[R] Help with installing add-on packages

From: Miha Staut <mihastaut_at_yahoo.co.uk>
Date: Wed, 09 Jul 2008 07:40:19 +0000 (GMT)


Dear R users.

Recently I wanted to update my R distribution to the current one (R-2.7.1). I am running a Fedora core 8 distirbution. The installation went fine, but when I tried to add some additional packages the majority made an exit with an error. Only a few least demanding (e.g. RColorBrewer) managed to get through the installation process.

What happened between the versions 2.6.x and 2.7.x to impede the installation of add-on packages that previously went smooth?

Thank you for your suggestions and best regards. Miha

Example:

> install.packages("akima",repos="http://cran.r-project.org",depend=T)

* Installing to library '/usr/lib/R/library'
* 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'

Not happy with your email address?.
Get the one you really want - millions of new email addresses available now at Yahoo! http://uk.docs.yahoo.com/ymail/new.html

R-help_at_r-project.org 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. Received on Wed 09 Jul 2008 - 07:46:32 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Wed 09 Jul 2008 - 08:31:37 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.

list of date sections of archive