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Question: unable to install "variant"
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gravatar for duclare123
8 months ago by
duclare1230
duclare1230 wrote:

Hi Guys,

I was not able to properly install the package variant from bioconductor in R


So I ran 

source("http://bioconductor.org/workflows.R")
workflowInstall("variants")

and a bunch of errors show up, I was able to fix some but there are a few I have no clue to it. Here is one of a problematic package:


* 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... /usr/bin/sed
checking for pkg-config... no
checking for xml2-config... /Applications/anaconda/anaconda3/bin/xml2-config
USE_XML2 = yes
SED_EXTENDED_ARG: -E
Minor 9, Patch 7 for 2.9.7
Located parser file -I/Applications/anaconda/anaconda3/include/libxml2 -I/Applications/anaconda/anaconda3/include/parser.h
Checking for 1.8:  -I/Applications/anaconda/anaconda3/include/libxml2 -I/Applications/anaconda/anaconda3/include
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’


System info:

R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS High Sierra 10.13.3

libxml2 2.9.7

ADD COMMENTlink modified 8 months ago by mario.zanfardino150 • written 8 months ago by duclare1230
0
gravatar for mario.zanfardino
8 months ago by
Naples (Italy)
mario.zanfardino150 wrote:

Try to re-install libxml2:

brew update
brew uninstall libxml2
brew install libxml2 --with-xml2-config

 

ADD COMMENTlink modified 8 months ago • written 8 months ago by mario.zanfardino150

This appears to be a 'anaconda' installation; is it appropriate to use brew for this, or does the problem need to be fixed in anaconda? I'm ignorant of these things. It looks like the installation is already messed up (different headers from library).

Also the best approach in this case is usually to simplify the installation process as much as possible, to aid trouble-shooting. So start by trying to get the XML installation issue resolved before returning to the workflow installation.

biocLite("XML")
ADD REPLYlink modified 8 months ago • written 8 months ago by Martin Morgan ♦♦ 22k
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