Dear r-package-devel list subscribers, can someone please guide me a little in installing RODBC[1] on FreeBSD 13? I believe it depends on unixodbc[2], but the compilation stops with at not finding unixodbc (I think): rasmus at iselin ~ % mkdir ~/src/RODBC rasmus at iselin ~ % cd ~/src/RODBC rasmus at iselin ~/src/RODBC % fetch 'https://cran.rstudio.com/src/contrib/RODBC_1.3-17.tar.gz' rasmus at iselin ~/src/RODBC % R CMD INSTALL RODBC * installing to library ?/usr/home/rasmus/R/amd64-portbld-freebsd13.0-library/4.0? * installing *source* package ?RODBC? ... ** package ?RODBC? successfully unpacked and MD5 sums checked ** using staged installation checking for gcc... cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking how to run the C preprocessor... cc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/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 sql.h usability... yes checking sql.h presence... yes checking for sql.h... yes checking sqlext.h usability... yes checking sqlext.h presence... yes checking for sqlext.h... yes checking for library containing SQLTables... no configure: error: "no ODBC driver manager found" ERROR: configuration failed for package ?RODBC? * removing ?/usr/home/rasmus/R/amd64-portbld-freebsd13.0-library/4.0/RODBC? I've attached the config.log. I think the important lines are 249:253: configure:3672: cc -o conftest -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I. conftest.c -lodbc >&5 ld: error: unable to find library -lodbc cc: error: linker command failed with exit code 1 (use -v to see invocation) configure:3672: $? = 1 I found line 48 in configure.ac [3] odbc_lib_path=`odbc_config --libs | sed s/-lodbc//` and tried to change it to odbc_lib_path=`pkg-config --libs --cflags odbc | sed s/-lodbc//` but this changes nothing (I think ...) Running odbc_config and pkg-config: rasmus at iselin ~/src/RODBC % odbc_config --libs -L/usr/local/lib -lodbc rasmus at iselin ~/src/RODBC % pkg-config --libs --cflags odbc -I/usr/local/include -L/usr/local/lib -lodbc Hey, I am at a loss here ... I have not done much debugging work like this before ... Perhaps some kind soul among you can provide some useful pointers on this? Best, Rasmus Liland [1] https://cran.r-project.org/web/packages/RODBC/index.html [2] http://www.unixodbc.org/ [3] https://raw.githubusercontent.com/cran/RODBC/master/configure.ac -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: config.log URL: <https://stat.ethz.ch/pipermail/r-package-devel/attachments/20210329/688d058f/attachment.log> -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 833 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-package-devel/attachments/20210329/688d058f/attachment.sig>
[R-pkg-devel] Debugging RODBC installation problems on FreeBSD (unixodbc library path)
4 messages · Dirk Eddelbuettel, Rasmus Liland
On 29 March 2021 at 23:29, Rasmus Liland wrote:
| can someone please guide me a little in | installing RODBC[1] on FreeBSD 13? | | I believe it depends on unixodbc[2], but | the compilation stops with at not | finding unixodbc (I think): | | rasmus at iselin ~ % mkdir ~/src/RODBC | rasmus at iselin ~ % cd ~/src/RODBC | rasmus at iselin ~/src/RODBC % fetch 'https://cran.rstudio.com/src/contrib/RODBC_1.3-17.tar.gz' | rasmus at iselin ~/src/RODBC % R CMD INSTALL RODBC | * installing to library ?/usr/home/rasmus/R/amd64-portbld-freebsd13.0-library/4.0? [...] | checking for sqlext.h... yes | checking for library containing SQLTables... no | configure: error: "no ODBC driver manager found" | ERROR: configuration failed for package ?RODBC? | * removing ?/usr/home/rasmus/R/amd64-portbld-freebsd13.0-library/4.0/RODBC? | | I've attached the config.log. I think | the important lines are 249:253: I find it easier to look at the input code in configure.ac that is used to create configure (which, as a machine generated script, is less readable, same for the log). So we see that test for sqlext.h still passed, but the next one failed. Using the source for RODBC we have first the block that passes and then the block that fails: dnl Check the headers can be found AC_CHECK_HEADERS(sql.h sqlext.h) if test "${ac_cv_header_sql_h}" = no || test "${ac_cv_header_sqlext_h}" = no; then AC_MSG_ERROR("ODBC headers sql.h and sqlext.h not found") fi dnl search for a library containing an ODBC function if test [ -n "${odbc_mgr}" ] ; then AC_SEARCH_LIBS(SQLTables, ${odbc_mgr}, , AC_MSG_ERROR("ODBC driver manager '${odbc_mgr}' not found")) else AC_SEARCH_LIBS(SQLTables, odbc odbc32 iodbc, , AC_MSG_ERROR("no ODBC driver manager found")) fi So we see that we end up in the else branch of the test for odbc_mgr. Scrolling back we see dnl A user-specifiable option odbc_mgr="" AC_ARG_WITH([odbc-manager], AC_HELP_STRING([--with-odbc-manager=MGR], [specify the ODBC manager, e.g. odbc or iodbc]), [odbc_mgr=$withval]) if test "$odbc_mgr" = "odbc" ; then AC_PATH_PROGS(ODBC_CONFIG, odbc_config) fi So this wants you to specify either (unix)odbc or (lib)iodbc explicitly, and if odbc was set, check for odbc_config. I have looked after RODBC for Debian since 2003 or so, and I think I switched from unixodbc to iodbc and back in that time, reflecting the state of the library at the time. I think what I would do now is to see which of libiodbc and unixodbc is present, and if it is the latter if setting it as argument to --with-odbc-manager helps some more. Dirk
https://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
Dirk, I did not realize libiodbc[1] is an alternative to unixODBC, how are you able to see this? I also did not realize I had both of them installed ... Uninstalling libiodbc, keeping unixODBC, adding the flag (I only suppose this is how the flag is added), does nothing: rasmus at iselin ~/src/RODBC % R CMD INSTALL RODBC --with-odbc-manager=odbc Warning: unknown option ?--with-odbc-manager=odbc? * installing to library ?/usr/home/rasmus/R/amd64-portbld-freebsd13.0-library/4.0? * installing *source* package ?RODBC? ... files ?configure?, ?configure.ac? have the wrong MD5 checksums ** using staged installation checking for gcc... cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking how to run the C preprocessor... cc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/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 sql.h usability... yes checking sql.h presence... yes checking for sql.h... yes checking sqlext.h usability... yes checking sqlext.h presence... yes checking for sqlext.h... yes checking for library containing SQLTables... no configure: error: "no ODBC driver manager found" ERROR: configuration failed for package ?RODBC? * removing ?/usr/home/rasmus/R/amd64-portbld-freebsd13.0-library/4.0/RODBC? The other way around, uninstalling unixODBC, keeping libiodbc, brings me one step backwards: rasmus at iselin ~/src/RODBC % R CMD INSTALL RODBC --with-odbc-manager=iodbc Warning: unknown option ?--with-odbc-manager=iodbc? * installing to library ?/usr/home/rasmus/R/amd64-portbld-freebsd13.0-library/4.0? * installing *source* package ?RODBC? ... files ?configure?, ?configure.ac? have the wrong MD5 checksums ** using staged installation checking for gcc... cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking how to run the C preprocessor... cc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/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 sql.h usability... no checking sql.h presence... no checking for sql.h... no checking sqlext.h usability... no checking sqlext.h presence... no checking for sqlext.h... no configure: error: "ODBC headers sql.h and sqlext.h not found" ERROR: configuration failed for package ?RODBC? * removing ?/usr/home/rasmus/R/amd64-portbld-freebsd13.0-library/4.0/RODBC? ... the sql.h and sqlext.h header files are there, libiodbc provides them both: root at iselin /usr/home/rasmus # pkg info -l libiodbc | egrep 'sql.h|sqlext.h' /usr/local/include/libiodbc/isql.h /usr/local/include/libiodbc/isqlext.h /usr/local/include/libiodbc/sql.h /usr/local/include/libiodbc/sqlext.h ... also when having unixodbc installed: root at iselin /usr/home/rasmus # pkg info -l unixODBC-2.3.9 | egrep 'sql.h|sqlext.h' /usr/local/include/sql.h /usr/local/include/sqlext.h Rasmus [1] https://www.freshports.org/databases/libiodbc/ -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 833 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-package-devel/attachments/20210330/60b98b81/attachment.sig>
On 30 March 2021 at 01:10, Rasmus Liland wrote:
| Dirk, I did not realize libiodbc[1] is an
| alternative to unixODBC, how are you
| able to see this?
By studing the sources and README of the package you are trying to build.
| I also did not realize I had both of
| them installed ...
|
| Uninstalling libiodbc, keeping unixODBC,
| adding the flag (I only suppose this is
| how the flag is added), does nothing:
|
| rasmus at iselin ~/src/RODBC % R CMD INSTALL RODBC --with-odbc-manager=odbc
| Warning: unknown option ?--with-odbc-manager=odbc?
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
These runs are not doing what you think they are doing. The switch applies
to calling 'configure' directly (which I recommend you do for debugging). For
builds from 'R CMD INSTALL ...' you need another indirection, see --help there.
If I were you, I'd try to mimick what 'configure' does and compile and link a
minimal C program against either of the two to demonstrate "you can". The
next step then is to make 'configure' do it too, ideally without switches.
Then the R package has a better-than-fair chance of installing.
Dirk
https://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org