Question: Install problem of some BioConductor packages under linux R session
0
gravatar for buhard Ceph
16.7 years ago by
buhard Ceph10
buhard Ceph10 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@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]]
hexbin • 567 views
ADD COMMENTlink modified 16.7 years ago by Jeff Gentry3.9k • written 16.7 years ago by buhard Ceph10
Answer: Install problem of some BioConductor packages under linux R session
0
gravatar for Laurent Gautier
16.7 years ago by
Laurent Gautier2.2k
Laurent Gautier2.2k 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@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@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
ADD COMMENTlink written 16.7 years ago by Laurent Gautier2.2k
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@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@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@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
ADD REPLYlink written 16.7 years ago by David Lapointe170
Answer: Install problem of some BioConductor packages under linux R session
0
gravatar for Jeff Gentry
16.7 years ago by
Jeff Gentry3.9k
Jeff Gentry3.9k wrote:
> 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 ? You need the readline library. This is discussed in the R-FAQ, question 7.22 ... http://cran.r-project.org/doc/FAQ/R-FAQ.html
ADD COMMENTlink written 16.7 years ago by Jeff Gentry3.9k
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