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>-----------------
hadley wickham
2008-Sep-18 15:12 UTC
[R] Problem installing packages in newer versions of R
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 >> > ----------------- > > > > > > ______________________________________________ > 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. >-- http://had.co.nz/
Peter Dalgaard
2008-Sep-18 15:28 UTC
[R] Problem installing packages in newer versions of R
Miha Staut 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. >You need to install the R-devel RPM. -- O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907