Question: installing XML in linux
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16.4 years ago by
Mahbub Latif70
Mahbub Latif70 wrote:
Hi, I was trying to install XML package in a linux (dabian) machine and got the following error message. I am not sure whether there is any error in my linux installion. I appreciate suggestions to install XML properly in this machine. Thanks in advance. Mahbub. ######Errors#### $R CMD INSTALL -l /usr/local/lib/R/library/ XML_0.93-4.tar.gz * Installing *source* package 'XML' ... creating cache ./config.cache checking for gcc... gcc checking whether the C compiler (gcc ) works... yes checking whether the C compiler (gcc ) is a cross-compiler... no checking whether we are using GNU C... yes checking whether gcc accepts -g... yes checking how to run the C preprocessor... gcc -E checking for xml-config... no checking for libxml/parser.h... no checking for gnome-xml/parser.h... no checking for libxml/parser.h... (cached) no checking for gnome-xml/parser.h... (cached) no checking for libxml/parser.h... (cached) no Cannot find parser.h. Set the value of the environment variable LIBXML_INCDIR to point to where it can be found. ERROR: configuration failed for package 'XML' > version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 1 minor 7.0 year 2003 month 04 day 16 language R • 2.8k views ADD COMMENTlink modified 16.4 years ago by A.J. Rossini810 • written 16.4 years ago by Mahbub Latif70 Answer: installing XML in linux 0 16.4 years ago by Douglas Bates180 Douglas Bates180 wrote: You will need to install the Debian package libxml-dev before you can install the R XML package. Mahbub Latif <ahmlatif@yahoo.com> writes: > I was trying to install XML package in a linux > (dabian) machine and got the following error message. > I am not sure whether there is any error in my linux > installion. I appreciate suggestions to install XML > properly in this machine. > > Thanks in advance. > > Mahbub. > > ######Errors#### >$ R CMD INSTALL -l /usr/local/lib/R/library/ > XML_0.93-4.tar.gz > * Installing *source* package 'XML' ... > creating cache ./config.cache > checking for gcc... gcc > checking whether the C compiler (gcc ) works... yes > checking whether the C compiler (gcc ) is a > cross-compiler... no > checking whether we are using GNU C... yes > checking whether gcc accepts -g... yes > checking how to run the C preprocessor... gcc -E > checking for xml-config... no > checking for libxml/parser.h... no > checking for gnome-xml/parser.h... no > checking for libxml/parser.h... (cached) no > checking for gnome-xml/parser.h... (cached) no > checking for libxml/parser.h... (cached) no > Cannot find parser.h. Set the value of the environment > variable > LIBXML_INCDIR > to point to where it can be found. > ERROR: configuration failed for package 'XML'
Thanks a lot Prof Bates. One more thing... What Debian packages should I install to install R packages Rgraphviz and rhdf5? Mahbub. --- Douglas Bates <bates@stat.wisc.edu> wrote: > You will need to install the Debian package > libxml-dev before you can > install the R XML package. > > Mahbub Latif <ahmlatif@yahoo.com> writes: > > > I was trying to install XML package in a linux > > (dabian) machine and got the following error > message. > > I am not sure whether there is any error in my > linux > > installion. I appreciate suggestions to install > XML > > properly in this machine. > > > > Thanks in advance. > > > > Mahbub. > > > > ######Errors#### > > $R CMD INSTALL -l /usr/local/lib/R/library/ > > XML_0.93-4.tar.gz > > * Installing *source* package 'XML' ... > > creating cache ./config.cache > > checking for gcc... gcc > > checking whether the C compiler (gcc ) works... > yes > > checking whether the C compiler (gcc ) is a > > cross-compiler... no > > checking whether we are using GNU C... yes > > checking whether gcc accepts -g... yes > > checking how to run the C preprocessor... gcc -E > > checking for xml-config... no > > checking for libxml/parser.h... no > > checking for gnome-xml/parser.h... no > > checking for libxml/parser.h... (cached) no > > checking for gnome-xml/parser.h... (cached) no > > checking for libxml/parser.h... (cached) no > > Cannot find parser.h. Set the value of the > environment > > variable > > LIBXML_INCDIR > > to point to where it can be found. > > ERROR: configuration failed for package 'XML' > ADD REPLYlink written 16.4 years ago by Mahbub Latif70 On Mon, 9 Jun 2003, Mahbub Latif wrote: > Thanks a lot Prof Bates. One more thing... What Debian > packages should I install to install R packages > Rgraphviz and rhdf5? You need the Graphviz library installed: http://www.research.att.com/sw/tools/graphviz/download.html They have a debian package there, but it is probably not new enough as Rgraphviz requires a version of Graphviz newer then their last official release (and they only have up to 1.8.9 as debian package anyways). Your best bet is to download the current CVS snapshot at: http://www.graphviz.org/pub/graphviz/, and compile it normally. rhdf requires the HDF5 library to be installed: http://hdf.ncsa.uiuc.edu/HDF5/ Installation directions are available on their site. -J ADD REPLYlink written 16.4 years ago by Jeff Gentry3.9k On Mon, Jun 09, 2003 at 06:03:55AM -0700, Mahbub Latif wrote: > Thanks a lot Prof Bates. One more thing... What Debian > packages should I install to install R packages > Rgraphviz and rhdf5? For any given 'foo' I usually start by$ apt-cache search foo # may return lots $apt-cache search libfoo # more focussed for libraries In this case, assumimg you want standard hdf5 (and not the mpich and lam variants that are also available) and$ apt-get install libhdf5-serial-dev graphviz but I do not know if the graphviz package has all you need. One day we may have suitable .deb packages for this to make installation of complex CRAN / bioC packages a litte easier. Dirk -- Don't drink and derive. Alcohol and analysis don't mix.
On 9 Jun 2003, Douglas Bates wrote: > You will need to install the Debian package libxml-dev before you can > install the R XML package. and note that the package is really looking for 'libxml/parser.h'. On my machine, for example, parser.h is in /usr/include/libxml2/libxml/, so I have LIBXML_INCDIR=/usr/include/libxml2. -- Robert Burrows, PhD New England Biometrics rbb@nebiometrics.com
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16.4 years ago by
A.J. Rossini810
A.J. Rossini810 wrote:
Jeff Gentry <jgentry@jimmy.harvard.edu> writes: > On Mon, 9 Jun 2003, Mahbub Latif wrote: >> Thanks a lot Prof Bates. One more thing... What Debian >> packages should I install to install R packages >> Rgraphviz and rhdf5? > > You need the Graphviz library installed: > http://www.research.att.com/sw/tools/graphviz/download.html > > They have a debian package there, but it is probably not new enough as > Rgraphviz requires a version of Graphviz newer then their last official > release (and they only have up to 1.8.9 as debian package anyways). Your > best bet is to download the current CVS snapshot at: > http://www.graphviz.org/pub/graphviz/, and compile it normally. It's worse than that -- Rgraphviz needs the development libraries, and the Debian package doesn't really provide them. Yech. > rhdf requires the HDF5 library to be installed: > http://hdf.ncsa.uiuc.edu/HDF5/ > Installation directions are available on their site. On the other hand, this is simple for debian. apt-get install libhdf5-serial-dev unless you really want the MPI or PVM versions. best, -tony -- A.J. Rossini / rossini@u.washington.edu / rossini@scharp.org Biomedical/Health Informatics and Biostatistics, University of Washington. Biostatistics, HVTN/SCHARP, Fred Hutchinson Cancer Research Center. FHCRC: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachments ... {{dropped}}
> apt-get install libhdf5-serial-dev To install libhdf5 what I am getting.... $apt-get install libhdf5-serial-dev libhdf5-serial-dev: Depends: libhdf5-serial (= 1.4.5-2) but it is not going to be installed then I try...$ apt-get install libhdf5-serial libhdf5-serial: Depends: libc6 (>= 2.3.1-1) but 2.2.5-11.5 is to be installed That means I need libc6 2.3.1-1 or higher. How can I get that? Mahbub. > > unless you really want the MPI or PVM versions. > > best, > -tony > > -- > A.J. Rossini / rossini@u.washington.edu / > rossini@scharp.org > Biomedical/Health Informatics and Biostatistics, > University of Washington. > Biostatistics, HVTN/SCHARP, Fred Hutchinson Cancer > Research Center. > FHCRC: 206-667-7025 (fax=4812)|Voicemail is pretty > sketchy/use Email > > CONFIDENTIALITY NOTICE: This e-mail message and any > attachments may be > confidential and privileged. If you received this > message in error, > please destroy it and notify the sender. Thank you.

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