[R] Problem installing packages in newer versions of R

hadley wickham h.wickham at gmail.com
Thu Sep 18 17:12:14 CEST 2008


Hi Miha,

One tip for diagnosing build problems is to ignore all warnings and
look for the first error.  In your case it's:

init.c:2:15: error: R.h: No such file or directory
init.c:3:24: error: Rinternals.h: No such file or directory

Which possibly suggests that you don't have the necessary headers.
One common reason for this is that you haven't installed the
development rpm for R which contains all the header files to compile
stuff - you probably just have the user package which allows you to
use R.

Hadley

On Thu, Sep 18, 2008 at 10:04 AM, Miha Staut <mihastaut at yahoo.co.uk> wrote:
> Dear all,
>
> I was wandering what could be wrong with my system (regularly updated Fedora core 8) so that installing packages does not succeed with almost every package. I follow the procedure specified in the help file R-admin section 6.3. This is not a feature new to the current version but happened (to me) in the previous version as well. Additionally R-help html pages try to follow wrong links for the packages that manage to get thorough install.packages() (e.g. RColorBrewer). Should I specify a different lib.loc during install.packages()? My base packages currently reside in /usr/lib/R/library, however, html links for the mentioned contributed package RColorBrewer try to follow a non-existent /usr/share/doc/library/RColorBrewer/html/00Index.html. Why? What should I set to make my default library location (for html links as well) /usr/lib/R/library and default R location /usr/lib/R?
>
> Are these two problems connected or the are not?
>
> I have even built the rpm from src.rpm myself but with no change.
>
> Below you may find the (error) output from installing the akima package. It might give a clue.
>
> Thanks for your help.
> Miha
>
> -----------------
>> install.packages("akima",repos="http://cran.r-project.org",depend=T)
> Warning in install.packages("akima", repos = "http://cran.r-project.org",  :
>  argument 'lib' is missing: using '/usr/lib/R/library'
> trying URL 'http://cran.r-project.org/src/contrib/akima_0.5-1.tar.gz'
> Content type 'application/x-gzip' length 148838 bytes (145 Kb)
> opened URL
> ==================================================
> downloaded 145 Kb
>
> * Installing *source* package 'akima' ...
> ** libs
> gfortran -m32   -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 akima433.f -o akima433.o
>  In file akima433.f:49
>
>        IF(X(I-1)-X(I))   11,95,96
>                                                                       1
> Warning: Obsolete: arithmetic IF statement at (1)
>  In file akima433.f:38
>
>    10 L0=L
>    1
> Warning: Label 1 at (1) defined but not used
>  In file akima433.f:56
>
>   20   IF(LM2.EQ.0)      GO TO 27
>    1
> Warning: Label 20 at (1) defined but not used
>  In file akima433.f:63
>
>   22   IMX=I
>    1
> Warning: Label 22 at (1) defined but not used
>  In file akima433.f:79
>
>   40   J=I
>    1
> Warning: Label 40 at (1) defined but not used
>  In file akima433.f:166
>
>   99 ERR = 10
>    1
> Warning: Label 99 at (1) defined but not used
> gfortran -m32   -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 akima697.f -o akima697.o
>  In file akima697.f:88
>
>   10 IF (ND.LE.1)   GO TO 90
>    1
> Warning: Label 10 at (1) defined but not used
>  In file akima697.f:97
>
>   20 NP0=MAX(3,NP)
>    1
> Warning: Label 20 at (1) defined but not used
>  In file akima697.f:103
>
>   30 DO 39  II=1,NI
>    1
> Warning: Label 30 at (1) defined but not used
>  In file akima697.f:398
>
>   99 ERR=10
>    1
> Warning: Label 99 at (1) defined but not used
> gfortran -m32   -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 akima.new.f -o akima.new.o
> akima.new.f: In function 'sdplnl':
> akima.new.f:1904: warning: 'zii1' may be used uninitialized in this function
> akima.new.f:1903: warning: 'y0' may be used uninitialized in this function
> akima.new.f:1903: warning: 'wt2' may be used uninitialized in this function
> akima.new.f:1903: warning: 'p50' may be used uninitialized in this function
> akima.new.f:1903: warning: 'p41' may be used uninitialized in this function
> akima.new.f:1902: warning: 'p40' may be used uninitialized in this function
> akima.new.f:1902: warning: 'p31' may be used uninitialized in this function
> akima.new.f:1902: warning: 'p32' may be used uninitialized in this function
> akima.new.f:1903: warning: 'x0' may be used uninitialized in this function
> akima.new.f:1902: warning: 'p22' may be used uninitialized in this function
> akima.new.f:1902: warning: 'p21' may be used uninitialized in this function
> akima.new.f:1902: warning: 'p23' may be used uninitialized in this function
> akima.new.f:1902: warning: 'p13' may be used uninitialized in this function
> akima.new.f:1902: warning: 'p14' may be used uninitialized in this function
> akima.new.f:1901: warning: 'p12' may be used uninitialized in this function
> akima.new.f:1902: warning: 'p20' may be used uninitialized in this function
> akima.new.f:1901: warning: 'p10' may be used uninitialized in this function
> akima.new.f:1901: warning: 'p04' may be used uninitialized in this function
> akima.new.f:1901: warning: 'p02' may be used uninitialized in this function
> akima.new.f:1901: warning: 'p03' may be used uninitialized in this function
> akima.new.f:1901: warning: 'p05' may be used uninitialized in this function
> akima.new.f:1901: warning: 'p11' may be used uninitialized in this function
> akima.new.f:1902: warning: 'p30' may be used uninitialized in this function
> akima.new.f:1901: warning: 'p00' may be used uninitialized in this function
> akima.new.f:1900: warning: 'cp' may be used uninitialized in this function
> akima.new.f:1899: warning: 'bp' may be used uninitialized in this function
> akima.new.f:1898: warning: 'ap' may be used uninitialized in this function
> akima.new.f:1900: warning: 'dp' may be used uninitialized in this function
> akima.new.f:1901: warning: 'p01' may be used uninitialized in this function
> gfortran -m32   -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 idbvip.f -o idbvip.o
>  In file idbvip.f:65
>
>   10 MD0=MD
>    1
> Warning: Label 10 at (1) defined but not used
>  In file idbvip.f:70
>
>   20 IF(MD0.LT.1.OR.MD0.GT.3)           GO TO 90
>    1
> Warning: Label 20 at (1) defined but not used
>  In file idbvip.f:102
>
>   40 IF(MD0.GT.1)   GO TO 50
>    1
> Warning: Label 40 at (1) defined but not used
>  In file idbvip.f:126
>
>   80 ITPV=0
>    1
> Warning: Label 80 at (1) defined but not used
> gfortran -m32   -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 idcldp.f -o idcldp.o
>  In file idcldp.f:2
>
>      SUBROUTINE  IDCLDP(NDP,XD,YD,NCP,IPC)
>                                                                       1
> Warning: Line truncated at (1)
>  In file idcldp.f:28
>
>   10 NDP0=NDP
>    1
> Warning: Label 10 at (1) defined but not used
>  In file idcldp.f:33
>
>   20 DO 59  IP1=1,NDP0
>    1
> Warning: Label 20 at (1) defined but not used
>  In file idcldp.f:76
>
>   40   NCLPT=0
>    1
> Warning: Label 40 at (1) defined but not used
> idcldp.f: In function 'idcldp':
> idcldp.f:47: warning: 'jmx' may be used uninitialized in this function
> idcldp.f:90: warning: 'ip3mn' may be used uninitialized in this function
> idcldp.f:87: warning: 'dsqmn' may be used uninitialized in this function
> gfortran -m32   -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 idgrid.f -o idgrid.o
>  In file idgrid.f:90
>
>            IF (SIDE(X1,Y1,X2,Y2,XII,YII)) 130, 40, 50
>                                                                       1
> Warning: Obsolete: arithmetic IF statement at (1)
>  In file idgrid.f:92
>
>   50       IF (SIDE(X2,Y2,X3,Y3,XII,YII)) 130, 60, 70
>                                                                       1
> Warning: Obsolete: arithmetic IF statement at (1)
>  In file idgrid.f:94
>
>   70       IF (SIDE(X3,Y3,X1,Y1,XII,YII)) 130, 80, 90
>                                                                       1
> Warning: Obsolete: arithmetic IF statement at (1)
>  In file idgrid.f:154
>
>            IF (SIDE(X1,Y1,X2,Y2,XII,YII)) 210, 200, 290
>                                                                       1
> Warning: Obsolete: arithmetic IF statement at (1)
>  In file idgrid.f:156
>
>  210       IF (SPDT(X2,Y2,X1,Y1,XII,YII)) 290, 220, 230
>                                                                       1
> Warning: Obsolete: arithmetic IF statement at (1)
>  In file idgrid.f:158
>
>  230       IF (SPDT(X1,Y1,X2,Y2,XII,YII)) 290, 240, 250
>                                                                       1
> Warning: Obsolete: arithmetic IF statement at (1)
>  In file idgrid.f:213
>
>            IF (SPDT(X1,Y1,X2,Y2,XII,YII)) 360, 350, 420
>                                                                       1
> Warning: Obsolete: arithmetic IF statement at (1)
>  In file idgrid.f:215
>
>  360       IF (SPDT(X3,Y3,X2,Y2,XII,YII)) 380, 370, 420
>                                                                       1
> Warning: Obsolete: arithmetic IF statement at (1)
> idgrid.f: In function 'idgrid':
> idgrid.f:80: warning: 'iximn' may be used uninitialized in this function
> gfortran -m32   -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 idlctn.f -o idlctn.o
> gfortran -m32   -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 idpdrv.f -o idpdrv.o
>  In file idpdrv.f:2
>
>      SUBROUTINE  IDPDRV(NDP,XD,YD,ZD,NCP,IPC,PD)
>                                                                       1
> Warning: Line truncated at (1)
>  In file idpdrv.f:23
>
>   10 NDP0=NDP
>    1
> Warning: Label 10 at (1) defined but not used
>  In file idpdrv.f:27
>
>  20  DO 24  IP0=1,NDP0
>   1
> Warning: Label 20 at (1) defined but not used
>  In file idpdrv.f:66
>
>   30 DO 34  IP0=1,NDP0
>    1
> Warning: Label 30 at (1) defined but not used
> gfortran -m32   -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 idptip.f -o idptip.o
>  In file idptip.f:43
>
>   10 IT0=ITI
>    1
> Warning: Label 10 at (1) defined but not used
>  In file idptip.f:60
>
>   21 JIPT=3*(IT0-1)
>    1
> Warning: Label 21 at (1) defined but not used
>  In file idptip.f:78
>
>   24 X0=X(1)
>    1
> Warning: Label 24 at (1) defined but not used
>  In file idptip.f:93
>
>   25 AA=A*A
>    1
> Warning: Label 25 at (1) defined but not used
>  In file idptip.f:111
>
>   27 P00=Z(1)
>    1
> Warning: Label 27 at (1) defined but not used
>  In file idptip.f:169
>
>   31 P0=P00+V*(P01+V*(P02+V*(P03+V*(P04+V*P05))))
>    1
> Warning: Label 31 at (1) defined but not used
>  In file idptip.f:183
>
>   41 JIPL=3*(IL1-1)
>    1
> Warning: Label 41 at (1) defined but not used
>  In file idptip.f:201
>
>   44 X0=X(1)
>    1
> Warning: Label 44 at (1) defined but not used
>  In file idptip.f:216
>
>   45 AA=A*A
>    1
> Warning: Label 45 at (1) defined but not used
>  In file idptip.f:234
>
>   47 P00=Z(1)
>    1
> Warning: Label 47 at (1) defined but not used
>  In file idptip.f:260
>
>   51 P0=P00+V*(P01+V*(P02+V*(P03+V*(P04+V*P05))))
>    1
> Warning: Label 51 at (1) defined but not used
>  In file idptip.f:270
>
>   61 JIPL=3*IL2-2
>    1
> Warning: Label 61 at (1) defined but not used
>  In file idptip.f:281
>
>   67 P00=Z(1)
>    1
> Warning: Label 67 at (1) defined but not used
>  In file idptip.f:292
>
>   71 P0=P00+V*(P01+V*P02)
>    1
> Warning: Label 71 at (1) defined but not used
> idptip.f: In function 'idptip':
> idptip.f:79: warning: 'y0' may be used uninitialized in this function
> idptip.f:78: warning: 'x0' may be used uninitialized in this function
> idptip.f:121: warning: 'p40' may be used uninitialized in this function
> idptip.f:134: warning: 'p41' may be used uninitialized in this function
> idptip.f:160: warning: 'p32' may be used uninitialized in this function
> idptip.f:120: warning: 'p30' may be used uninitialized in this function
> idptip.f:139: warning: 'p31' may be used uninitialized in this function
> idptip.f:159: warning: 'p22' may be used uninitialized in this function
> idptip.f:114: warning: 'p20' may be used uninitialized in this function
> idptip.f:135: warning: 'p14' may be used uninitialized in this function
> idptip.f:138: warning: 'p21' may be used uninitialized in this function
> idptip.f:143: warning: 'p13' may be used uninitialized in this function
> idptip.f:161: warning: 'p23' may be used uninitialized in this function
> idptip.f:112: warning: 'p10' may be used uninitialized in this function
> idptip.f:115: warning: 'p11' may be used uninitialized in this function
> idptip.f:128: warning: 'p05' may be used uninitialized in this function
> idptip.f:126: warning: 'p03' may be used uninitialized in this function
> idptip.f:127: warning: 'p04' may be used uninitialized in this function
> idptip.f:142: warning: 'p12' may be used uninitialized in this function
> idptip.f:111: warning: 'p00' may be used uninitialized in this function
> idptip.f:113: warning: 'p01' may be used uninitialized in this function
> idptip.f:89: warning: 'cp' may be used uninitialized in this function
> idptip.f:90: warning: 'dp' may be used uninitialized in this function
> idptip.f:87: warning: 'ap' may be used uninitialized in this function
> idptip.f:88: warning: 'bp' may be used uninitialized in this function
> idptip.f:116: warning: 'p02' may be used uninitialized in this function
> gfortran -m32   -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 idptli.f -o idptli.o
>  In file idptli.f:3
>
>     1                   MISSII)
>                                                                       1
> Warning: Line truncated at (1)
>  In file idptli.f:34
>
>   10 IT0=ITI
>    1
> Warning: Label 10 at (1) defined but not used
>  In file idptli.f:43
>
>   21 JIPT=3*(IT0-1)
>    1
> Warning: Label 21 at (1) defined but not used
>  In file idptli.f:55
>
>   24 X0=X(1)
>    1
> Warning: Label 24 at (1) defined but not used
>  In file idptli.f:2
>
>      SUBROUTINE  IDPTLI(XD,YD,ZD,NDP,NT,IPT,NL,IPL,ITI,XII,YII,ZII,
>                                                  1
> Warning: Unused variable ipl declared at (1)
> idptli.f: In function 'idptli':
> idptli.f:55: warning: 'x0' may be used uninitialized in this function
> idptli.f:56: warning: 'y0' may be used uninitialized in this function
> idptli.f:66: warning: 'cp' may be used uninitialized in this function
> idptli.f:65: warning: 'bp' may be used uninitialized in this function
> idptli.f:64: warning: 'ap' may be used uninitialized in this function
> idptli.f:67: warning: 'dp' may be used uninitialized in this function
> gfortran -m32   -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 idsfft.f -o idsfft.o
>  In file idsfft.f:69
>
>   10 MD0=MD
>    1
> Warning: Label 10 at (1) defined but not used
>  In file idsfft.f:75
>
>   20 IF(MD0.LT.1.OR.MD0.GT.3)           GO TO 90
>    1
> Warning: Label 20 at (1) defined but not used
>  In file idsfft.f:110
>
>   40 IF(MD0.GT.1)   GO TO 50
>    1
> Warning: Label 40 at (1) defined but not used
>  In file idsfft.f:129
>
>   80 ITPV=0
>    1
> Warning: Label 80 at (1) defined but not used
> gfortran -m32   -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 idtang.f -o idtang.o
>  In file idtang.f:2
>
>      SUBROUTINE  IDTANG(NDP,XD,YD,NT,IPT,NL,IPL,IWL,IWP,WK)
>                                                                       1
> Warning: Line truncated at (1)
>  In file idtang.f:53
>
>   10 NDP0=NDP
>    1
> Warning: Label 10 at (1) defined but not used
>  In file idtang.f:57
>
>   20 DSQMN=DSQF(XD(1),YD(1),XD(2),YD(2))
>    1
> Warning: Label 20 at (1) defined but not used
>  In file idtang.f:79
>
>   30 JP1=2
>    1
> Warning: Label 30 at (1) defined but not used
>  In file idtang.f:101
>
>   35 AR=DSQ12*RATIO
>    1
> Warning: Label 35 at (1) defined but not used
>  In file idtang.f:148
>
>   50 DO 79  JP1=4,NDP0
>    1
> Warning: Label 50 at (1) defined but not used
>  In file idtang.f:260
>
>   70   NTT3P3=NTT3+3
>    1
> Warning: Label 70 at (1) defined but not used
>  In file idtang.f:345
>
>   80 DO 81  ITT3=3,NTT3,3
>    1
> Warning: Label 80 at (1) defined but not used
> idtang.f: In function 'idtang':
> idtang.f:226: warning: 'nln' may be used uninitialized in this function
> idtang.f:227: warning: 'nlnt3' may be used uninitialized in this function
> gfortran -m32   -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 idxchg.f -o idxchg.o
>  In file idxchg.f:2
>
>      FUNCTION  IDXCHG(X,Y,NDP,I1,I2,I3,I4)
>                                                                       1
> Warning: Line truncated at (1)
>  In file idxchg.f:20
>
>   10 X1=X(I1)
>    1
> Warning: Label 10 at (1) defined but not used
>  In file idxchg.f:29
>
>   20 IDX=0
>    1
> Warning: Label 20 at (1) defined but not used
> gcc -m32 -std=gnu99 -I/usr/include/R  -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 init.c -o init.o
> init.c:2:15: error: R.h: No such file or directory
> init.c:3:24: error: Rinternals.h: No such file or directory
> In file included from init.c:5:
> akima.h:7: error: 'F77_NAME' declared as function returning a function
> akima.h:7: warning: parameter names (without types) in function declaration
> akima.h:12: error: 'F77_NAME' declared as function returning a function
> akima.h:12: warning: parameter names (without types) in function declaration
> akima.h:18: error: 'F77_NAME' declared as function returning a function
> akima.h:18: warning: parameter names (without types) in function declaration
> akima.h:23: error: 'F77_NAME' declared as function returning a function
> akima.h:23: warning: parameter names (without types) in function declaration
> akima.h:26: error: 'F77_NAME' declared as function returning a function
> akima.h:26: warning: parameter names (without types) in function declaration
> akima.h:29: error: 'F77_NAME' declared as function returning a function
> akima.h:29: warning: parameter names (without types) in function declaration
> init.c:7:28: error: R_ext/Rdynload.h: No such file or directory
> init.c:11: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'idbvip_t'
> init.c:27: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'sdbi3p_t'
> init.c:46: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'idsfft_t'
> init.c:63: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'sdsf3p_t'
> init.c:83: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'uvip3p_t'
> init.c:94: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'intrpl_t'
> init.c:104: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'fortranMethods'
> init.c:115: error: expected ')' before '*' token
> make: *** [init.o] Error 1
> ERROR: compilation failed for package 'akima'
> ** Removing '/usr/lib/R/library/akima'
> Updating HTML index of packages in '.Library'
> Warning message:
> In install.packages("akima", repos = "http://cran.r-project.org",  :
>  installation of package 'akima' had non-zero exit status
>>
> -----------------
>
>
>
>
>
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