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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package XML does not load in R 2.15.1
7 messages · Michael Rutter, Dirk Eddelbuettel, John Kane
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
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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
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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
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
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