[R] Problem installing RMySQL (S4R.h:40:17: error: S.h: No such file or directory?)
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 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
Re: [R] Problem installing RMySQL (S4R.h:40:17: error: S.h: No such file or directory?)
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 ')'
Re: [R] Problem installing RMySQL (S4R.h:40:17: error: S.h: No such file or directory?)
Looks like you installed R from an RPM and missed the R-devel RPM. On Fri, 30 Jan 2009, 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 And I get the output below. Can anyone help me with this? What additional system details can I send? Well, what your OS is is often helpful, and how you installed R, and of course the 'at a minimum' information asked for in the posting guide. 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
