Question

installing XML in linux

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Mahbub Latif ▴ 70

@mahbub-latif-268

Last seen 10.3 years ago

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

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ADD COMMENT • link updated 21.5 years ago by A.J. Rossini ▴ 810 • written 21.5 years ago by Mahbub Latif ▴ 70

score 0 · Answer 1 · 2003-06-09

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Douglas Bates ▴ 180

@douglas-bates-5

Last seen 10.3 years ago

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 COMMENT • link 21.5 years ago Douglas Bates ▴ 180

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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 REPLY • link 21.5 years ago Mahbub Latif ▴ 70

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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 REPLY • link 21.5 years ago Jeff Gentry ★ 3.9k

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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.

ADD REPLY • link 21.5 years ago Dirk Eddelbuettel ▴ 80

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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

ADD REPLY • link 21.5 years ago Robert Burrows ▴ 10

score 0 · Answer 2 · 2003-06-09

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}}