[R] Rcommander installation fails on Fedora 9

[Peter Dalgaard]

John Sorkin wrote:
> Fedora 9
> R 2.7.1 
>
> I tried to install R on my Linux system using 
> install.packages("Rcmdr", dependencies=TRUE). 
>
> I received many, many, many error messages. I hope someone can suggest a
> fix.
>   
Looks like you forgot to install the R-devel package. (And yes, the 
error messages are rather, er, indirect, but Fedora's packaging is not 
our decision... The giveaway is the absence of R.h and friends.)
> The output from warnings()
> is listed below. A more detailed list of errors from one of the failed
> installations is listed below the warnings: 
>
>   
>> warnings()
>>     
> Warning messages:
> 1: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   dependency ‘Biobase’ is not available
> 2: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'maps' had non-zero exit status
> 3: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'kinship' had non-zero exit status
> 4: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'ape' had non-zero exit status
> 5: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'gee' had non-zero exit status
> 6: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'tkrplot' had non-zero exit status
> 7: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'kernlab' had non-zero exit status
> 8: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'akima' had non-zero exit status
> 9: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'Hmisc' had non-zero exit status
> 10: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'colorspace' had non-zero exit status
> 11: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'randomForest' had non-zero exit status
> 12: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'Matrix' had non-zero exit status
> 13: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'chron' had non-zero exit status
> 14: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'e1071' had non-zero exit status
> 15: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'mlbench' had non-zero exit status
> 16: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'mvtnorm' had non-zero exit status
> 17: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'robustbase' had non-zero exit status
> 18: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'rgl' had non-zero exit status
> 19: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'RODBC' had non-zero exit status
> 20: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'mapproj' had non-zero exit status
> 21: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'Design' had non-zero exit status
> 22: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'plm' had non-zero exit status
> 23: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'vcd' had non-zero exit status
> 24: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'its' had non-zero exit status
> 25: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'tseries' had non-zero exit status
> 26: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'ipred' had non-zero exit status
> 27: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'lme4' had non-zero exit status
> 28: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'coin' had non-zero exit status
> 29: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'multcomp' had non-zero exit status
> 30: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'systemfit' had non-zero exit status
> 31: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of p32: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'fSeries' had non-zero exit status
> 33: In install.packages("Rcmdr", dependencies = TRUE) ... :
>   installation of package 'mboost' had non-zero exit status
>
>
> More detailed error messages:
> * Installing *source* package 'party' ...
> ** libs
> 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 Classes.c -o Classes.o
> In file included from Classes.c:9:
> party.h:6:15: error: R.h: No such file or directory
> party.h:7:19: error: Rmath.h: No such file or directory
> party.h:8:24: error: Rinternals.h: No such file or directory
> party.h:9:22: error: Rdefines.h: No such file or directory
> party.h:10:42: error: R_ext/Applic.h: No such file or directory
> party.h:11:43: error: R_ext/Lapack.h: No such file or directory
> In file included from party.h:15,
>                  from Classes.c:9:
> Classes.h:3: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘PL2_expectationSym’
> Classes.h:67: error: expected ‘)’ before ‘object’
> Classes.h:68: error: expected ‘)’ before ‘object’
> Classes.h:69: error: expected ‘)’ before ‘object’
> Classes.h:70: error: expected ‘)’ before ‘object’
> Classes.h:71: error: expected ‘)’ before ‘object’
> Classes.h:72: error: expected ‘)’ before ‘object’
> Classes.h:73: error: expected ‘)’ before ‘object’
> Classes.h:74: error: expected ‘)’ before ‘object’
> Classes.h:75: error: expected ‘)’ before ‘object’
> Classes.h:76: error: expected ‘)’ before ‘object’
> Classes.h:77: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_transformation’
> Classes.h:78: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_test_trafo’
> Classes.h:79: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_predict_trafo’
> Classes.h:80: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_variable’
> Classes.h:81: error: expected ‘)’ before ‘object’
> Classes.h:82: error: expected ‘)’ before ‘object’
> Classes.h:83: error: expected ‘)’ before ‘object’
> Classes.h:84: error: expected ‘)’ before ‘object’
> Classes.h:85: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_missings’
> Classes.h:86: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_ordering’
> Classes.h:87: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_levels’
> Classes.h:88: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_scores’
> Classes.h:89: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_whichNA’
> Classes.h:90: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_varmemory’
> Classes.h:91: error: expected ‘)’ before ‘object’
> Classes.h:92: error: expected ‘)’ before ‘object’
> Classes.h:93: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_weights’
> Classes.h:94: error: expected ‘)’ before ‘object’
> Classes.h:95: error: expected ‘)’ before ‘object’
> Classes.h:96: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_varctrl’
> Classes.h:97: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_splitctrl’
> Classes.h:98: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_gtctrl’
> Classes.h:99: error: expected ‘)’ before ‘object’
> Classes.h:100: error: expected ‘)’ before ‘object’
> Classes.h:101: error: expected ‘)’ before ‘object’
> Classes.h:102: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_dontuse’
> Classes.h:103: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_dontusetmp’
> Classes.h:104: error: expected ‘)’ before ‘object’
> Classes.h:105: error: expected ‘)’ before ‘object’
> Classes.h:106: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_tgctrl’
> Classes.h:107: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_splitstatistics’
> Classes.h:108: error: expected ‘)’ before ‘object’
> Classes.h:109: error: expected ‘)’ before ‘object’
> Classes.h:110: error: expected ‘)’ before ‘object’
> Classes.h:111: error: expected ‘)’ before ‘object’
> Classes.h:112: error: expected ‘)’ before ‘object’
> In file included from party.h:16,
>                  from Classes.c:9:
> Utils.h:5: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘La_svd’
> Utils.h:8: error: expected ‘)’ before ‘x’
> Utils.h:15: error: expected ‘)’ before ‘x’
> Utils.h:16: error: expected ‘)’ before ‘y’
> Utils.h:19: error: expected declaration specifiers or ‘...’ before ‘SEXP’
> Utils.h:21: error: expected ‘)’ before ‘subtree’
> Utils.h:22: error: expected declaration specifiers or ‘...’ before ‘SEXP’
> Utils.h:22: error: expected declaration specifiers or ‘...’ before ‘SEXP’
> Utils.h:22: error: expected declaration specifiers or ‘...’ before ‘SEXP’
> In file included from party.h:17,
>                  from Classes.c:9:
> mvt.h:5: error: ‘F77_NAME’ declared as function returning a function
> mvt.h:5: warning: parameter names (without types) in function
> declaration
> In file included from party.h:18,
>                  from Classes.c:9:
> LinearStatistic.h:8: error: expected declaration specifiers or ‘...’
> before ‘SEXP’
> LinearStatistic.h:12: warning: type defaults to ‘int’ in declaration of
> ‘SEXP’
> LinearStatistic.h:12: error: expected ‘;’, ‘,’ or ‘)’ before ‘expcovinf’
> LinearStatistic.h:18: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘R_ExpectCovarInfluence’
> In file included from party.h:20,
>                  from Classes.c:9:
> Distributions.h:5: error: expected declaration specifiers or ‘...’
> before ‘SEXP’
> Distributions.h:5: error: expected declaration specifiers or ‘...’
> before ‘SEXP’
> Distributions.h:6: error: expected declaration specifiers or ‘...’
> before ‘SEXP’
> Distributions.h:6: error: expected declaration specifiers or ‘...’
> before ‘SEXP’
> Distributions.h:6: error: expected declaration specifiers or ‘...’
> before ‘SEXP’
> In file included from party.h:21,
>                  from Classes.c:9:
> Convenience.h:5: error: expected declaration specifiers or ‘...’ before
> ‘SEXP’
> Convenience.h:5: error: expected declaration specifiers or ‘...’ before
> ‘SEXP’
> Convenience.h:6: error: expected ‘)’ before ‘linexpcov’
> Convenience.h:7: error: expected ‘)’ before ‘linexpcov’
> Convenience.h:8: warning: type defaults to ‘int’ in declaration of ‘SEXP’
> Convenience.h:8: error: expected ‘;’, ‘,’ or ‘)’ before ‘linexpcov’
> Convenience.h:9: error: expected declaration specifiers or ‘...’ before
> ‘SEXP’
> In file included from party.h:22,
>                  from Classes.c:9:
> S3Classes.h:2: error: expected ‘)’ before ‘node’
> S3Classes.h:3: error: expected ‘)’ before ‘node’
> S3Classes.h:4: error: expected ‘)’ before ‘node’
> S3Classes.h:5: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘S3get_nodeweights’
> S3Classes.h:6: error: expected ‘)’ before ‘node’
> S3Classes.h:7: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘S3get_teststat’
> S3Classes.h:8: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘S3get_criterion’
> S3Classes.h:9: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘S3get_maxcriterion’
> S3Classes.h:10: error: expected ‘)’ before ‘node’
> S3Classes.h:11: error: expected ‘)’ before ‘node’
> S3Classes.h:12: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘S3get_primarysplit’
> S3Classes.h:13: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘S3get_surrogatesplits’
> S3Classes.h:14: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘S3get_prediction’
> S3Classes.h:15: error: expected ‘)’ before ‘split’
> S3Classes.h:16: error: expected ‘)’ before ‘split’
> S3Classes.h:17: error: expected ‘)’ before ‘split’
> S3Classes.h:18: error: expected ‘)’ before ‘split’
> S3Classes.h:19: error: expected ‘)’ before ‘split’
> S3Classes.h:20: error: expected ‘)’ before ‘split’
> S3Classes.h:21: error: expected ‘)’ before ‘split’
> S3Classes.h:22: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘S3get_splitpoint’
> S3Classes.h:23: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘S3get_splitstatistics’
> S3Classes.h:24: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘S3get_leftnode’
> S3Classes.h:25: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘S3get_rightnode’
> S3Classes.h:26: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘S3get_table’
> S3Classes.h:27: error: expected ‘)’ before ‘split’
> S3Classes.h:28: error: expected ‘)’ before ‘split’
> In file included from party.h:23,
>                  from Classes.c:9:
> IndependenceTest.h:2: error: expected ‘)’ before ‘learnsample’
> IndependenceTest.h:4: warning: type defaults to ‘int’ in declaration of
> ‘SEXP’
> IndependenceTest.h:4: error: expected ‘;’, ‘,’ or ‘)’ before ‘linexpcov’
> IndependenceTest.h:6: warning: type defaults to ‘int’ in declaration of
> ‘SEXP’
> IndependenceTest.h:6: error: expected ‘;’, ‘,’ or ‘)’ before ‘linexpcov’
> In file included from party.h:24,
>                  from Classes.c:9:
> Splits.h:5: error: expected declaration specifiers or ‘...’ before ‘SEXP’
> Splits.h:5: error: expected declaration specifiers or ‘...’ before ‘SEXP’
> Splits.h:6: error: expected declaration specifiers or ‘...’ before ‘SEXP’
> Splits.h:13: error: expected declaration specifiers or ‘...’ before
> ‘SEXP’
> Splits.h:13: error: expected declaration specifiers or ‘...’ before
> ‘SEXP’
> Splits.h:14: error: expected declaration specifiers or ‘...’ before
> ‘SEXP’
> In file included from party.h:25,
>                  from Classes.c:9:
> Node.h:2: error: expected ‘)’ before ‘node’
> In file included from party.h:26,
>                  from Classes.c:9:
> Predict.h:2: error: expected ‘)’ before ‘node’
> In file included from party.h:27,
>                  from Classes.c:9:
> SurrogateSplits.h:2: error: expected ‘)’ before ‘node’
> SurrogateSplits.h:3: error: expected ‘)’ before ‘node’
> In file included from party.h:28,
>                  from Classes.c:9:
> TreeGrow.h:2: error: expected ‘)’ before ‘node’
> Classes.c:12: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘PL2_expectationSym’
> Classes.c:77: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘party_init’
> Classes.c:147: error: expected ‘)’ before ‘object’
> Classes.c:151: error: expected ‘)’ before ‘object’
> Classes.c:155: error: expected ‘)’ before ‘object’
> Classes.c:159: error: expected ‘)’ before ‘object’
> Classes.c:163: error: expected ‘)’ before ‘object’
> Classes.c:167: error: expected ‘)’ before ‘object’
> Classes.c:171: error: expected ‘)’ before ‘object’
> Classes.c:175: error: expected ‘)’ before ‘object’
> Classes.c:179: error: expected ‘)’ before ‘object’
> Classes.c:183: error: expected ‘)’ before ‘object’
> Classes.c:187: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_transformation’
> Classes.c:193: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_test_trafo’
> Classes.c:197: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_predict_trafo’
> Classes.c:202: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_variable’
> Classes.c:208: error: expected ‘)’ before ‘object’
> Classes.c:212: error: expected ‘)’ before ‘object’
> Classes.c:216: error: expected ‘)’ before ‘object’
> Classes.c:220: error: expected ‘)’ before ‘object’
> Classes.c:224: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_ordering’
> Classes.c:235: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_levels’
> Classes.c:247: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_scores’
> Classes.c:258: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_missings’
> Classes.c:269: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_varmemory’
> Classes.c:274: error: expected ‘)’ before ‘object’
> Classes.c:278: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_splitstatistics’
> Classes.c:282: error: expected ‘)’ before ‘object’
> Classes.c:286: error: expected ‘)’ before ‘object’
> Classes.c:290: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_weights’
> Classes.c:294: error: expected ‘)’ before ‘object’
> Classes.c:298: error: expected ‘)’ before ‘object’
> Classes.c:302: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_varctrl’
> Classes.c:306: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_splitctrl’
> Classes.c:310: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_gtctrl’
> Classes.c:314: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_tgctrl’
> Classes.c:318: error: expected ‘)’ before ‘object’
> Classes.c:322: error: expected ‘)’ before ‘object’
> Classes.c:326: error: expected ‘)’ before ‘object’
> Classes.c:330: error: expected ‘)’ before ‘object’
> Classes.c:334: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_dontuse’
> Classes.c:338: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘get_dontusetmp’
> Classes.c:342: error: expected ‘)’ before ‘object’
> Classes.c:346: error: expected ‘)’ before ‘object’
> Classes.c:354: error: expected ‘)’ before ‘object’
> Classes.c:358: error: expected ‘)’ before ‘object’
> Classes.c:362: error: expected ‘)’ before ‘object’
> make: *** [Classes.o] Error 1
> ERROR: compilation failed for package 'party'
> ** Removing '/usr/lib/R/library/party'
>
>
> John Sorkin M.D., Ph.D.
> Chief, Biostatistics and Informatics
> Baltimore VA Medical Center GRECC,
> University of Maryland School of Medicine Claude D. Pepper OAIC,
> University of Maryland Clinical Nutrition Research Unit, and
> Baltimore VA Center Stroke of Excellence
>
> University of Maryland School of Medicine
> Division of Gerontology
> Baltimore VA Medical Center
> 10 North Greene Street
> GRECC (BT/18/GR)
> Baltimore, MD 21201-1524
>
> (Phone) 410-605-7119
> (Fax) 410-605-7913 (Please call phone number above prior to faxing)
> jsorkin at grecc.umaryland.edu
> Confidentiality Statement:
> This email message, including any attachments, is for ...{{dropped:16}}