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

[David Lapointe]

I had the same problem. The issue is not having g77, a gnu FORTRAN
compiler, installed.

g77 [..] -c hbin.f 

These files with *.f are fortran, I believe. There is an RPM for g77.
That should fix the problem.

David

On Wed, 2003-03-19 at 21:01, Laurent Gautier wrote:
> 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
> > 
> > 
> > 	[[alternate HTML version deleted]]
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> 
> -- 
> --------------------------------------------------------------
> currently at the National Yang-Ming University in Taipei, Taiwan
> --------------------------------------------------------------
> Laurent Gautier			CBS, Building 208, DTU
> PhD. Student			DK-2800 Lyngby,Denmark	
> tel: +45 45 25 24 89		http://www.cbs.dtu.dk/laurent
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor