Re: [R] RODBC installation: error message

[Marc Schwartz]

Hi Gregory,

See below.

On Jan 5, 2012, at 4:20 PM, gregory benison wrote:

 As Duncan noted, the message is pretty clear in that the ODBC header files 
 are missing, which are required to compile RODBC from source. On RH based 
 Linuxen, this requires the installation of the unixODBC-devel RPM, much as 
 one would need to have other *-devel RPMs (eg. readline-devel) installed for 
 compiling many applications from source.
 
 
 Since a lot of R users may not be familiar with these header files, I
 think the configure script could go a step further in explaining why
 it was looking for these headers (to find an installed ODBC driver
 manager), and that it didn't find one.  To illustrate what I mean,
 here is the result of running R CMD INSTALL on a system lacking an
 installed dsm where I swapped the order of the tests in configure.ac
 (see patch below) such that the library tests come before the header
 tests:
 
 * installing *source* package 'RODBC' ...
 checking for library containing SQLTables... no
 configure: error: no ODBC driver manager found
 ERROR: configuration failed for package 'RODBC'
 
 To me, that is a more helpful error message, because it makes it clear
 that you need to install an ODBC driver manager.

snipped other content

To split hairs, there are two issues at play here, irrespective of the ordering 
of the tests:

1. If you do not have unixODBC installed, you will get an error message 
regarding a missing ODBC driver manager, if as you have done here, that test is 
first rather than second.

2. If you have unixODBC installed (so you pass the first test in your 
scenario), but do not have the 'devel' part, which is a separate install on 
most Linuxen with package managers (RHEL/CentOS, Fedora, Debian and derivatives 
like Ubuntu and Mint, etc.), you will still get the error message regarding the 
missing header files. That is an entirely different error than missing the 
actual ODBC driver manager.

So you can argue about the ordering of the tests, but the end result is the 
same. Only if you have some knowledge about compiling source code (on ANY 
operating system), will you understand the meaning of missing header files AND 
only if you have some lower level knowledge of development on Linuxen 
specifically, will you know that the header files are contained in a separate 
binary package that needs to be installed as well, the details of which will be 
specific to the Linux distribution that you have chosen to install.

On top of that, if as with most Linuxen today, you don't have the software 
development packages installed (you are a naive user of Linux and only did a 
default install of the distribution), you won't have compilers and other 
associated tools (eg. make, etc.) installed either. At some point, the user has 
to be responsible for obtaining the requisite knowledge of their operating 
system, independent of the use of R. Despite the protestations by some on the 
web that their grandmothers are running Linux, it is still largely a geek's 
platform (with a 1% to 1.5% marketshare on the desktop) and due to the 
marketplace fragmentation of the plethora of distributions and desktop 
environments, further requires distribution and even version specific knowledge 
as well.

As I noted earlier, if you are going to use Linux, you are generally going to 
be expected to have a more technical level of knowledge than somebody who is 
running Windows or OSX, where for the most part, one can install pre-compiled 
binary packages from CRAN, thanks in large measure to folks like Kurt, Uwe, 
Duncan, Simon and Prof. Ripley (I may be missing others) who have taken the 
time over the years to put the testing and build infrastructure in place to 
automate much of that process.

Since there are over 3,500 packages on CRAN and some proportion (I don't know 
the number) have C/C++ and/or FORTRAN code in them, which will require 
compilation when installing source packages using either install.packages() or 
R CMD INSTALL on Linuxen, addressing RODBC in isolation is ultimately not 
helpful, since like most CRAN packages, it has a finite audience of users (me 
being very thankful to Prof. Ripley to be one of them).

I cannot speak for Prof. Ripley here, but since you seem to have the requisite 
skills, he may be open to accepting a patch against his package that would 
narrowly address the issue that you raise.

However, that does not change the defacto behavior for all of the other CRAN 
packages that will have similar requirements when being installed from source 
and will, as is the case with Linux generally, output relatively terse error 
messages when faced with these kinds of issues.

Also as Duncan noted, perhaps there may be a better mechanism in gaining access 
to install time requirements for CRAN packages. In the case of RODBC, Prof. 
Ripley has taken the time to create a vignette which covers much of this 
material. That is directly available from the CRAN page for the package, 

Re: [R] RODBC installation: error message

[gregory benison]

 1. If you do not have unixODBC installed, you will get an error message 
 regarding a missing ODBC driver manager, if as you have done here, that test 
 is first rather than second.

If the test for the headers comes first, and no driver manager is
installed, configure exits with an error before the library test is
run (hence the error message regarding a missing driver manager is not
displayed).

 I cannot speak for Prof. Ripley here, but since you seem to have the 
 requisite skills, he may be open to accepting a patch against his package 
 that would narrowly address the issue that you raise.


OK, here's my shot at such a patch (below), together with the
resulting configure output in cases where the library or the headers
are missing.  I realize that there are matters of style preference
here, that this approach errs on the side of verbosity rather than
terseness, and that it's entirely up to the R package maintainers
which style to adopt.

Thanks for the replies!

Greg

 Case 1, no ODBC driver manager installed =

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
checking for library containing SQLTables... no
configure: error:
No ODBC driver manager found;
see section Installation in inst/doc/RODBC.pdf
(also at http://cran.r-project.org/web/packages/RODBC/vignettes/RODBC.pdf)
ERROR: configuration failed for package 'RODBC'

== Case 2, driver manager installed but no headers 

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
checking for library containing SQLTables... -lodbc
configure: error:
Found ODBC driver manager library (-lodbc),
but not required ODBC headers sql.h and sqlext.h.
(Need -devel version of ODBC driver manager?)

ERROR: configuration failed for package 'RODBC'

= patch follows 

diff --git a/configure.ac b/configure.ac
index 8f9fc6a..8661e8f 100644
--- a/configure.ac
+++ b/configure.ac
@@ -64,10 +64,6 @@ CPPFLAGS=${CPPFLAGS} ${RODBC_CPPFLAGS}

 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
@@ -75,9 +71,23 @@ if test [ -n ${odbc_mgr} ] ; then
 AC_MSG_ERROR(ODBC driver manager '${odbc_mgr}' not found))
 else
   AC_SEARCH_LIBS(SQLTables, odbc odbc32 iodbc, ,
-AC_MSG_ERROR(no ODBC driver manager found))
+AC_MSG_ERROR([
+No ODBC driver manager found;
+see section Installation in inst/doc/RODBC.pdf
+(also at http://cran.r-project.org/web/packages/RODBC/vignettes/RODBC.pdf)]))
+fi
+
+dnl Exit with error if ODBC headers were not found
+if test ${ac_cv_header_sql_h} = no ||
+   test ${ac_cv_header_sqlext_h} = no; then
+   AC_MSG_ERROR([
+Found ODBC driver manager library ($ac_cv_search_SQLTables),
+but not required ODBC headers sql.h and sqlext.h.
+(Need -devel version of ODBC driver manager?)
+])
 fi

+
 dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they are defined.
 AC_CHECK_TYPES([SQLLEN, SQLULEN], , , [# include sql.h])
 dnl for unixODBC header

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Re: [R] RODBC installation: error message

[gregory benison]

 As Duncan noted, the message is pretty clear in that the ODBC header files 
 are missing, which are required to compile RODBC from source. On RH based 
 Linuxen, this requires the installation of the unixODBC-devel RPM, much as 
 one would need to have other *-devel RPMs (eg. readline-devel) installed for 
 compiling many applications from source.


Since a lot of R users may not be familiar with these header files, I
think the configure script could go a step further in explaining why
it was looking for these headers (to find an installed ODBC driver
manager), and that it didn't find one.  To illustrate what I mean,
here is the result of running R CMD INSTALL on a system lacking an
installed dsm where I swapped the order of the tests in configure.ac
(see patch below) such that the library tests come before the header
tests:

 * installing *source* package 'RODBC' ...
 checking for library containing SQLTables... no
 configure: error: no ODBC driver manager found
 ERROR: configuration failed for package 'RODBC'

To me, that is a more helpful error message, because it makes it clear
that you need to install an ODBC driver manager.

Another example is found in the configure script for
mysql-connector-odbc.  Like RODBC, it requires an installed driver
manager including header files.  It can use either unixODBC or iodbc.
Here is the result of running its configure script, without arguments,
on a system without an installed driver manager:

...
checking if driver should be linked against odbcinst library... yes
checking for iodbc-config... no
checking for SQL_ATTR_UNIXODBC_VERSION in sqlext.h... not found
configure: error: no suitable driver manager selected or found

Again, I think that is a better error message, if only because it
includes the phrase driver manager.

== patch 1 -- swap order of tests in configure.ac ===

diff --git a/configure.ac b/configure.ac
index 8f9fc6a..997da8a 100644
--- a/configure.ac
+++ b/configure.ac
@@ -62,13 +62,6 @@ if test -n ${ODBC_CONFIG}; then
 fi
 CPPFLAGS=${CPPFLAGS} ${RODBC_CPPFLAGS}

-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}, ,
@@ -78,6 +71,13 @@ else
 AC_MSG_ERROR(no ODBC driver manager found))
 fi

+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 for 64-bit ODBC need SQL[U]LEN, and it is unclear where they are defined.
 AC_CHECK_TYPES([SQLLEN, SQLULEN], , , [# include sql.h])
 dnl for unixODBC header

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Re: [R] RODBC installation: error message

[Duncan Murdoch]

On 12-01-03 2:39 PM, gregory benison wrote:

If one attempts to install RODBC (via install.packages('RODBC'))
without having an ODBC driver installed, this error message results:

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/lib/R/library/RODBC'

Yes, the RODBC README describes the needed prerequisites, but for
someone who just wants to use RODBC and tries to install it in the
most natural way, i.e. from R Installation and Administration:


For most users it suffices to call ‘install.packages(pkgname)’


the result is the above error message, which could be more informative.


RODBC is not my package, but I can say from experience that it's hard to 
put together error messages that satisfy everyone.  Here, the problem is 
that configuration couldn't find the files sql.h and sqlext.h, and 
that's what the error says.  Not installing ODBC is one reason that 
might happen; another is installing it improperly, and there are 
probably others, too.  I think it's best if the error messages describe 
the problems; trying to diagnose the solution is something that needs 
human intervention.


One thing R could do better is to provide a standard way to view README 
and similar files before installing a package.  That might have helped here.


Duncan Murdoch



Greg Benison

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Re: [R] RODBC installation: error message

[Milan Bouchet-Valat]

Le mardi 03 janvier 2012 à 11:39 -0800, gregory benison a écrit :
 If one attempts to install RODBC (via install.packages('RODBC'))
 without having an ODBC driver installed, this error message results:
 
 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/lib/R/library/RODBC'
 
 Yes, the RODBC README describes the needed prerequisites, but for
 someone who just wants to use RODBC and tries to install it in the
 most natural way, i.e. from R Installation and Administration:
 
  For most users it suffices to call ‘install.packages(pkgname)’
I guess this applies only to users installing binary packages. If you
build packages from source, the build system runs ./configure, which
returns this automated message.

Ideally, you shouldn't need to build packages from source when all you
want is use them... (Distributions could ship binary packages that R
would detect and install automatically?)


Cheers

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Re: [R] RODBC installation: error message

[Marc Schwartz]

On Jan 4, 2012, at 8:02 AM, Milan Bouchet-Valat wrote:

 Le mardi 03 janvier 2012 à 11:39 -0800, gregory benison a écrit :
 If one attempts to install RODBC (via install.packages('RODBC'))
 without having an ODBC driver installed, this error message results:
 
 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/lib/R/library/RODBC'
 
 Yes, the RODBC README describes the needed prerequisites, but for
 someone who just wants to use RODBC and tries to install it in the
 most natural way, i.e. from R Installation and Administration:
 
 For most users it suffices to call ‘install.packages(pkgname)’
 I guess this applies only to users installing binary packages. If you
 build packages from source, the build system runs ./configure, which
 returns this automated message.
 
 Ideally, you shouldn't need to build packages from source when all you
 want is use them... (Distributions could ship binary packages that R
 would detect and install automatically?)

That is up to the resources available for each Linux distribution. Debian based 
distributions have done a better job of this for R than most, largely due to 
Dirk et al making the commitment and taking the time over the years to support 
a large number of CRAN packages via apt. 

However, there is not the same level of commitment for others (eg. Fedora, 
RHEL/CentOS, etc.), leaving most others to install from source, thus requiring 
users to manually satisfy pre-requisites for installation. R itself is 
available for installation via binary, but the selection of CRAN packages is 
much more limited.

As Duncan noted, the message is pretty clear in that the ODBC header files are 
missing, which are required to compile RODBC from source. On RH based Linuxen, 
this requires the installation of the unixODBC-devel RPM, much as one would 
need to have other *-devel RPMs (eg. readline-devel) installed for compiling 
many applications from source. 

In years past, the *-devel RPMs were frequently installed by default, but as 
the Linux community has evolved, current defaults tend to not install 
'development' related packages, which include compilers and related tools. This 
allows for smaller footprints for the installed OS for non-technical end users.

If you are going to use R on Linux, you need to be prepared to get your hands 
dirty under the hood at a lower level than if you are using Windows or OSX. 

In this particular case, Prof. Ripley has taken great pains to provide 
documents to guide the user on the installation of not only RODBC itself, but 
other components of the ODBC ecosystem to get things working.

Regards,

Marc Schwartz

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Re: [R] RODBC installation: error message

[gregory benison]

 One thing R could do better is to provide a standard way to view README and
 similar files before installing a package.  That might have helped here.


Agreed... right now, the R documentation points to a straightforward,
one-line way to download and install packages from the R command line,
but not to a similarly straightforward way to view a package's README
content (as far as I can tell).

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[R] RODBC installation: error message

[gregory benison]

If one attempts to install RODBC (via install.packages('RODBC'))
without having an ODBC driver installed, this error message results:

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/lib/R/library/RODBC'

Yes, the RODBC README describes the needed prerequisites, but for
someone who just wants to use RODBC and tries to install it in the
most natural way, i.e. from R Installation and Administration:

 For most users it suffices to call ‘install.packages(pkgname)’

the result is the above error message, which could be more informative.

Greg Benison

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