[R] Rcommander installation fails on Fedora 9

John Sorkin jsorkin at grecc.umaryland.edu
Fri Aug 15 19:15:25 CEST 2008


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.

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:
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