in
bioconductor is dependent on hexbin. But this will soon change and
hexagons will rule the world, na just kidding. If installing readline and
readline_devel doesn't help email again and i will see if we can't get
this debugged.

Nicholas
 
> Message: 1
> Date: Wed, 19 Mar 2003 17:10:23 +0100
> From: "buhard Ceph" <buhard at cephb.fr>
> Subject: [BioC]         Install problem of some BioConductor packages
> under
> 	linux R session
> To: <bioconductor at stat.math.ethz.ch>
> Message-ID: <001f01c2ee32$0d520610$4d05030a at cephb.fr>
> Content-Type: text/plain
> 
> 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
> INSERM U434/CEPH
> 27 rue Juliette DODU
> 75010 PARIS
> 
> 
> 	[[alternate HTML version deleted]]
> 
> 
> ------------------------------
>