Can't install DESeq2 because of libxml
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Fátima • 0
@cde63321
Last seen 23 days ago
United Kingdom

I need to use DESeq2 in R so I tried installing it and it does not work. I looked online and it seemed to be a problem with XML so i tried to install it, but the same error arieses. Can you, please help? thank you.


Using libxml2.*
checking for gzopen in -lz... yes
checking for xmlParseFile in -lxml2... yes
You are trying to use a version 2.* edition of libxml
but an incompatible library. The header files and library seem to be
mismatched. If you have specified LIBXML_INCDIR, make certain to also
specify an appropriate LIBXML_LIBDIR if the libxml2 library is not in the default
directories.
ERROR: configuration failed for package ‘XML’

deseq2 libxml xml • 92 views
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@james-w-macdonald-5106
Last seen 2 days ago
United States

The problem appears to be the install of libxml on your Linux box. In other words, when it says

You are trying to use a version 2.* edition of libxml
but an incompatible library. The header files and library seem to be
mismatched.


It is talking about the libxml install on your Linux box, not something from the XML package. So you or your sysadmin need to ensure that your libxml and libxml-dev are the same version.

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ATpoint ▴ 640
@atpoint-13662
Last seen 8 hours ago
Germany

You need libxml2-dev.

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