Connecting R environment to Mysql databases on Unix system
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10.4 years ago
marcelelaux ▴ 20

Hello Guys

I have a really (long time) important question here, and I will really appreciate any help

I'd like to perform several statistical tasks using R environment under unix system. Actually up to now I have used R Studio (windows), for ecology studies, but now I have huge tables of metagenomic data to analyze.

I created my Mysql database (unix) of metagenomic data, with reads and uniprot's and Knumbers and taxid's and so so so on. This means that I have dozens of tables with thousands (even millions) entries. Now I have to perform some tasks unavailable on Mysql functions, like variance analysis, PCA, cluster, regression, even stepwise model choices.

I have tried to install the RMySQL and dbConnect packages on R Studio, but I got the message:

Warning in install.packages :
  package 'dbConnect' is not available (for R version 3.1.0)

I searched for this error and none of the available suggestions and comments and possible solutions worked to me.

Besides of this, what would be really efficient would be do this connection between R and Mysql under command line unix system.

My R version on unix is

R version 3.1.0 (2014-04-10) -- "Spring Dance"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)

My MySQL version is:

Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 1081 #----> I think that this id will be important, right?
Server version: 5.1.73 Source distribution

I don't know what to do, I searched for this in many blogs, forums, I asked my colleagues and advisors, no one around me could help me, for now.

You can just send to me links and any kind of material (books, tutorials), I can try to do this by myself, but I need, at least, a objective reading about this (or someone that did this).... I have dozens of R books and tutorials and none of them help to do this.

Thank You!

Merry Christmas!
Mysql Unix dbConnect R RMySQL • 8.0k views
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"dbConnect: Provides a graphical user interface to connect with databases that use MySQL" <- do you really need this package ? RMySQL should be enough.

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Yes, sure, you are right, I tried dbConnect too because RMySQL doesn't work, but what I need is the later.

Thanx

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10.4 years ago
Ram 45k

Quick possible solution: Can you try running

>install.packages('RMySQL', type='source')

unless you tried that already? If you did and it did not succeed, the error you face would help get to the next step.
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I tried this command and a "+" appear, so I tried this one:

install.packages("RMySQL", lib="/my/own/R-packages/")

then selected a CRAN mirror, a lot of checks were performed and I got this configuration error:

could not find the MySQL installation include and/or library
  directories.  Manually specify the location of the MySQL
  libraries and the header files and re-run R CMD INSTALL.

INSTRUCTIONS:

1. Define and export the 2 shell variables PKG_CPPFLAGS and
   PKG_LIBS to include the directory for header files (*.h)
   and libraries, for example (using Bourne shell syntax):

      export PKG_CPPFLAGS="-I<MySQL-include-dir>" ----> **How I get this information of MySQL directory?**
      export PKG_LIBS="-L<MySQL-lib-dir> -lmysqlclient"

   Re-run the R INSTALL command:

      R CMD INSTALL RMySQL_<version>.tar.gz

2. Alternatively, you may pass the configure arguments
      --with-mysql-dir=<base-dir> (distribution directory)
   or
      --with-mysql-inc=<base-inc> (where MySQL header files reside)
      --with-mysql-lib=<base-lib> (where MySQL libraries reside)
   in the call to R INSTALL --configure-args='...'
</pre>
<pre>
   R CMD INSTALL --configure-args='--with-mysql-dir=DIR' RMySQL_<version>.tar.gz
</pre>
<pre>
ERROR: configuration failed for package 'RMySQL'
* removing '/root/R/x86_64-redhat-linux-gnu-library/3.1/RMySQL'

The downloaded source packages are in
        '/tmp/RtmpnPMTpK/downloaded_packages'
Warning message:
In install.packages("RMySQL", lib = "/my/own/R-packages/") :
  installation of package 'RMySQL' had non-zero exit status

PS: I have root access.

Thanx for help

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0
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Sorry, there was a mistake in matching quotes. I've updated the command, please try it again.

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0
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Yes, now install.packages('RMySQL', type='source') command worked, but with the same error :(

I think that I really need to this this:

could not find the MySQL installation include and/or library
  directories.  Manually specify the location of the MySQL
  libraries and the header files and re-run R CMD INSTALL.

But I don't know how to locate this information...

Thanx

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0
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Please give me the output of:

$which mysql

from the UNIX command prompt

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0
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It just logged to MySQL:

[marlaux@Frevo ~]$ $which mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 1084
Server version: 5.1.73 Source distribution

Copyright (c) 2000, 2013, Oracle and/or its affiliates. All rights reserved.

Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement
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0
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The $ sign was to denote a shell command, please just run this as-is on the shell:

which mysql
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0
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OK, so after this, you ran a which mysql to which you got the output /usr/bin/mysql

From this link, your MYSQL INC and LIB directories are:

  • INC: /usr/include/mysql
  • LIB: /usr/lib/mysql

Now try running these on the Unix shell:

R CMD INSTALL --configure-args='--with-mysql-inc=/usr/include/mysql --with-mysql-lib=/usr/lib/mysql' RMySQL_0.9-3.tar.gz
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I got this:

[root@Frevo marlaux]# R CMD INSTALL --configure-args='--with-mysql-inc=<base-inc> --with-mysql-lib=<base-lib>' RMySQL_0.9-3.tar.gz

*installing to library '/root/R/x86_64-redhat-linux-gnu-library/3.1'
* installing *source* package 'RMySQL' ... 
** package 'RMySQL' successfully unpacked and MD5 sums checked
sh: -c: line 0: syntax error near unexpected token `newline'
sh: -c: line 0:`*R_SHLIB_BUILD_OBJECTS_SYMBOL_TABLES*=false ./configure --with-mysql-inc=<base-inc> --with-mysql-lib=<base-lib>'
ERROR: configuration failed for package 'RMySQL'
* removing '/root/R/x86_64-redhat-linux-gnu-library/3.1/RMySQL'
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0
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I forgot to update the command with the actual directories. Please try the refreshed command now.

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0
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no way :(

R CMD INSTALL --configure-args='--with-mysql-inc=/usr/include/mysql
--with-mysql-lib=/usr/lib/mysql' RMySQL_0.9-3.tar.gz
* installing to library ‘/root/R/x86_64-redhat-linux-gnu-library/3.1’
* installing *source* package ‘RMySQL’ ...
** package ‘RMySQL’ successfully unpacked and MD5 sums checked
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 -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -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 -m64
-mtune=generic -c RS-DBI.c -o RS-DBI.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -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 -m64
-mtune=generic -c RS-MySQL.c -o RS-MySQL.o
In file included from RS-MySQL.c:22:
RS-MySQL.h:32:19: error: mysql.h: No such file or directory
RS-MySQL.h:33:27: error: mysql_version.h: No such file or directory
RS-MySQL.h:34:23: error: mysql_com.h: No such file or directory
In file included from RS-MySQL.c:22:
RS-MySQL.h:119: error: ‘FIELD_TYPE_DECIMAL’ undeclared here (not in a
function)
RS-MySQL.h:120: error: ‘FIELD_TYPE_TINY’ undeclared here (not in a function)
RS-MySQL.h:121: error: ‘FIELD_TYPE_SHORT’ undeclared here (not in a
function)
RS-MySQL.h:122: error: ‘FIELD_TYPE_LONG’ undeclared here (not in a function)
RS-MySQL.h:123: error: ‘FIELD_TYPE_FLOAT’ undeclared here (not in a
function)
RS-MySQL.h:124: error: ‘FIELD_TYPE_DOUBLE’ undeclared here (not in a
function)
RS-MySQL.h:125: error: ‘FIELD_TYPE_NULL’ undeclared here (not in a function)
RS-MySQL.h:126: error: ‘FIELD_TYPE_TIMESTAMP’ undeclared here (not in a
function)
RS-MySQL.h:127: error: ‘FIELD_TYPE_LONGLONG’ undeclared here (not in a
function)
RS-MySQL.h:128: error: ‘FIELD_TYPE_INT24’ undeclared here (not in a
function)
RS-MySQL.h:129: error: ‘FIELD_TYPE_DATE’ undeclared here (not in a function)
RS-MySQL.h:130: error: ‘FIELD_TYPE_TIME’ undeclared here (not in a function)
RS-MySQL.h:131: error: ‘FIELD_TYPE_DATETIME’ undeclared here (not in a
function)
RS-MySQL.h:132: error: ‘FIELD_TYPE_YEAR’ undeclared here (not in a function)
RS-MySQL.h:133: error: ‘FIELD_TYPE_NEWDATE’ undeclared here (not in a
function)
RS-MySQL.h:134: error: ‘FIELD_TYPE_ENUM’ undeclared here (not in a function)
RS-MySQL.h:135: error: ‘FIELD_TYPE_SET’ undeclared here (not in a function)
RS-MySQL.h:136: error: ‘FIELD_TYPE_TINY_BLOB’ undeclared here (not in a
function)
RS-MySQL.h:137: error: ‘FIELD_TYPE_MEDIUM_BLOB’ undeclared here (not in a
function)
RS-MySQL.h:138: error: ‘FIELD_TYPE_LONG_BLOB’ undeclared here (not in a
function)
RS-MySQL.h:139: error: ‘FIELD_TYPE_BLOB’ undeclared here (not in a function)
RS-MySQL.h:140: error: ‘FIELD_TYPE_VAR_STRING’ undeclared here (not in a
function)
RS-MySQL.h:141: error: ‘FIELD_TYPE_STRING’ undeclared here (not in a
function)
RS-MySQL.c: In function ‘RS_MySQL_moreResultSets’:
RS-MySQL.c:110: error: ‘MYSQL’ undeclared (first use in this function)
RS-MySQL.c:110: error: (Each undeclared identifier is reported only once
RS-MySQL.c:110: error: for each function it appears in.)
RS-MySQL.c:110: error: ‘my_connection’ undeclared (first use in this
function)
RS-MySQL.c:110: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:110: warning: statement with no effect
RS-MySQL.c:111: error: ‘my_bool’ undeclared (first use in this function)
RS-MySQL.c:111: warning: statement with no effect
RS-MySQL.c:111: error: expected ‘;’ before ‘tmp’
RS-MySQL.c:115: error: expected expression before ‘)’ token
RS-MySQL.c:115: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:115: warning: statement with no effect
RS-MySQL.c:117: error: ‘tmp’ undeclared (first use in this function)
RS-MySQL.c:117: warning: implicit declaration of function
‘mysql_more_results’
RS-MySQL.c:117: warning: statement with no effect
RS-MySQL.c: In function ‘RS_MySQL_nextResultSet’:
RS-MySQL.c:137: error: ‘MYSQL_RES’ undeclared (first use in this function)
RS-MySQL.c:137: error: ‘my_result’ undeclared (first use in this function)
RS-MySQL.c:137: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:137: warning: statement with no effect
RS-MySQL.c:138: error: ‘MYSQL’ undeclared (first use in this function)
RS-MySQL.c:138: error: ‘my_connection’ undeclared (first use in this
function)
RS-MySQL.c:138: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:138: warning: statement with no effect
RS-MySQL.c:142: error: expected expression before ‘)’ token
RS-MySQL.c:142: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:142: warning: statement with no effect
RS-MySQL.c:144: warning: implicit declaration of function
‘mysql_next_result’
RS-MySQL.c:154: warning: implicit declaration of function ‘mysql_use_result’
RS-MySQL.c:154: warning: statement with no effect
RS-MySQL.c:156: error: expected expression before ‘)’ token
RS-MySQL.c:156: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:156: error: called object ‘<erroneous-expression>’ is not a
function
RS-MySQL.c:156: warning: statement with no effect
RS-MySQL.c:158: warning: implicit declaration of function
‘mysql_field_count’
RS-MySQL.c:176: warning: implicit declaration of function
‘mysql_affected_rows’
RS-MySQL.c: In function ‘RS_MySQL_createConnection’:
RS-MySQL.c:313: error: ‘MYSQL’ undeclared (first use in this function)
RS-MySQL.c:313: error: ‘my_connection’ undeclared (first use in this
function)
RS-MySQL.c:313: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:313: warning: statement with no effect
RS-MySQL.c:319: warning: implicit declaration of function ‘mysql_init’
RS-MySQL.c:319: warning: statement with no effect
RS-MySQL.c:341: warning: implicit declaration of function ‘mysql_options’
RS-MySQL.c:341: error: ‘MYSQL_READ_DEFAULT_GROUP’ undeclared (first use in
this function)
RS-MySQL.c:347: error: ‘MYSQL_READ_DEFAULT_FILE’ undeclared (first use in
this function)
RS-MySQL.c:349: warning: implicit declaration of function
‘mysql_real_connect’
RS-MySQL.c:356: warning: implicit declaration of function ‘mysql_error’
RS-MySQL.c:356: warning: format ‘%s’ expects type ‘char *’, but argument 3
has type ‘int’
RS-MySQL.c:365: warning: implicit declaration of function ‘mysql_close’
RS-MySQL.c: In function ‘RS_MySQL_closeConnection’:
RS-MySQL.c:384: error: ‘MYSQL’ undeclared (first use in this function)
RS-MySQL.c:384: error: ‘my_connection’ undeclared (first use in this
function)
RS-MySQL.c:384: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:384: warning: statement with no effect
RS-MySQL.c:400: error: expected expression before ‘)’ token
RS-MySQL.c:400: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:400: warning: statement with no effect
RS-MySQL.c: In function ‘RS_MySQL_exec’:
RS-MySQL.c:425: error: ‘MYSQL’ undeclared (first use in this function)
RS-MySQL.c:425: error: ‘my_connection’ undeclared (first use in this
function)
RS-MySQL.c:425: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:425: warning: statement with no effect
RS-MySQL.c:426: error: ‘MYSQL_RES’ undeclared (first use in this function)
RS-MySQL.c:426: error: ‘my_result’ undeclared (first use in this function)
RS-MySQL.c:426: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:426: warning: statement with no effect
RS-MySQL.c:432: error: expected expression before ‘)’ token
RS-MySQL.c:432: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:432: warning: statement with no effect
RS-MySQL.c:454: warning: implicit declaration of function ‘mysql_query’
RS-MySQL.c:459: warning: format ‘%s’ expects type ‘char *’, but argument 3
has type ‘int’
RS-MySQL.c:470: warning: statement with no effect
RS-MySQL.c:472: error: expected expression before ‘)’ token
RS-MySQL.c:472: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:472: error: called object ‘<erroneous-expression>’ is not a
function
RS-MySQL.c:472: warning: statement with no effect
RS-MySQL.c: In function ‘RS_MySQL_createDataMappings’:
RS-MySQL.c:511: error: ‘MYSQL_RES’ undeclared (first use in this function)
RS-MySQL.c:511: error: ‘my_result’ undeclared (first use in this function)
RS-MySQL.c:511: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:511: warning: statement with no effect
RS-MySQL.c:512: error: ‘MYSQL_FIELD’ undeclared (first use in this function)
RS-MySQL.c:512: error: ‘select_dp’ undeclared (first use in this function)
RS-MySQL.c:512: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:512: warning: statement with no effect
RS-MySQL.c:520: error: expected expression before ‘)’ token
RS-MySQL.c:520: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:520: warning: statement with no effect
RS-MySQL.c:523: warning: implicit declaration of function
‘mysql_fetch_fields’
RS-MySQL.c:523: warning: statement with no effect
RS-MySQL.c:526: error: ‘MYSQL’ undeclared (first use in this function)
RS-MySQL.c:526: error: expected expression before ‘)’ token
RS-MySQL.c:526: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:552: error: ‘struct data_types’ has no member named ‘name’
RS-MySQL.c:552: warning: passing argument 1 of ‘RS_DBI_copyString’ from
incompatible pointer type
RS-DBI.h:237: note: expected ‘const char *’ but argument is of type ‘struct
data_types *’
RS-MySQL.c:553: error: ‘struct data_types’ has no member named ‘type’
RS-MySQL.c:553: warning: assignment makes integer from pointer without a
cast
RS-MySQL.c:554: error: ‘struct data_types’ has no member named ‘length’
RS-MySQL.c:554: warning: assignment makes integer from pointer without a
cast
RS-MySQL.c:555: error: ‘struct data_types’ has no member named ‘length’
RS-MySQL.c:555: warning: assignment makes integer from pointer without a
cast
RS-MySQL.c:556: error: ‘struct data_types’ has no member named ‘decimals’
RS-MySQL.c:556: warning: assignment makes integer from pointer without a
cast
RS-MySQL.c:557: warning: implicit declaration of function ‘IS_NOT_NULL’
RS-MySQL.c:557: error: ‘struct data_types’ has no member named ‘flags’
RS-MySQL.c:559: error: ‘struct data_types’ has no member named ‘type’
RS-MySQL.c:559: warning: assignment makes integer from pointer without a
cast
RS-MySQL.c:571: error: ‘struct data_types’ has no member named ‘flags’
RS-MySQL.c:571: error: ‘UNSIGNED_FLAG’ undeclared (first use in this
function)
RS-MySQL.c:571: error: invalid operands to binary &amp; (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c: In function ‘RS_MySQL_fetch’:
RS-MySQL.c:649: error: ‘MYSQL_RES’ undeclared (first use in this function)
RS-MySQL.c:649: error: ‘my_result’ undeclared (first use in this function)
RS-MySQL.c:649: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:649: warning: statement with no effect
RS-MySQL.c:650: error: ‘MYSQL_ROW’ undeclared (first use in this function)
RS-MySQL.c:650: warning: statement with no effect
RS-MySQL.c:650: error: expected ‘;’ before ‘row’
RS-MySQL.c:687: error: expected expression before ‘)’ token
RS-MySQL.c:687: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:687: warning: statement with no effect
RS-MySQL.c:708: error: ‘row’ undeclared (first use in this function)
RS-MySQL.c:708: warning: implicit declaration of function ‘mysql_fetch_row’
RS-MySQL.c:708: warning: statement with no effect
RS-MySQL.c:713: warning: implicit declaration of function ‘mysql_errno’
RS-MySQL.c:713: error: ‘MYSQL’ undeclared (first use in this function)
RS-MySQL.c:713: error: expected expression before ‘)’ token
RS-MySQL.c:713: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:717: warning: implicit declaration of function
‘mysql_fetch_lengths’
RS-MySQL.c:717: warning: assignment makes pointer from integer without a
cast
RS-MySQL.c:721: error: invalid operands to binary == (have ‘struct
data_types’ and ‘void *’)
RS-MySQL.c:721: warning: assignment makes integer from pointer without a
cast
RS-MySQL.c:729: error: incompatible type for argument 1 of ‘atol’
/usr/include/stdlib.h:289: note: expected ‘const char *’ but argument is of
type ‘struct data_types’
RS-MySQL.c:729: warning: cast from pointer to integer of different size
RS-MySQL.c:745: error: incompatible type for argument 1 of ‘strlen’
/usr/include/string.h:399: note: expected ‘const char *’ but argument is of
type ‘struct data_types’
RS-MySQL.c:745: warning: comparison between pointer and integer
RS-MySQL.c:752: error: incompatible type for argument 1 of ‘Rf_mkChar’
/usr/include/R/Rinternals.h:777: note: expected ‘const char *’ but argument
is of type ‘struct data_types’
RS-MySQL.c:752: warning: passing argument 3 of ‘SET_STRING_ELT’ from
incompatible pointer type
/usr/include/R/Rinternals.h:530: note: expected ‘SEXP’ but argument is of
type ‘struct data_types *’
RS-MySQL.c:760: error: incompatible type for argument 1 of ‘atof’
/usr/include/stdlib.h:279: note: expected ‘const char *’ but argument is of
type ‘struct data_types’
RS-MySQL.c:760: error: pointer value used where a floating point value was
expected
RS-MySQL.c:793: error: incompatible type for argument 1 of ‘Rf_mkChar’
/usr/include/R/Rinternals.h:777: note: expected ‘const char *’ but argument
is of type ‘struct data_types’
RS-MySQL.c:793: warning: passing argument 3 of ‘SET_STRING_ELT’ from
incompatible pointer type
/usr/include/R/Rinternals.h:530: note: expected ‘SEXP’ but argument is of
type ‘struct data_types *’
RS-MySQL.c: In function ‘RS_MySQL_getException’:
RS-MySQL.c:829: error: ‘MYSQL’ undeclared (first use in this function)
RS-MySQL.c:829: error: ‘my_connection’ undeclared (first use in this
function)
RS-MySQL.c:829: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:829: warning: statement with no effect
RS-MySQL.c:849: error: expected expression before ‘)’ token
RS-MySQL.c:849: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:849: warning: statement with no effect
RS-MySQL.c:851: warning: passing argument 1 of ‘Rf_mkChar’ makes pointer
from integer without a cast
/usr/include/R/Rinternals.h:777: note: expected ‘const char *’ but argument
is of type ‘int’
RS-MySQL.c: In function ‘RS_MySQL_closeResultSet’:
RS-MySQL.c:862: error: ‘MYSQL_RES’ undeclared (first use in this function)
RS-MySQL.c:862: error: ‘my_result’ undeclared (first use in this function)
RS-MySQL.c:862: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:862: warning: statement with no effect
RS-MySQL.c:867: error: expected expression before ‘)’ token
RS-MySQL.c:867: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:867: warning: statement with no effect
RS-MySQL.c:870: error: ‘MYSQL_ROW’ undeclared (first use in this function)
RS-MySQL.c:870: warning: statement with no effect
RS-MySQL.c:870: error: expected ‘;’ before ‘row’
RS-MySQL.c:871: error: ‘row’ undeclared (first use in this function)
RS-MySQL.c:874: warning: implicit declaration of function
‘mysql_free_result’
RS-MySQL.c: In function ‘RS_MySQL_managerInfo’:
RS-MySQL.c:941: warning: implicit declaration of function
‘mysql_get_client_info’
RS-MySQL.c:941: warning: passing argument 1 of ‘Rf_mkChar’ makes pointer
from integer without a cast
/usr/include/R/Rinternals.h:777: note: expected ‘const char *’ but argument
is of type ‘int’
RS-MySQL.c: In function ‘RS_MySQL_connectionInfo’:
RS-MySQL.c:951: error: ‘MYSQL’ undeclared (first use in this function)
RS-MySQL.c:951: error: ‘my_con’ undeclared (first use in this function)
RS-MySQL.c:951: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:951: warning: statement with no effect
RS-MySQL.c:967: error: expected expression before ‘)’ token
RS-MySQL.c:967: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:967: warning: statement with no effect
RS-MySQL.c:980: error: ‘struct data_types’ has no member named ‘host’
RS-MySQL.c:980: error: ‘struct data_types’ has no member named ‘host’
RS-MySQL.c:980: warning: pointer type mismatch in conditional expression
RS-MySQL.c:982: error: ‘struct data_types’ has no member named ‘user’
RS-MySQL.c:982: error: ‘struct data_types’ has no member named ‘user’
RS-MySQL.c:982: warning: pointer type mismatch in conditional expression
RS-MySQL.c:984: error: ‘struct data_types’ has no member named ‘db’
RS-MySQL.c:984: error: ‘struct data_types’ has no member named ‘db’
RS-MySQL.c:984: warning: pointer type mismatch in conditional expression
RS-MySQL.c:986: warning: implicit declaration of function
‘mysql_get_host_info’
RS-MySQL.c:986: warning: passing argument 1 of ‘Rf_mkChar’ makes pointer
from integer without a cast
/usr/include/R/Rinternals.h:777: note: expected ‘const char *’ but argument
is of type ‘int’
RS-MySQL.c:987: warning: implicit declaration of function
‘mysql_get_server_info’
RS-MySQL.c:987: warning: passing argument 1 of ‘Rf_mkChar’ makes pointer
from integer without a cast
/usr/include/R/Rinternals.h:777: note: expected ‘const char *’ but argument
is of type ‘int’
RS-MySQL.c:989: warning: implicit declaration of function
‘mysql_get_proto_info’
RS-MySQL.c:990: warning: implicit declaration of function ‘mysql_thread_id’
RS-MySQL.c: In function ‘RS_MySQL_dbApply’:
RS-MySQL.c:1210: error: ‘MYSQL_RES’ undeclared (first use in this function)
RS-MySQL.c:1210: error: ‘my_result’ undeclared (first use in this function)
RS-MySQL.c:1210: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:1210: warning: statement with no effect
RS-MySQL.c:1211: error: ‘MYSQL_ROW’ undeclared (first use in this function)
RS-MySQL.c:1211: warning: statement with no effect
RS-MySQL.c:1211: error: expected ‘;’ before ‘row’
RS-MySQL.c:1236: error: ‘row’ undeclared (first use in this function)
RS-MySQL.c:1236: warning: statement with no effect
RS-MySQL.c:1286: error: expected expression before ‘)’ token
RS-MySQL.c:1286: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:1286: warning: statement with no effect
RS-MySQL.c:1305: warning: statement with no effect
RS-MySQL.c:1311: error: ‘MYSQL’ undeclared (first use in this function)
RS-MySQL.c:1311: error: expected expression before ‘)’ token
RS-MySQL.c:1311: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:1317: warning: assignment makes pointer from integer without a
cast
RS-MySQL.c:1326: error: invalid operands to binary == (have ‘struct
data_types’ and ‘void *’)
RS-MySQL.c:1326: warning: assignment makes integer from pointer without a
cast
RS-MySQL.c:1334: error: incompatible type for argument 1 of ‘atol’
/usr/include/stdlib.h:289: note: expected ‘const char *’ but argument is of
type ‘struct data_types’
RS-MySQL.c:1334: warning: assignment makes integer from pointer without a
cast
RS-MySQL.c:1351: error: incompatible type for argument 1 of ‘strlen’
/usr/include/string.h:399: note: expected ‘const char *’ but argument is of
type ‘struct data_types’
RS-MySQL.c:1351: warning: comparison between pointer and integer
RS-MySQL.c:1358: error: incompatible type for argument 1 of ‘Rf_mkChar’
/usr/include/R/Rinternals.h:777: note: expected ‘const char *’ but argument
is of type ‘struct data_types’
RS-MySQL.c:1358: warning: passing argument 3 of ‘SET_STRING_ELT’ from
incompatible pointer type
/usr/include/R/Rinternals.h:530: note: expected ‘SEXP’ but argument is of
type ‘struct data_types *’
RS-MySQL.c:1367: error: incompatible type for argument 1 of ‘atof’
/usr/include/stdlib.h:279: note: expected ‘const char *’ but argument is of
type ‘struct data_types’
RS-MySQL.c:1367: error: pointer value used where a floating point value was
expected
RS-MySQL.c:1402: error: incompatible type for argument 1 of ‘Rf_mkChar’
/usr/include/R/Rinternals.h:777: note: expected ‘const char *’ but argument
is of type ‘struct data_types’
RS-MySQL.c:1402: warning: passing argument 3 of ‘SET_STRING_ELT’ from
incompatible pointer type
/usr/include/R/Rinternals.h:530: note: expected ‘SEXP’ but argument is of
type ‘struct data_types *’
RS-MySQL.c: In function ‘RS_MySQL_insertid’:
RS-MySQL.c:1605: error: ‘MYSQL’ undeclared (first use in this function)
RS-MySQL.c:1605: error: ‘my_con’ undeclared (first use in this function)
RS-MySQL.c:1605: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:1605: warning: statement with no effect
RS-MySQL.c:1613: error: expected expression before ‘)’ token
RS-MySQL.c:1613: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:1613: warning: statement with no effect
RS-MySQL.c:1622: warning: implicit declaration of function ‘mysql_insert_id’
RS-MySQL.c: In function ‘RS_MySQL_escapeStrings’:
RS-MySQL.c:1640: error: ‘MYSQL’ undeclared (first use in this function)
RS-MySQL.c:1640: error: ‘my_connection’ undeclared (first use in this
function)
RS-MySQL.c:1640: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:1640: warning: statement with no effect
RS-MySQL.c:1648: error: expected expression before ‘)’ token
RS-MySQL.c:1648: error: invalid operands to binary * (have ‘struct
data_types *’ and ‘struct data_types *’)
RS-MySQL.c:1648: warning: statement with no effect
RS-MySQL.c:1672: warning: implicit declaration of function
‘mysql_real_escape_string’
RS-MySQL.c: In function ‘RS_MySQL_clientLibraryVersions’:
RS-MySQL.c:1687: error: ‘MYSQL_SERVER_VERSION’ undeclared (first use in
this function)
RS-MySQL.c:1687: warning: passing argument 1 of ‘Rf_mkChar’ from
incompatible pointer type
/usr/include/R/Rinternals.h:777: note: expected ‘const char *’ but argument
is of type ‘struct data_types *’
RS-MySQL.c:1688: warning: passing argument 1 of ‘Rf_mkChar’ makes pointer
from integer without a cast
/usr/include/R/Rinternals.h:777: note: expected ‘const char *’ but argument
is of type ‘int’
RS-MySQL.c:1690: error: ‘MYSQL_VERSION_ID’ undeclared (first use in this
function)
RS-MySQL.c:1690: warning: cast from pointer to integer of different size
RS-MySQL.c:1691: warning: implicit declaration of function
‘mysql_get_client_version’
RS-MySQL.c: In function ‘R_init_RMySQL’:
RS-MySQL.c:1698: error: ‘MYSQL_VERSION_ID’ undeclared (first use in this
function)
RS-MySQL.c:1698: warning: initialization makes integer from pointer without
a cast
RS-MySQL.c:1701: warning: implicit declaration of function
‘mysql_library_init’
RS-MySQL.c:1711: error: ‘MYSQL_SERVER_VERSION’ undeclared (first use in
this function)
RS-MySQL.c: In function ‘R_unload_RMySQL’:
RS-MySQL.c:1716: warning: implicit declaration of function
‘mysql_library_end’
make: *** [RS-MySQL.o] Error 1
ERROR: compilation failed for package ‘RMySQL’
* removing ‘/root/R/x86_64-redhat-linux-gnu-library/3.1/RMySQL’
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Can you try installing without logging in as root? And you could probably use pastebin or GitHub Gist to share long output/error messages the next time!

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