[R] Re: [BioC] installing XML in linux
You will need to install the Debian package libxml-dev before you can install the R XML package. Mahbub Latif [EMAIL PROTECTED] 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' __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Re: [BioC] installing XML in linux
Thanks a lot Prof Bates. One more thing... What Debian packages should I install to install R packages Rgraphviz and rhdf5? Mahbub. --- Douglas Bates [EMAIL PROTECTED] wrote: You will need to install the Debian package libxml-dev before you can install the R XML package. Mahbub Latif [EMAIL PROTECTED] 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' __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Re: [BioC] installing XML in linux
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 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Re: [BioC] installing XML in linux
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. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Re: [BioC] installing XML in linux
Robert Burrows wrote: 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. Thanks for pointing out the fact that one can set LIBXML_INCDIR and it is definitely a good thing. In this particular case, however, I hope that the configuration should work automatically without any additional manual settings. The configure script should be using xml2-config --cflags and that should return -I/usr/include/libxml2 and libxml/parser.h is then duly found within that directory. If this isn't the case, I'd be happy to find out and change things. Unfortunately, conflicts between libxml and libxml2, use of libxml/ and gnome-xml/, etc... make this a complex configuration. -- Robert Burrows, PhD New England Biometrics [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help -- ___ Duncan Temple Lang[EMAIL PROTECTED] Bell Labs, Lucent Technologiesoffice: (908)582-3217 700 Mountain Avenue, Room 2C-259 fax:(908)582-3340 Murray Hill, NJ 07974-2070 http://cm.bell-labs.com/stat/duncan __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Re: [BioC] installing XML in linux
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 / [EMAIL PROTECTED] / [EMAIL PROTECTED] 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. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Re: [BioC] installing XML in linux
Mahbub Latif [EMAIL PROTECTED] wrote: 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? libc6-2.3.1 is in testing (sarge), while libc6-2.2.5 is still in the stable (woody) distribution of debian. What confuses me a bit from your message is that libhdf5 is _not_ in woody (libhdf4 is), and that the version that you are trying to install is not even in sarge. On a sarge system, the current package libhdf5-serial-dev has version number 1.4.4-0.2 and depends on libc6-2.2.5-13, not the newer libc6-2.3.1. In other words, it looks like your /etc/apt/sources.list points towards the unstable (sid) distribution, while your debian system has not been upgraded. My 1ยข piece of advice would be to steer away from sid until you master the intricacies of the debian packaging system. Aside from fixing this mess, you may just retrieve the sources and compile them against your current libc. -- Philippe __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
