XML package cannot be installed
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Guest User ★ 12k
@guest-user-4897
Last seen 8.3 years ago
in order to install the "charm" package in R in my laptop I installed the dependent pakages first. But during the process of installing the package XML", I encounted an error below. Could you help me out? Thanks. -- output of sessionInfo(): 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 ???/usr/lib64/R/library/XML sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.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_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- Sent via the guest posting facility at bioconductor.org.
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@david-westergaard-5119
Last seen 8.3 years ago
Dear Wayne, XML is complaining it cannot find xml2-config (From Cannot find xml2-config). You need to have the libxml2 package installed on your system. If you are running a debian flavor, you can get it from aptitude. I'm not familiar with redhat, but I guess it should be in whatever packaging system it uses. Best, David 2012/7/28 Wayne Zhang [guest] <guest at="" bioconductor.org="">: > > in order to install the "charm" package in R in my laptop I installed the dependent pakages first. But during the process of installing the package XML", I encounted an error below. > Could you help me out? Thanks. > > -- output of sessionInfo(): > > 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 ???/usr/lib64/R/library/XML > > > > > sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-redhat-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.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_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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nabiyogesh ▴ 10
@nabiyogesh-11718
Last seen 8 weeks ago
United Kingdom

During DESeq installation I am also getting same error:

Cannot find xml2-config
ERROR: configuration failed for package ‘XML’
* removing ‘/usr/lib64/R/library/XML’
* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/usr/lib64/R/library/RCurl’
ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘annotate’
* removing ‘/usr/lib64/R/library/annotate’
ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
* removing ‘/usr/lib64/R/library/genefilter’
ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’
* removing ‘/usr/lib64/R/library/geneplotter’
ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq’
* removing ‘/usr/lib64/R/library/DESeq’

The downloaded source packages are in
        ‘/tmp/RtmpsMJs05/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘XML’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RCurl’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘annotate’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘genefilter’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘geneplotter’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘DESeq’ had non-zero exit status

Can you suggest how I can download and Installed libxml2 package to cento OS 7 Platform.

Thanks

Yogesh

Thanks

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dnf install libxml2-devel 
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@nileshiiita-15471
Last seen 4.7 years ago

You need to install "libxml2-devel" if you are on Fedora, Centos or Redhat using following command.

dnf install libxml2-devel 

Thanks.

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