I am getting what appears to be an Unbuntu level error in trying to install the
XML package.
Both commands:
install.packages("XML:)
install.packages("XML", dependencies = TRUE)
give an error .
The full installation script is below but the problem to my very inexperenced
eye seems to be here:
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package ?XML?
I seem to have libxml1 version 2.7.8defg.1ubuntu installed if this is relevent.
Any suggestions would be gratefully received.
Ubuntu 12.04
sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: i686-pc-linux-gnu (32-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tcltk_2.15.1 tools_2.15.1
Full installation script.
================================================================================================================downloaded
901 Kb
* installing *source* package ?XML? ...
** package ?XML? successfully unpacked and MD5 sums checked
checking for gcc... gcc
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 accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
No ability to remove finalizers on externalptr objects in this verison of R
checking for sed... /bin/sed
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package ?XML?
* removing ?/home/john/R/i686-pc-linux-gnu-library/2.15/XML?
The downloaded source packages are in
?/tmp/RtmpC85FTD/downloaded_packages?
Warning message:
In install.packages("XML") :
installation of package ?XML? had non-zero exit status
==========================================================John Kane
Kingston ON Canada
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On 07/21/2012 10:42 AM, John Kane wrote:> I am getting what appears to be an Unbuntu level error in trying to install the > XML package. > > Both commands: > install.packages("XML:) > install.packages("XML", dependencies = TRUE) > give an error . > > The full installation script is below but the problem to my very inexperenced eye seems to be here: > > checking for pkg-config... /usr/bin/pkg-config > checking for xml2-config... no > Cannot find xml2-config > ERROR: configuration failed for package ?XML? > > I seem to have libxml1 version 2.7.8defg.1ubuntu installed if this is relevent. > > Any suggestions would be gratefully received. > > Ubuntu 12.04 > sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: i686-pc-linux-gnu (32-bit)John, The Ubuntu package you need to install is "libxml2-dev". Or you could install "r-cran-xml" from the cran2deb4ubuntu PPA and it will resolve all the dependencies for you. Details here: https://launchpad.net/~marutter/+archive/c2d4u Hope this helps, Michael -- Dr. Michael A. Rutter School of Science Penn State Erie, The Behrend College 4205 College Drive Erie, PA 16563 http://math.bd.psu.edu/faculty/rutter mar36 at psu.edu
Thank you Michael. It took all of two minutes to install "libxml2-dev" and XML and it seems to be running John Kane Kingston ON Canada> -----Original Message----- > From: mar36 at psu.edu > Sent: Sat, 21 Jul 2012 11:00:42 -0400 > To: jrkrideau at inbox.com > Subject: Re: [R-sig-Debian] package XML does not load in R 2.15.1 > > > > On 07/21/2012 10:42 AM, John Kane wrote: >> I am getting what appears to be an Unbuntu level error in trying to >> install the >> XML package. >> >> Both commands: >> install.packages("XML:) >> install.packages("XML", dependencies = TRUE) >> give an error . >> >> The full installation script is below but the problem to my very >> inexperenced eye seems to be here: >> >> checking for pkg-config... /usr/bin/pkg-config >> checking for xml2-config... no >> Cannot find xml2-config >> ERROR: configuration failed for package ?XML? >> >> I seem to have libxml1 version 2.7.8defg.1ubuntu installed if this is >> relevent. >> >> Any suggestions would be gratefully received. >> >> Ubuntu 12.04 >> sessionInfo() >> R version 2.15.1 (2012-06-22) >> Platform: i686-pc-linux-gnu (32-bit) > > John, > > The Ubuntu package you need to install is "libxml2-dev". Or you could > install "r-cran-xml" from the cran2deb4ubuntu PPA and it will resolve > all the dependencies for you. Details here: > > https://launchpad.net/~marutter/+archive/c2d4u > > Hope this helps, > Michael > > > > -- > Dr. Michael A. Rutter > School of Science > Penn State Erie, The Behrend College > 4205 College Drive > Erie, PA 16563 > http://math.bd.psu.edu/faculty/rutter > mar36 at psu.edu____________________________________________________________ Publish your photos in seconds for FREE TRY IM TOOLPACK at http://www.imtoolpack.com/default.aspx?rc=if4
Dirk Eddelbuettel
2012-Jul-21 16:48 UTC
[R-sig-Debian] package XML does not load in R 2.15.1
On 21 July 2012 at 06:42, John Kane wrote:
| I am getting what appears to be an Unbuntu level error in trying to install
the
| XML package.
You are making your life too complicated as there is a prepackaged version:
edd at max:~$ dpkg -s r-cran-xml
Package: r-cran-xml
Status: install ok installed
Priority: optional
Section: gnu-r
Installed-Size: 2363
Maintainer: Ubuntu Developers <ubuntu-devel-discuss at lists.ubuntu.com>
Architecture: amd64
Version: 3.6-2-1
Replaces: r-xml
Depends: r-base-core (>= 2.14.0), libc6 (>= 2.4), libxml2 (>= 2.7.4)
Conflicts: r-xml
Description: GNU R package for XML parsing and generation
This package provides facilities for the R language to
.
* parse XML files, URLs and strings, using either the DOM (Document
Object Model)/tree-based approach, or the event-driven SAX (Simple
API for XML) mechanism;
* generate XML content to buffers, files, URLs, and internal XML trees;
* read DTDs as R objects.
Original-Maintainer: Dirk Eddelbuettel <edd at debian.org>
Homepage: http://www.omegahat.org/RSXML
which works just fine:
edd at max:~$ r -e 'library(XML); print("All good")'
Loading required package: methods
Loading required package: utils
[1] "All good"
edd at max:~$
Dirk
--
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
I am makingmy life too complicated? I must be misunderstanding something john at john-K53U:~$ dpkg -s r-cran-xml Package `r-cran-xml' is not installed and no info is available. Use dpkg --info (= dpkg-deb --info) to examine archive files, and dpkg --contents (= dpkg-deb --contents) to list their contents. Should I be installing this rather than the XML package (which seems to be installed. John Kane Kingston ON Canada> -----Original Message----- > From: edd at debian.org > Sent: Sat, 21 Jul 2012 11:48:56 -0500 > To: jrkrideau at inbox.com > Subject: Re: [R-sig-Debian] package XML does not load in R 2.15.1 > > > On 21 July 2012 at 06:42, John Kane wrote: > | I am getting what appears to be an Unbuntu level error in trying to > install the > | XML package. > > You are making your life too complicated as there is a prepackaged > version: > > edd at max:~$ dpkg -s r-cran-xml > Package: r-cran-xml > Status: install ok installed > Priority: optional > Section: gnu-r > Installed-Size: 2363 > Maintainer: Ubuntu Developers <ubuntu-devel-discuss at lists.ubuntu.com> > Architecture: amd64 > Version: 3.6-2-1 > Replaces: r-xml > Depends: r-base-core (>= 2.14.0), libc6 (>= 2.4), libxml2 (>= 2.7.4) > Conflicts: r-xml > Description: GNU R package for XML parsing and generation > This package provides facilities for the R language to > . > * parse XML files, URLs and strings, using either the DOM (Document > Object Model)/tree-based approach, or the event-driven SAX (Simple > API for XML) mechanism; > * generate XML content to buffers, files, URLs, and internal XML trees; > * read DTDs as R objects. > Original-Maintainer: Dirk Eddelbuettel <edd at debian.org> > Homepage: http://www.omegahat.org/RSXML > > > which works just fine: > > > edd at max:~$ r -e 'library(XML); print("All good")' > Loading required package: methods > Loading required package: utils > [1] "All good" > edd at max:~$ > > > Dirk > > -- > Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com____________________________________________________________ FREE ONLINE PHOTOSHARING - Share your photos online with your friends and family! Visit http://www.inbox.com/photosharing to find out more!
Okay l see what you mean. I had already installed XML after adding libxsm12-dev when I responded to you. Yes it probably would have been easier kyour way. Thanks John Kane Kingston ON Canada> -----Original Message----- > From: edd at debian.org > Sent: Sat, 21 Jul 2012 12:14:48 -0500 > To: jrkrideau at inbox.com > Subject: Re: [R-sig-Debian] package XML does not load in R 2.15.1 > > > On 21 July 2012 at 09:00, John Kane wrote: > | I am makingmy life too complicated? > | > | I must be misunderstanding something > | > | john at john-K53U:~$ dpkg -s r-cran-xml > | Package `r-cran-xml' is not installed and no info is available. > | Use dpkg --info (= dpkg-deb --info) to examine archive files, > | and dpkg --contents (= dpkg-deb --contents) to list their contents. > > "dpkg -s" reports the status of __installed packages__ so you are little > circular here. It only reports that you don't have it installed. > > Try to search for packages via e.g. "apt-cache search r-cran-" > > | Should I be installing this rather than the XML package (which seems to > be installed. > > Well as you failed to install from source on your own, installing a > ready-made binary would seem easier to me, but it is your call. > > Dirk > > -- > Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com____________________________________________________________ FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks & orcas on your desktop!