problem updating packages on Ubuntu 7.10

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problem updating packages on Ubuntu 7.10

Daniel Nordlund
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
>

I tried searching on the error message

/usr/bin/ld: cannot find -lgfortran

along with R and Ubuntu and was not able to find anything that was helpful to me.  I have successfully updated packages on Ubuntu 6.10 and 7.04.  I am sure somebody knows what is happening here, and I would appreciate any pointers to what I am doing wrong.

Thanks,

Dan

Daniel Nordlund
Bothell, WA

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Re: problem updating packages on Ubuntu 7.10

Vincent Goulet
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
   [hidden email]   http://vgoulet.act.ulaval.ca


>
> I tried searching on the error message
>
> /usr/bin/ld: cannot find -lgfortran
>
> along with R and Ubuntu and was not able to find anything that was  
> helpful to me.  I have successfully updated packages on Ubuntu 6.10  
> and 7.04.  I am sure somebody knows what is happening here, and I  
> would appreciate any pointers to what I am doing wrong.
>
> Thanks,
>
> Dan
>
> Daniel Nordlund
> Bothell, WA
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: problem updating packages on Ubuntu 7.10

Daniel Nordlund
> -----Original Message-----
> From: Vincent Goulet [mailto:[hidden email]]
> Sent: Friday, November 23, 2007 7:47 AM
> To: Daniel Nordlund
> Cc: [hidden email]
> 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
>    [hidden email]   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

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.