Re: [R] Hmisc compilation problem

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Tue, 11 Dec 2007 15:19:19 +0000 (GMT)

I think you have glibc-headers missing. On an F8 system I get

eclectus% rpm -qf /usr/include/limits.h
glibc-headers-2.7-2
eclectus% rpm -qf /usr/include/stdio.h
glibc-headers-2.7-2
eclectus% rpm -qf /usr/include/stdlib.h
glibc-headers-2.7-2

You may find that glibc-devel is also missing and needed.

Did you install the R-devel RPM (you cannot have built R on that system)? That's the way to pull in the dependencies you need to make packages.

On Tue, 11 Dec 2007, Frank Liu wrote:

> I upgraded my system to Fedora Core 7 and got a compilation problem when
> installing Hmisc package.
> According to the error messages (shown below), I have tried to updated
> all of my glibc, gcc, automake rpm packages,
> but that did not help. Could you help me pointed out what package I have
> missed? Thank you.
>
>
>> version
> _
> platform i386-redhat-linux-gnu
> arch i386
> os linux-gnu
> system i386, linux-gnu
> status
> major 2
> minor 6.1
> year 2007
> month 11
> day 26
> svn rev 43537
> language R
> version.string R version 2.6.1 (2007-11-26)
>
>> install.packages("Hmisc")
> Warning in install.packages("Hmisc") :
> argument 'lib' is missing: using '/usr/lib/R/library'
> --- Please select a CRAN mirror for use in this session ---
> Loading Tcl/Tk interface ... done
> trying URL 'http://cran.csie.ntu.edu.tw/src/contrib/Hmisc_3.4-3.tar.gz'
> Content type 'application/x-gzip' length 519009 bytes (506 Kb)
> opened URL
> ==================================================
> downloaded 506 Kb
>
> /usr/lib/R/library
> * Installing *source* package 'Hmisc' ...
> ** libs
> gfortran -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
> -mtune=generic -fasynchronous-unwind-tables -c cidxcn.f -o cidxcn.o
> gfortran -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
> -mtune=generic -fasynchronous-unwind-tables -c cidxcp.f -o cidxcp.o
> gfortran -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
> -mtune=generic -fasynchronous-unwind-tables -c hoeffd.f -o hoeffd.o
> gfortran -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
> -mtune=generic -fasynchronous-unwind-tables -c jacklins.f -o jacklins.o
> gfortran -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
> -mtune=generic -fasynchronous-unwind-tables -c largrec.f -o largrec.o
> gcc -std=gnu99 -I/usr/lib/R/include -I/usr/lib/R/include
> -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32
> -march=i386 -mtune=generic -fasynchronous-unwind-tables -c ranksort.c -o
> ranksort.o
> In file included from ranksort.c:1:
> /usr/lib/R/include/R.h:28:20: error: stdlib.h: No such file or directory
> /usr/lib/R/include/R.h:29:19: error: stdio.h: No such file or directory
> In file included from
> /usr/lib/gcc/i386-redhat-linux/4.1.2/include/syslimits.h:7,
> from /usr/lib/gcc/i386-redhat-linux/4.1.2/include/limits.h:11,
> from /usr/lib/R/include/R.h:30,
> from ranksort.c:1:
> /usr/lib/gcc/i386-redhat-linux/4.1.2/include/limits.h:122:61: error:
> limits.h: No such file or directory
> In file included from ranksort.c:1:
> /usr/lib/R/include/R.h:32:18: error: math.h: No such file or directory
> /usr/lib/R/include/R.h:33:19: error: errno.h: No such file or directory
> In file included from /usr/lib/R/include/R.h:50,
> from ranksort.c:1:
> /usr/lib/R/include/R_ext/RS.h:24:39: error: string.h: No such file or
> directory
> make: *** [ranksort.o] Error 1
> ERROR: compilation failed for package 'Hmisc'
> ** Removing '/usr/lib/R/library/Hmisc'
>
> The downloaded packages are in
> /tmp/Rtmpn7J8Y0/downloaded_packages
> Updating HTML index of packages in '.Library'
> Warning message:
> In install.packages("Hmisc") :
> installation of package 'Hmisc' had non-zero exit status
>
>
>

-- 
Brian D. Ripley,                  ripley_at_stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Received on Tue 11 Dec 2007 - 15:21:37 GMT

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