Good morning, I have some problems installing RODBC to R in a linux cluster. My R version is: R version 2.12.0 (2010-10-15) Platform: x86_64-unknown-linux-gnu (64-bit) I get the following error:> install.packages('RODBC')Installing package(s) into '/home/jorgehou/R/x86_64-unknown-linux-gnu-library/2.12' (as 'lib' is unspecified) trying URL 'http://stat.ethz.ch/CRAN/src/contrib/RODBC_1.3-2.tar.gz' Content type 'application/x-gzip' length 1108358 bytes (1.1 Mb) opened URL =================================================downloaded 1.1 Mb * installing *source* package 'RODBC' ... checking for gcc... gcc -std=gnu99 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 -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -std=gnu99 -E 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 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 '/home/jorgehou/R/x86_64-unknown-linux-gnu-library/2.12/RODBC' The downloaded packages are in '/tmp/Rtmpgb1Nxz/downloaded_packages' Warning message: In install.packages("RODBC") : installation of package 'RODBC' had non-zero exit status I found some info on it here: http://r.789695.n4.nabble.com/Problem-installing-RODBC-td2016736.html but how should I use it??? (Yes, I am very novice to Linux (and R) so it might be a stupid question....) Thanks! Jørgen -- Jørgen Blystad Houge MSc Student Industrial Economics NTNU, Norway [[alternative HTML version deleted]]
Please read the RODBC manual (which comes with it). You (or the cluster owner) need to install unixODBC, and if installing from RPMs etc, something like unixODBC-devel. Please also note the R posting guide - no HTML mail, use an appropriate list (R-sig-db or R-devel here as this is about non-R programming). On Thu, 4 Nov 2010, J?rgen Blystad Houge wrote:> Good morning, > > I have some problems installing RODBC to R in a linux cluster. My R version > is: > R version 2.12.0 (2010-10-15) > Platform: x86_64-unknown-linux-gnu (64-bit) > > I get the following error: >> install.packages('RODBC') > Installing package(s) into > '/home/jorgehou/R/x86_64-unknown-linux-gnu-library/2.12' > (as 'lib' is unspecified) > trying URL 'http://stat.ethz.ch/CRAN/src/contrib/RODBC_1.3-2.tar.gz' > Content type 'application/x-gzip' length 1108358 bytes (1.1 Mb) > opened URL > =================================================> downloaded 1.1 Mb > > * installing *source* package 'RODBC' ... > checking for gcc... gcc -std=gnu99 > 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 -std=gnu99 accepts -g... yes > checking for gcc -std=gnu99 option to accept ANSI C... none needed > checking how to run the C preprocessor... gcc -std=gnu99 -E > 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 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 '/home/jorgehou/R/x86_64-unknown-linux-gnu-library/2.12/RODBC' > > The downloaded packages are in > '/tmp/Rtmpgb1Nxz/downloaded_packages' > Warning message: > In install.packages("RODBC") : > installation of package 'RODBC' had non-zero exit status > > I found some info on it here: > http://r.789695.n4.nabble.com/Problem-installing-RODBC-td2016736.html but > how should I use it??? > > (Yes, I am very novice to Linux (and R) so it might be a stupid > question....) > > Thanks! > J?rgen > -- > J?rgen Blystad Houge > MSc Student Industrial Economics NTNU, Norway > > [[alternative HTML version deleted]] > >-- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
On 11/04/2010 08:14 AM, J?rgen Blystad Houge wrote: ...> '/tmp/Rtmpgb1Nxz/downloaded_packages' > Warning message: > In install.packages("RODBC") : > installation of package 'RODBC' had non-zero exit status > > I found some info on it here: > http://r.789695.n4.nabble.com/Problem-installing-RODBC-td2016736.html but > how should I use it??? > > (Yes, I am very novice to Linux (and R) so it might be a stupid > question....)Well, the answer is in the output:> configure: error: "ODBC headers sql.h and sqlext.h not found"That's an installation issue with ODBC, not an R issue as such. Usually a development package is missing, but exactly which one depends on your particular flavour of Linux. In Fedora 13, it is here: $ rpm -qf /usr/include/sqlext.h unixODBC-devel-2.2.14-12.fc13.i686 so the unixODBC-devel package is required. In e.g. Ubuntu, it is -er- somewhere else... -- Peter Dalgaard Center for Statistics, Copenhagen Business School Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com