[R] problem updating packages on Ubuntu 7.10

[Daniel Nordlund]

> -----Original Message-----
> From: Vincent Goulet [mailto:vincent.goulet at act.ulaval.ca]
> Sent: Friday, November 23, 2007 7:47 AM
> To: Daniel Nordlund
> Cc: r-help at stat.math.ethz.ch
> Subject: Re: [R] problem updating packages on Ubuntu 7.10
> 
> Le jeu. 22 nov. à 14:19, Daniel Nordlund a écrit :
> 
> > I am running Ubuntu 7.10 and R-2.6.0, and I am having trouble
> > updating packages.  There appears to be a problem involving
> > gfortran.  For example, here is the output of an attempt to update
> > the Hmisc package.
> >
> > * Installing *source* package 'Hmisc' ...
> > ** libs
> > gfortran   -fpic  -g -O2 -c cidxcn.f -o cidxcn.o
> > gfortran   -fpic  -g -O2 -c cidxcp.f -o cidxcp.o
> > gfortran   -fpic  -g -O2 -c hoeffd.f -o hoeffd.o
> > gfortran   -fpic  -g -O2 -c jacklins.f -o jacklins.o
> > gfortran   -fpic  -g -O2 -c largrec.f -o largrec.o
> > gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -
> > fpic  -g -O2 -c ranksort.c -o ranksort.o
> > gfortran   -fpic  -g -O2 -c rcorr.f -o rcorr.o
> > gfortran   -fpic  -g -O2 -c wclosest.f -o wclosest.o
> > gcc -std=gnu99 -shared  -o Hmisc.so cidxcn.o cidxcp.o hoeffd.o
> > jacklins.o largrec.o ranksort.o rcorr.o wclosest.o  -lgfortran -lm -
> > lgcc_s -L/usr/lib/R/lib -lR
> > /usr/bin/ld: cannot find -lgfortran
> > collect2: ld returned 1 exit status
> > make: *** [Hmisc.so] Error 1
> > ERROR: compilation failed for package 'Hmisc'
> > ** Removing '/usr/local/lib/R/site-library/Hmisc'
> > ** Restoring previous '/usr/local/lib/R/site-library/Hmisc'
> >
> > The downloaded packages are in
> >        /tmp/RtmpkaH0Db/downloaded_packages
> > Warning message:
> > In install.packages(update[instlib == l, "Package"], l, contriburl =
> > contriburl,  :
> >  installation of package 'Hmisc' had non-zero exit status
> >>
> 
> Hi Daniel,
> 
> The package built and installed flawlessly here in the Gutsy chroot
> where the Ubuntu packages are built. Did you install the r-base-dev
> package? This package will install all the tools you need to install
> source packages.
> 
> Best,
> 
> ---
>    Vincent Goulet, Associate Professor
>    École d'actuariat
>    Université Laval, Québec
>    Vincent.Goulet at act.ulaval.ca   http://vgoulet.act.ulaval.ca
> 
> 
Vincent,

Thanks for your suggestion, it led to finding the solution to my problem.  I thought I had r-base-dev installed but checked anyway.  I had r-base-dev installed under "Feisty", but it turns out that I had failed to add the CRAN repository for "Gutsy" to my third party repositories and the "Feisty" R install had not been updated.  I have done that and packages now install just fine.  I apologize for taking up band-width on R-help for a non-R problem (but I am thankful that the list did provide a solution :-).

Dan

Daniel Nordlund
Bothell, WA