Your error says the XML package was not installed because you are missing
"xml2-config"... if you search the web for that term you will find
that your operating system needs to have libxml2 installed, including the
development tools. There is a SystemRequirements entry on the CRAN web page for
the XML package mentions libxml2.
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Sent from my phone. Please excuse my brevity.
On July 15, 2015 3:09:43 AM PDT, giovanni_gmail <giovanni.franzo1 at
gmail.com> wrote:>dear all,
>sorry for the naive question,
>I'm trying to install (in R version 3.2.1 (2015-06-18)) the
"ips"
>package for phylogenetic analysis.
>However I get the following message:
>
>
> > install.packages("ips",dependencies = T)
>Installing package into
>?/home/giovanni/R/x86_64-pc-linux-gnu-library/3.2?
>(as ?lib? is unspecified)
>also installing the dependency ?XML?
>
>provo con l'URL
>'https://cran.rstudio.com/src/contrib/XML_3.98-1.3.tar.gz'
>Content type 'application/x-gzip' length 1607725 bytes (1.5 MB)
>=================================================>downloaded 1.5 MB
>
>provo con l'URL
'https://cran.rstudio.com/src/contrib/ips_0.0-7.tar.gz'
>Content type 'application/x-gzip' length 62904 bytes (61 KB)
>=================================================>downloaded 61 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
>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/giovanni/R/x86_64-pc-linux-gnu-library/3.2/XML?
>Warning in install.packages :
> installation of package ?XML? had non-zero exit status
>ERROR: dependency ?XML? is not available for package ?ips?
>* removing ?/home/giovanni/R/x86_64-pc-linux-gnu-library/3.2/ips?
>Warning in install.packages :
> installation of package ?ips? had non-zero exit status
>
>The downloaded source packages are in
> ?/tmp/RtmpbTmMtc/downloaded_packages?
>
>can anybody help me?
>best regards
>Giovanni
>
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