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