[R] Hmisc compilation problem

From: Frank Liu <frankcsliu_at_gmail.com>
Date: Tue, 11 Dec 2007 22:37:42 +0800

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
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

* 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
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
Updating HTML index of packages in '.Library' Warning message:
In install.packages("Hmisc") :
installation of package 'Hmisc' had non-zero exit status


Frank C.S. Liu
Assistant Professor, Graduate Institute of Political Science E-mail: frankcsliu_at_gmail.com National Sun Yat-sen University (NYSYU) Office:+886.7.525.2000 #5555 Kaohsiung, Taiwan 804, R.O.C. FAX:+886.7.525.5540

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