[R] Help with installing add-on packages
Miha Staut
mihastaut at yahoo.co.uk
Wed Jul 9 09:40:19 CEST 2008
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'
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