[R] Cannot update packages on F8

[Marc Schwartz]

Paul Smith wrote:
> Dear All,
> 
> I have just updated R to the version 2.6.2 on F8 (with the official F8
> rpm). However, when running as root the following command:
> 
> update.packages(checkBuilt=T)
> 
> I get a bunch of errors like the ones below. Any ideas?
> 
> Thanks in advance,
> 
> Paul
> 
> -----------------------------------------------
> 
> * Installing *source* package 'nlme' ...
> ** libs
> gcc -m32 -std=gnu99 -I/usr/include/R -I/usr/include/R
> -I/usr/local/include   -fvisibility=hidden -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 corStruct.c -o corStruct.o
> In file included from matrix.h:25,
>                  from corStruct.c:25:
> base.h:27:28: error: S.h: No such file or directory
> base.h:43:20: error: nonlin.h: No such file or directory
> In file included from matrix.h:25,
>                  from corStruct.c:25:
> base.h:56: error: 'F77_NAME' declared as function returning a function
> base.h:56: warning: parameter names (without types) in function declaration
> base.h:57: error: 'F77_NAME' declared as function returning a function
> base.h:57: warning: parameter names (without types) in function declaration
> In file included from corStruct.c:25:
> matrix.h:26:26: error: R_ext/Applic.h: No such file or directory
> matrix.h:27:27: error: R_ext/Linpack.h: No such file or directory
> corStruct.c:28: error: 'F77_NAME' declared as function returning a function
> corStruct.c:28: warning: parameter names (without types) in function declaration
> corStruct.c: In function 'corStruct_factList':
> corStruct.c:46: warning: implicit declaration of function 'Calloc'
> corStruct.c:46: error: expected expression before 'double'
> corStruct.c:46: warning: assignment makes pointer from integer without a cast
> corStruct.c:47: error: expected expression before 'double'
> corStruct.c:47: warning: assignment makes pointer from integer without a cast
> corStruct.c:51: warning: implicit declaration of function 'F77_CALL'
> corStruct.c:51: error: 'chol' undeclared (first use in this function)
> corStruct.c:51: error: (Each undeclared identifier is reported only once
> corStruct.c:51: error: for each function it appears in.)
> corStruct.c:51: error: called object
> 'F77_CALL(<erroneous-expression>)' is not a function
> corStruct.c:55: error: 'dtrsl' undeclared (first use in this function)
> corStruct.c:55: error: called object
> 'F77_CALL(<erroneous-expression>)' is not a function
> corStruct.c:56: warning: implicit declaration of function 'log'
> corStruct.c:56: warning: incompatible implicit declaration of built-in
> function 'log'
> corStruct.c:56: warning: implicit declaration of function 'fabs'
> corStruct.c:56: warning: incompatible implicit declaration of built-in
> function 'fabs'
> corStruct.c:58: warning: implicit declaration of function 'Memcpy'
> corStruct.c:59: warning: implicit declaration of function 'Free'
> corStruct.c: In function 'symm_fullCorr':
> corStruct.c:87: error: expected expression before 'double'
> corStruct.c:87: warning: assignment makes pointer from integer without a cast
> corStruct.c:91: warning: implicit declaration of function 'exp'
> corStruct.c:91: warning: incompatible implicit declaration of built-in
> function 'exp'
> corStruct.c:92: error: 'PI' undeclared (first use in this function)
> corStruct.c:93: warning: implicit declaration of function 'cos'
> corStruct.c:93: warning: incompatible implicit declaration of built-in
> function 'cos'
> corStruct.c:94: warning: implicit declaration of function 'sin'
> corStruct.c:94: warning: incompatible implicit declaration of built-in
> function 'sin'
> corStruct.c: In function 'symm_matList':
> corStruct.c:133: error: expected expression before 'double'
> corStruct.c:133: warning: initialization makes pointer from integer
> without a cast
> corStruct.c: In function 'symm_fact':
> corStruct.c:153: error: expected expression before 'double'
> corStruct.c:153: warning: initialization makes pointer from integer
> without a cast
> corStruct.c:153: error: expected expression before 'double'
> corStruct.c:153: warning: initialization makes pointer from integer
> without a cast
> corStruct.c:159: error: 'chol' undeclared (first use in this function)
> corStruct.c:159: error: called object
> 'F77_CALL(<erroneous-expression>)' is not a function
> corStruct.c:163: error: 'dtrsl' undeclared (first use in this function)
> corStruct.c:163: error: called object
> 'F77_CALL(<erroneous-expression>)' is not a function
> corStruct.c:164: warning: incompatible implicit declaration of
> built-in function 'log'
> corStruct.c:164: warning: incompatible implicit declaration of
> built-in function 'fabs'
> corStruct.c: In function 'symm_factList':
> corStruct.c:174: error: expected expression before 'double'
> corStruct.c:174: warning: initialization makes pointer from integer
> without a cast
> corStruct.c: In function 'symm_recalc':
> corStruct.c:191: error: expected expression before 'double'
> corStruct.c:191: warning: initialization makes pointer from integer
> without a cast
> corStruct.c:195: error: expected expression before 'double'
> corStruct.c:195: warning: initialization makes pointer from integer
> without a cast
> corStruct.c: In function 'nat_fullCorr':
> corStruct.c:214: warning: incompatible implicit declaration of
> built-in function 'exp'
> corStruct.c: In function 'nat_matList':
> corStruct.c:223: error: expected expression before 'double'
> corStruct.c:223: warning: initialization makes pointer from integer
> without a cast
> corStruct.c: In function 'nat_factList':
> corStruct.c:239: error: expected expression before 'double'
> corStruct.c:239: warning: initialization makes pointer from integer
> without a cast
> corStruct.c: In function 'nat_recalc':
> corStruct.c:256: error: expected expression before 'double'
> corStruct.c:256: warning: initialization makes pointer from integer
> without a cast
> corStruct.c:260: error: expected expression before 'double'
> corStruct.c:260: warning: initialization makes pointer from integer
> without a cast
> corStruct.c: In function 'AR1_mat':
> corStruct.c:279: warning: implicit declaration of function 'pow'
> corStruct.c:279: warning: incompatible implicit declaration of
> built-in function 'pow'
> corStruct.c: In function 'safe_phi':
> corStruct.c:290: warning: incompatible implicit declaration of
> built-in function 'exp'
> corStruct.c:293: warning: incompatible implicit declaration of
> built-in function 'exp'
> corStruct.c: In function 'AR1_fact':
> corStruct.c:314: warning: implicit declaration of function 'sqrt'
> corStruct.c:314: warning: incompatible implicit declaration of
> built-in function 'sqrt'
> corStruct.c:316: warning: incompatible implicit declaration of
> built-in function 'log'
> corStruct.c: In function 'AR1_recalc':
> corStruct.c:348: error: expected expression before 'double'
> corStruct.c:348: warning: assignment makes pointer from integer without a cast
> corStruct.c: In function 'CAR1_mat':
> corStruct.c:367: warning: incompatible implicit declaration of
> built-in function 'pow'
> corStruct.c:367: warning: incompatible implicit declaration of
> built-in function 'fabs'
> corStruct.c: In function 'CAR1_matList':
> corStruct.c:377: warning: incompatible implicit declaration of
> built-in function 'exp'
> corStruct.c: In function 'CAR1_fact':
> corStruct.c:391: error: expected expression before 'double'
> corStruct.c:391: warning: initialization makes pointer from integer
> without a cast
> corStruct.c:391: error: expected expression before 'double'
> corStruct.c:391: warning: initialization makes pointer from integer
> without a cast
> corStruct.c:397: error: 'chol' undeclared (first use in this function)
> corStruct.c:397: error: called object
> 'F77_CALL(<erroneous-expression>)' is not a function
> corStruct.c:401: error: 'dtrsl' undeclared (first use in this function)
> corStruct.c:401: error: called object
> 'F77_CALL(<erroneous-expression>)' is not a function
> corStruct.c:402: warning: incompatible implicit declaration of
> built-in function 'log'
> corStruct.c:402: warning: incompatible implicit declaration of
> built-in function 'fabs'
> corStruct.c: In function 'CAR1_factList':
> corStruct.c:413: warning: incompatible implicit declaration of
> built-in function 'exp'
> corStruct.c: In function 'CAR1_recalc':
> corStruct.c:428: warning: incompatible implicit declaration of
> built-in function 'exp'
> corStruct.c:432: error: expected expression before 'double'
> corStruct.c:432: warning: initialization makes pointer from integer
> without a cast
> corStruct.c: In function 'ARMA_transPar':
> corStruct.c:449: warning: implicit declaration of function 'error'
> corStruct.c:449: warning: implicit declaration of function '_'
> corStruct.c:463: warning: incompatible implicit declaration of
> built-in function 'log'
> corStruct.c: In function 'ARMA_untransPar':
> corStruct.c:480: error: expected expression before 'double'
> corStruct.c:480: warning: assignment makes pointer from integer without a cast
> corStruct.c:482: warning: incompatible implicit declaration of
> built-in function 'exp'
> corStruct.c: In function 'ARMA_corr':
> corStruct.c:522: error: expected expression before 'long'
> corStruct.c:522: warning: initialization makes pointer from integer
> without a cast
> corStruct.c:523: error: expected expression before 'double'
> corStruct.c:523: warning: initialization makes pointer from integer
> without a cast
> corStruct.c:523: error: expected expression before 'double'
> corStruct.c:523: warning: initialization makes pointer from integer
> without a cast
> corStruct.c:524: error: expected expression before 'double'
> corStruct.c:524: warning: initialization makes pointer from integer
> without a cast
> corStruct.c:526: warning: incompatible implicit declaration of
> built-in function 'sqrt'
> corStruct.c:526: error: 'DOUBLE_EPS' undeclared (first use in this function)
> corStruct.c:534: error: expected expression before 'double'
> corStruct.c:534: warning: assignment makes pointer from integer without a cast
> corStruct.c:558: error: 'dqrdc2' undeclared (first use in this function)
> corStruct.c:558: error: called object
> 'F77_CALL(<erroneous-expression>)' is not a function
> corStruct.c:562: error: 'dqrsl' undeclared (first use in this function)
> corStruct.c:563: error: called object
> 'F77_CALL(<erroneous-expression>)' is not a function
> corStruct.c: In function 'ARMA_fullCorr':
> corStruct.c:594: error: expected expression before 'double'
> corStruct.c:594: warning: assignment makes pointer from integer without a cast
> corStruct.c: In function 'ARMA_matList':
> corStruct.c:617: error: expected expression before 'double'
> corStruct.c:617: warning: initialization makes pointer from integer
> without a cast
> corStruct.c: In function 'ARMA_fact':
> corStruct.c:634: error: expected expression before 'double'
> corStruct.c:634: warning: initialization makes pointer from integer
> without a cast
> corStruct.c:634: error: expected expression before 'double'
> corStruct.c:634: warning: initialization makes pointer from integer
> without a cast
> corStruct.c:642: error: 'chol' undeclared (first use in this function)
> corStruct.c:642: error: called object
> 'F77_CALL(<erroneous-expression>)' is not a function
> corStruct.c:646: error: 'dtrsl' undeclared (first use in this function)
> corStruct.c:646: error: called object
> 'F77_CALL(<erroneous-expression>)' is not a function
> corStruct.c:647: warning: incompatible implicit declaration of
> built-in function 'log'
> corStruct.c:647: warning: incompatible implicit declaration of
> built-in function 'fabs'
> corStruct.c: In function 'ARMA_factList':
> corStruct.c:658: error: expected expression before 'double'
> corStruct.c:658: warning: initialization makes pointer from integer
> without a cast
> corStruct.c: In function 'ARMA_recalc':
> corStruct.c:677: error: expected expression before 'double'
> corStruct.c:677: warning: initialization makes pointer from integer
> without a cast
> corStruct.c:682: error: expected expression before 'double'
> corStruct.c:682: warning: initialization makes pointer from integer
> without a cast
> corStruct.c: In function 'compSymm_matList':
> corStruct.c:709: warning: incompatible implicit declaration of
> built-in function 'exp'
> corStruct.c: In function 'compSymm_fact':
> corStruct.c:721: error: expected expression before 'double'
> corStruct.c:721: warning: initialization makes pointer from integer
> without a cast
> corStruct.c:723: warning: incompatible implicit declaration of
> built-in function 'log'
> corStruct.c:724: warning: incompatible implicit declaration of
> built-in function 'sqrt'
> corStruct.c: In function 'compSymm_factList':
> corStruct.c:747: warning: incompatible implicit declaration of
> built-in function 'exp'
> corStruct.c: In function 'compSymm_recalc':
> corStruct.c:760: warning: incompatible implicit declaration of
> built-in function 'exp'
> corStruct.c:764: error: expected expression before 'double'
> corStruct.c:764: warning: initialization makes pointer from integer
> without a cast
> corStruct.c: In function 'HF_matList':
> corStruct.c:795: warning: incompatible implicit declaration of
> built-in function 'exp'
> corStruct.c: In function 'HF_fact':
> corStruct.c:808: error: expected expression before 'double'
> corStruct.c:808: warning: initialization makes pointer from integer
> without a cast
> corStruct.c:808: error: expected expression before 'double'
> corStruct.c:808: warning: initialization makes pointer from integer
> without a cast
> corStruct.c:816: error: 'chol' undeclared (first use in this function)
> corStruct.c:816: error: called object
> 'F77_CALL(<erroneous-expression>)' is not a function
> corStruct.c:820: error: 'dtrsl' undeclared (first use in this function)
> corStruct.c:820: error: called object
> 'F77_CALL(<erroneous-expression>)' is not a function
> corStruct.c:821: warning: incompatible implicit declaration of
> built-in function 'log'
> corStruct.c:821: warning: incompatible implicit declaration of
> built-in function 'fabs'
> corStruct.c: In function 'HF_factList':
> corStruct.c:835: warning: incompatible implicit declaration of
> built-in function 'exp'
> corStruct.c: In function 'HF_recalc':
> corStruct.c:852: warning: incompatible implicit declaration of
> built-in function 'exp'
> corStruct.c:855: error: expected expression before 'double'
> corStruct.c:855: warning: initialization makes pointer from integer
> without a cast
> corStruct.c: In function 'spher_corr':
> corStruct.c:870: warning: incompatible implicit declaration of
> built-in function 'pow'
> corStruct.c: In function 'exp_corr':
> corStruct.c:879: warning: incompatible implicit declaration of
> built-in function 'exp'
> corStruct.c: In function 'Gaus_corr':
> corStruct.c:887: warning: incompatible implicit declaration of
> built-in function 'exp'
> corStruct.c: In function 'spatial_matList':
> corStruct.c:943: warning: incompatible implicit declaration of
> built-in function 'exp'
> corStruct.c: In function 'spatial_fact':
> corStruct.c:982: error: expected expression before 'double'
> corStruct.c:982: warning: initialization makes pointer from integer
> without a cast
> corStruct.c:982: error: expected expression before 'double'
> corStruct.c:982: warning: initialization makes pointer from integer
> without a cast
> corStruct.c:990: error: 'chol' undeclared (first use in this function)
> corStruct.c:990: error: called object
> 'F77_CALL(<erroneous-expression>)' is not a function
> corStruct.c:994: error: 'dtrsl' undeclared (first use in this function)
> corStruct.c:994: error: called object
> 'F77_CALL(<erroneous-expression>)' is not a function
> corStruct.c:995: warning: incompatible implicit declaration of
> built-in function 'log'
> corStruct.c:995: warning: incompatible implicit declaration of
> built-in function 'fabs'
> corStruct.c: In function 'spatial_factList':
> corStruct.c:1009: warning: incompatible implicit declaration of
> built-in function 'exp'
> corStruct.c: In function 'spatial_recalc':
> corStruct.c:1051: warning: incompatible implicit declaration of
> built-in function 'exp'
> corStruct.c:1081: error: expected expression before 'double'
> corStruct.c:1081: warning: initialization makes pointer from integer
> without a cast
> make: *** [corStruct.o] Error 1
> ERROR: compilation failed for package 'nlme'
> ** Removing '/usr/lib/R/library/nlme'
> ** Restoring previous '/usr/lib/R/library/nlme'


   # yum install R-devel

should do what you need. If you install via RPMS, in order to 
install/compile CRAN packages from source, you also need the headers and 
related files, which are in the 'devel' RPMS.

This is also the case for other applications on RH/FC/F Linux.

If you use:

   yum list R-*

you will see the other R related RPMS that are available via the Fedora 
repos.

HTH,

Marc Schwartz