[R] Compiling R packages on Ubuntu

[Vikas Rawal]

I am unable to compile R packages from source on Ubuntu
dapper/edgy. Does anybody have an experience?


When I do install.packages("nlme",depend=TRUE), I get following error messages. Can someone help?

I get similar messages for any package I try to compile.

VR

-------------

* Installing *source* package 'nlme' ...
** libs
gcc -I/usr/share/R/include -I/usr/share/R/include    -fvisibility=hidden -fpic  -g -O2 -std=gnu99 -c corStruct.c -o corStruct.o
In file included from base.h:29,
                 from matrix.h:27,
                 from corStruct.c:27:
/usr/share/R/include/S.h:37:20: error: stdlib.h: No such file or directory
/usr/share/R/include/S.h:38:19: error: stdio.h: No such file or directory
In file included from /usr/lib/gcc/i486-linux-gnu/4.1.2/include/syslimits.h:7,
                 from /usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:11,
                 from /usr/share/R/include/S.h:39,
                 from base.h:29,
                 from matrix.h:27,
                 from corStruct.c:27:
/usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:122:61: error: limits.h: No such file or directory
In file included from base.h:29,
                 from matrix.h:27,
                 from corStruct.c:27:
/usr/share/R/include/S.h:41:19: error: math.h: No such file or directory
In file included from /usr/share/R/include/S.h:55,
                 from base.h:29,
                 from matrix.h:27,
                 from corStruct.c:27:
/usr/share/R/include/R_ext/RS.h:23:38: error: string.h: No such file or directory
In file included from base.h:34,
                 from matrix.h:27,
                 from corStruct.c:27:
/usr/share/R/include/Rinternals.h:36:19: error: errno.h: No such file or directory
/usr/share/R/include/Rinternals.h:44:19: error: ctype.h: No such file or directory
In file included from base.h:34,
                 from matrix.h:27,
                 from corStruct.c:27:
/usr/share/R/include/Rinternals.h:767: error: expected declaration specifiers or $(B!F(B...$(B!G(B before $(B!F(BFILE$(B!G
(B/usr/share/R/include/Rinternals.h:770: error: expected declaration specifiers or $(B!F(B...$(B!G(B before $(B!F(BFILE$(B!G
(BIn file included from matrix.h:27,
                 from corStruct.c:27:
base.h:38:21: error: libintl.h: No such file or directory
corStruct.c: In function $(B!F(BcorStruct_factList$(B!G(B:
corStruct.c:58: warning: implicit declaration of function $(B!F(Blog$(B!G
(BcorStruct.c:58: warning: incompatible implicit declaration of built-in function $(B!F(Blog$(B!G
(BcorStruct.c:58: warning: implicit declaration of function $(B!F(Bfabs$(B!G
(BcorStruct.c:58: warning: incompatible implicit declaration of built-in function $(B!F(Bfabs$(B!G
(BcorStruct.c:60: warning: implicit declaration of function $(B!F(Bmemcpy$(B!G
(BcorStruct.c:60: warning: incompatible implicit declaration of built-in function $(B!F(Bmemcpy$(B!G
(BcorStruct.c: In function $(B!F(Bsymm_fullCorr$(B!G(B:
corStruct.c:93: warning: implicit declaration of function $(B!F(Bexp$(B!G
(BcorStruct.c:93: warning: incompatible implicit declaration of built-in function $(B!F(Bexp$(B!G
(BcorStruct.c:95: warning: implicit declaration of function $(B!F(Bcos$(B!G
(BcorStruct.c:95: warning: incompatible implicit declaration of built-in function $(B!F(Bcos$(B!G
(BcorStruct.c:96: warning: implicit declaration of function $(B!F(Bsin$(B!G
(BcorStruct.c:96: warning: incompatible implicit declaration of built-in function $(B!F(Bsin$(B!G
(BcorStruct.c: In function $(B!F(Bsymm_fact$(B!G(B:
corStruct.c:166: warning: incompatible implicit declaration of built-in function $(B!F(Blog$(B!G
(BcorStruct.c:166: warning: incompatible implicit declaration of built-in function $(B!F(Bfabs$(B!G
(BcorStruct.c:168: warning: incompatible implicit declaration of built-in function $(B!F(Bmemcpy$(B!G
(BcorStruct.c: In function $(B!F(Bnat_fullCorr$(B!G(B:
corStruct.c:216: warning: incompatible implicit declaration of built-in function $(B!F(Bexp$(B!G
(BcorStruct.c: In function $(B!F(BAR1_mat$(B!G(B:
corStruct.c:281: warning: implicit declaration of function $(B!F(Bpow$(B!G
(BcorStruct.c:281: warning: incompatible implicit declaration of built-in function $(B!F(Bpow$(B!G
(BcorStruct.c: In function $(B!F(Bsafe_phi$(B!G(B:
corStruct.c:292: warning: incompatible implicit declaration of built-in function $(B!F(Bexp$(B!G
(BcorStruct.c:295: warning: incompatible implicit declaration of built-in function $(B!F(Bexp$(B!G
(BcorStruct.c: In function $(B!F(BAR1_fact$(B!G(B:
corStruct.c:316: warning: implicit declaration of function $(B!F(Bsqrt$(B!G
(BcorStruct.c:316: warning: incompatible implicit declaration of built-in function $(B!F(Bsqrt$(B!G
(BcorStruct.c:318: warning: incompatible implicit declaration of built-in function $(B!F(Blog$(B!G
(BcorStruct.c: In function $(B!F(BCAR1_mat$(B!G(B:
corStruct.c:369: warning: incompatible implicit declaration of built-in function $(B!F(Bpow$(B!G
(BcorStruct.c:369: warning: incompatible implicit declaration of built-in function $(B!F(Bfabs$(B!G
(BcorStruct.c: In function $(B!F(BCAR1_matList$(B!G(B:
corStruct.c:379: warning: incompatible implicit declaration of built-in function $(B!F(Bexp$(B!G
(BcorStruct.c: In function $(B!F(BCAR1_fact$(B!G(B:
corStruct.c:404: warning: incompatible implicit declaration of built-in function $(B!F(Blog$(B!G
(BcorStruct.c:404: warning: incompatible implicit declaration of built-in function $(B!F(Bfabs$(B!G
(BcorStruct.c:406: warning: incompatible implicit declaration of built-in function $(B!F(Bmemcpy$(B!G
(BcorStruct.c: In function $(B!F(BCAR1_factList$(B!G(B:
corStruct.c:415: warning: incompatible implicit declaration of built-in function $(B!F(Bexp$(B!G
(BcorStruct.c: In function $(B!F(BCAR1_recalc$(B!G(B:
corStruct.c:430: warning: incompatible implicit declaration of built-in function $(B!F(Bexp$(B!G
(BcorStruct.c: In function $(B!F(BARMA_transPar$(B!G(B:
corStruct.c:451: warning: implicit declaration of function $(B!F(Bdgettext$(B!G
(BcorStruct.c:451: warning: incompatible implicit declaration of built-in function $(B!F(Bdgettext$(B!G
(BcorStruct.c:465: warning: incompatible implicit declaration of built-in function $(B!F(Blog$(B!G
(BcorStruct.c: In function $(B!F(BARMA_untransPar$(B!G(B:
corStruct.c:484: warning: incompatible implicit declaration of built-in function $(B!F(Bexp$(B!G
(BcorStruct.c:490: warning: incompatible implicit declaration of built-in function $(B!F(Bmemcpy$(B!G
(BcorStruct.c: In function $(B!F(BARMA_corr$(B!G(B:
corStruct.c:528: warning: incompatible implicit declaration of built-in function $(B!F(Bsqrt$(B!G
(BcorStruct.c:562: warning: incompatible implicit declaration of built-in function $(B!F(Bdgettext$(B!G
(BcorStruct.c:566: warning: incompatible implicit declaration of built-in function $(B!F(Bmemcpy$(B!G
(BcorStruct.c: In function $(B!F(BARMA_fact$(B!G(B:
corStruct.c:649: warning: incompatible implicit declaration of built-in function $(B!F(Blog$(B!G
(BcorStruct.c:649: warning: incompatible implicit declaration of built-in function $(B!F(Bfabs$(B!G
(BcorStruct.c:651: warning: incompatible implicit declaration of built-in function $(B!F(Bmemcpy$(B!G
(BcorStruct.c: In function $(B!F(BcompSymm_matList$(B!G(B:
corStruct.c:711: warning: incompatible implicit declaration of built-in function $(B!F(Bexp$(B!G
(BcorStruct.c: In function $(B!F(BcompSymm_fact$(B!G(B:
corStruct.c:725: warning: incompatible implicit declaration of built-in function $(B!F(Blog$(B!G
(BcorStruct.c:726: warning: incompatible implicit declaration of built-in function $(B!F(Bsqrt$(B!G
(BcorStruct.c:739: warning: incompatible implicit declaration of built-in function $(B!F(Bmemcpy$(B!G
(BcorStruct.c: In function $(B!F(BcompSymm_factList$(B!G(B:
corStruct.c:749: warning: incompatible implicit declaration of built-in function $(B!F(Bexp$(B!G
(BcorStruct.c: In function $(B!F(BcompSymm_recalc$(B!G(B:
corStruct.c:762: warning: incompatible implicit declaration of built-in function $(B!F(Bexp$(B!G
(BcorStruct.c: In function $(B!F(BHF_matList$(B!G(B:
corStruct.c:797: warning: incompatible implicit declaration of built-in function $(B!F(Bexp$(B!G
(BcorStruct.c: In function $(B!F(BHF_fact$(B!G(B:
corStruct.c:823: warning: incompatible implicit declaration of built-in function $(B!F(Blog$(B!G
(BcorStruct.c:823: warning: incompatible implicit declaration of built-in function $(B!F(Bfabs$(B!G
(BcorStruct.c:825: warning: incompatible implicit declaration of built-in function $(B!F(Bmemcpy$(B!G
(BcorStruct.c: In function $(B!F(BHF_factList$(B!G(B:
corStruct.c:837: warning: incompatible implicit declaration of built-in function $(B!F(Bexp$(B!G
(BcorStruct.c: In function $(B!F(BHF_recalc$(B!G(B:
corStruct.c:854: warning: incompatible implicit declaration of built-in function $(B!F(Bexp$(B!G
(BcorStruct.c: In function $(B!F(Bspher_corr$(B!G(B:
corStruct.c:872: warning: incompatible implicit declaration of built-in function $(B!F(Bpow$(B!G
(BcorStruct.c: In function $(B!F(Bexp_corr$(B!G(B:
corStruct.c:881: warning: incompatible implicit declaration of built-in function $(B!F(Bexp$(B!G
(BcorStruct.c: In function $(B!F(BGaus_corr$(B!G(B:
corStruct.c:889: warning: incompatible implicit declaration of built-in function $(B!F(Bexp$(B!G
(BcorStruct.c: In function $(B!F(Bdummy_corr$(B!G(B:
corStruct.c:914: warning: incompatible implicit declaration of built-in function $(B!F(Bdgettext$(B!G
(BcorStruct.c: In function $(B!F(Bspatial_matList$(B!G(B:
corStruct.c:945: warning: incompatible implicit declaration of built-in function $(B!F(Bexp$(B!G
(BcorStruct.c:969: warning: incompatible implicit declaration of built-in function $(B!F(Bdgettext$(B!G
(BcorStruct.c: In function $(B!F(Bspatial_fact$(B!G(B:
corStruct.c:997: warning: incompatible implicit declaration of built-in function $(B!F(Blog$(B!G
(BcorStruct.c:997: warning: incompatible implicit declaration of built-in function $(B!F(Bfabs$(B!G
(BcorStruct.c:999: warning: incompatible implicit declaration of built-in function $(B!F(Bmemcpy$(B!G
(BcorStruct.c: In function $(B!F(Bspatial_factList$(B!G(B:
corStruct.c:1011: warning: incompatible implicit declaration of built-in function $(B!F(Bexp$(B!G
(BcorStruct.c:1036: warning: incompatible implicit declaration of built-in function $(B!F(Bdgettext$(B!G
(BcorStruct.c: In function $(B!F(Bspatial_recalc$(B!G(B:
corStruct.c:1053: warning: incompatible implicit declaration of built-in function $(B!F(Bexp$(B!G
(BcorStruct.c:1078: warning: incompatible implicit declaration of built-in function $(B!F(Bdgettext$(B!G
(Bmake: *** [corStruct.o] Error 1
ERROR: compilation failed for package 'nlme'
** Removing '/usr/local/lib/R/site-library/nlme'

The downloaded packages are in
        /tmp/Rtmpjb1Cc1/downloaded_packages
Warning message:
installation of package 'nlme' had non-zero exit status in: install.packages("nlme", depend = TRUE) 
>