[R] Problem installing RMySQL ("S4R.h:40:17: error: S.h: No such file or directory"?)

[Jeffrey Horner]

Dan Bolser wrote:
> Hi,
> 
> I'm trying to install RMySQL and I keep hitting errors. My computer is:
> 
> uname -a
> Linux cricket 2.6.18-92.1.22.el5PAE #1 SMP Tue Dec 16 12:36:25 EST 2008 i686
> i686 i386 GNU/Linux
> 
> 
> I have set the following environment settings:
> 
> export PKG_LIBS="-L/usr/lib/mysql -lmysqlclient"
> export PKG_CPPFLAGS="-I/usr/include/mysql"
> 
> 
> I run the following command:
> 
> R CMD INSTALL --library "$HOME/R/i386-redhat-linux-gnu-library/2.7"
> RMySQL_0.7-2.tar.gz

Hi Dan,

You will certainly want to upgrade R first. The latest version is R 2.8.1.

Jeff

> 
> 
> And I get the output below.
> 
> Can anyone help me with this? What additional system details can I send?
> 
> 
> Thanks very much for any tips.
> 
> Dan.
> 
> 
> R CMD INSTALL --library "$HOME/R/i386-redhat-linux-gnu-library/2.7"
> RMySQL_0.7-2.tar.gz
> * Installing *source* package 'RMySQL' ...
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ANSI C... none needed
> checking how to run the C preprocessor... gcc -E
> checking for compress in -lz... yes
> checking for getopt_long in -lc... yes
> checking for mysql_init in -lmysqlclient... no
> checking for egrep... grep -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking mysql.h usability... no
> checking mysql.h presence... no
> checking for mysql.h... no
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> gcc -m32 -std=gnu99 -I/usr/include/R -I/usr/include/mysql
> -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 RS-DBI.c -o RS-DBI.o
> In file included from RS-DBI.h:32,
>                  from RS-DBI.c:22:
> S4R.h:40:17: error: S.h: No such file or directory
> S4R.h:53:24: error: Rversion.h: No such file or directory
> S4R.h:54:51: error: missing binary operator before token "("
> S4R.h:62:26: error: Rdefines.h: No such file or directory
> S4R.h:154:49: error: missing binary operator before token "("
> S4R.h:176:49: error: missing binary operator before token "("
> In file included from RS-DBI.c:22:
> RS-DBI.h:100: error: expected specifier-qualifier-list before 'SEXPTYPE'
> RS-DBI.h:170: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
> RS-DBI.h:173: error: expected ')' before '*' token
> RS-DBI.h:174: error: expected ')' before '*' token
> RS-DBI.h:175: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
> RS-DBI.h:176: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
> RS-DBI.h:179: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
> RS-DBI.h:181: error: expected ')' before '*' token
> RS-DBI.h:182: error: expected ')' before '*' token
> RS-DBI.h:183: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
> RS-DBI.h:184: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
> RS-DBI.h:187: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
> RS-DBI.h:188: error: expected ')' before '*' token
> RS-DBI.h:189: error: expected ')' before '*' token
> RS-DBI.h:190: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
> RS-DBI.h:191: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
> RS-DBI.h:194: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
> RS-DBI.h:195: error: expected ')' before '*' token
> RS-DBI.h:213: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
> RS-DBI.h:220: error: expected ')' before '*' token
> RS-DBI.h:224: error: expected ')' before '*' token
> RS-DBI.h:231: error: expected ')' before '*' token
> RS-DBI.h:251: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
> RS-DBI.h:253: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
> RS-DBI.h:257: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
> RS-DBI.h:259: error: expected declaration specifiers or '...' before
> 'SEXPTYPE'
> RS-DBI.h:260: error: expected declaration specifiers or '...' before
> 'SEXPTYPE'
> RS-DBI.c:36: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
> RS-DBI.c:109: error: expected ')' before '*' token
> RS-DBI.c:137: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
> RS-DBI.c:207: error: expected ')' before '*' token
> RS-DBI.c:261: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
> RS-DBI.c:309: error: expected ')' before '*' token
> RS-DBI.c: In function 'RS_DBI_allocFields':
> RS-DBI.c:350: warning: implicit declaration of function 'malloc'
> RS-DBI.c:350: warning: incompatible implicit declaration of built-in
> function 'malloc'
> RS-DBI.c:357: warning: implicit declaration of function 'calloc'
> RS-DBI.c:357: warning: incompatible implicit declaration of built-in
> function 'calloc'
> RS-DBI.c:364: error: 'RS_DBI_fields' has no member named 'Sclass'
> RS-DBI.c:364: error: 'SEXPTYPE' undeclared (first use in this function)
> RS-DBI.c:364: error: (Each undeclared identifier is reported only once
> RS-DBI.c:364: error: for each function it appears in.)
> RS-DBI.c:364: error: expected expression before ')' token
> RS-DBI.c: In function 'RS_DBI_freeFields':
> RS-DBI.c:375: warning: implicit declaration of function 'free'
> RS-DBI.c:384: error: 'RS_DBI_fields' has no member named 'Sclass'
> RS-DBI.c:384: error: 'RS_DBI_fields' has no member named 'Sclass'
> RS-DBI.c: At top level:
> RS-DBI.c:395: error: expected ')' before '*' token
> RS-DBI.c:448: error: expected ')' before '*' token
> RS-DBI.c:526: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
> RS-DBI.c:551: error: expected ')' before '*' token
> RS-DBI.c: In function 'RS_DBI_errorMessage':
> RS-DBI.c:586: error: 'PROBLEM' undeclared (first use in this function)
> RS-DBI.c:586: error: expected ';' before string constant
> RS-DBI.c:589: error: expected ';' before string constant
> RS-DBI.c:592: error: expected ';' before string constant
> RS-DBI.c:595: error: expected ';' before string constant
> RS-DBI.c:582: warning: unused variable 'driver'
> RS-DBI.c: In function 'RS_DBI_copyString':
> RS-DBI.c:607: warning: incompatible implicit declaration of built-in
> function 'malloc'
> RS-DBI.c:607: warning: implicit declaration of function 'strlen'
> RS-DBI.c:607: warning: incompatible implicit declaration of built-in
> function 'strlen'
> RS-DBI.c:612: warning: implicit declaration of function 'strcpy'
> RS-DBI.c:612: warning: incompatible implicit declaration of built-in
> function 'strcpy'
> RS-DBI.c: In function 'RS_DBI_nCopyString':
> RS-DBI.c:621: warning: incompatible implicit declaration of built-in
> function 'malloc'
> RS-DBI.c:624: warning: implicit declaration of function 'sprintf'
> RS-DBI.c:624: warning: incompatible implicit declaration of built-in
> function 'sprintf'
> RS-DBI.c:634: warning: implicit declaration of function 'strncpy'
> RS-DBI.c:634: warning: incompatible implicit declaration of built-in
> function 'strncpy'
> RS-DBI.c: At top level:
> RS-DBI.c:649: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
> RS-DBI.c:691: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
> RS-DBI.c:736: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
> RS-DBI.c:768: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
> RS-DBI.c:779: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
> RS-DBI.c:791: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
> RS-DBI.c:805: error: expected ')' before '*' token
> RS-DBI.c:820: error: expected ')' before '*' token
> RS-DBI.c:839: error: expected ')' before '*' token
> RS-DBI.c:914: error: expected ')' before '*' token
> RS-DBI.c:964: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
> RS-DBI.c:1010: error: expected '=', ',', ';', 'asm' or '__attribute__'
> before '*' token
> RS-DBI.c:1055: error: expected '=', ',', ';', 'asm' or '__attribute__'
> before '*' token
> RS-DBI.c:1094: error: expected '=', ',', ';', 'asm' or '__attribute__'
> before '*' token
> RS-DBI.c: In function 'RS_DBI_getTypeName':
> RS-DBI.c:1148: warning: incompatible implicit declaration of built-in
> function 'sprintf'
> RS-DBI.c: At top level:
> RS-DBI.c:1170: error: expected '=', ',', ';', 'asm' or '__attribute__'
> before '*' token
> RS-DBI.c:1213: error: expected declaration specifiers or '...' before
> 'SEXPTYPE'
> RS-DBI.c: In function 'RS_na_set':
> RS-DBI.c:1218: error: 'type' undeclared (first use in this function)
> RS-DBI.c:1219: error: 'INTSXP' undeclared (first use in this function)
> RS-DBI.c:1221: error: 'NA_INTEGER' undeclared (first use in this function)
> RS-DBI.c:1223: error: 'LGLSXP' undeclared (first use in this function)
> RS-DBI.c:1225: error: 'NA_LOGICAL' undeclared (first use in this function)
> RS-DBI.c:1227: error: 'REALSXP' undeclared (first use in this function)
> RS-DBI.c:1229: error: 'NA_REAL' undeclared (first use in this function)
> RS-DBI.c:1231: error: 'STRSXP' undeclared (first use in this function)
> RS-DBI.c:1233: warning: implicit declaration of function 'CHAR'
> RS-DBI.c:1233: warning: implicit declaration of function 'CHARACTER_POINTER'
> RS-DBI.c:1233: error: 'NA_STRING' undeclared (first use in this function)
> RS-DBI.c:1233: error: subscripted value is neither array nor pointer
> RS-DBI.c: At top level:
> RS-DBI.c:1238: error: expected declaration specifiers or '...' before
> 'SEXPTYPE'
> RS-DBI.c: In function 'RS_is_na':
> RS-DBI.c:1244: error: 'type' undeclared (first use in this function)
> RS-DBI.c:1245: error: 'INTSXP' undeclared (first use in this function)
> RS-DBI.c:1246: error: 'LGLSXP' undeclared (first use in this function)
> RS-DBI.c:1248: error: 'NA_INTEGER' undeclared (first use in this function)
> RS-DBI.c:1250: error: 'REALSXP' undeclared (first use in this function)
> RS-DBI.c:1252: warning: implicit declaration of function 'ISNA'
> RS-DBI.c:1254: error: 'STRSXP' undeclared (first use in this function)
> RS-DBI.c:1256: warning: implicit declaration of function 'strcmp'
> RS-DBI.c:1256: error: 'NA_STRING' undeclared (first use in this function)
> RS-DBI.c:1256: error: subscripted value is neither array nor pointer
> RS-DBI.c: At top level:
> RS-DBI.c:1265: error: 'NILSXP' undeclared here (not in a function)
> RS-DBI.c:1266: error: 'SYMSXP' undeclared here (not in a function)
> RS-DBI.c:1267: error: 'LISTSXP' undeclared here (not in a function)
> RS-DBI.c:1268: error: 'CLOSXP' undeclared here (not in a function)
> RS-DBI.c:1269: error: 'ENVSXP' undeclared here (not in a function)
> RS-DBI.c:1270: error: 'PROMSXP' undeclared here (not in a function)
> RS-DBI.c:1271: error: 'LANGSXP' undeclared here (not in a function)
> RS-DBI.c:1272: error: 'SPECIALSXP' undeclared here (not in a function)
> RS-DBI.c:1273: error: 'BUILTINSXP' undeclared here (not in a function)
> RS-DBI.c:1274: error: 'CHARSXP' undeclared here (not in a function)
> RS-DBI.c:1275: error: 'LGLSXP' undeclared here (not in a function)
> RS-DBI.c:1276: error: 'INTSXP' undeclared here (not in a function)
> RS-DBI.c:1277: error: 'REALSXP' undeclared here (not in a function)
> RS-DBI.c:1278: error: 'CPLXSXP' undeclared here (not in a function)
> RS-DBI.c:1279: error: 'STRSXP' undeclared here (not in a function)
> RS-DBI.c:1280: error: 'DOTSXP' undeclared here (not in a function)
> RS-DBI.c:1281: error: 'ANYSXP' undeclared here (not in a function)
> RS-DBI.c:1282: error: 'EXPRSXP' undeclared here (not in a function)
> RS-DBI.c:1283: error: 'VECSXP' undeclared here (not in a function)
> RS-DBI.c:1284: error: 'RAWSXP' undeclared here (not in a function)
> make: *** [RS-DBI.o] Error 1
> chmod: cannot access
> `/local/Scratch/dbolser/R/i386-redhat-linux-gnu-library/2.7/RMySQL/libs/*':
> No such file or directory
> ERROR: compilation failed for package 'RMySQL'
> ** Removing
> '/local/Scratch/dbolser/R/i386-redhat-linux-gnu-library/2.7/RMySQL'
> 
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-- 
http://biostat.mc.vanderbilt.edu/JeffreyHorner