Installing R package XML on MacOS 10.13.6

I updated my R packages the other day, and not surprisingly, one package failed to compile. This time, it was XML. The error message suggested configure: error: “libxml not found”, but homebrew suggested I had installed libxml2 and had it up-to-date.

By running ./configure manually and after some googling, I realized the compiler went to /usr/bin/xml2-config instead of the homebrew version, and thanks to this thread on StackOverflow, I learned that the compiler would be directed to the correct copy of libxml2 if I set the environmental variable XML_CONFIG.

So, running Sys.setenv(XML_CONFIG = "/usr/local/Cellar/libxml2/2.9.7/bin/xml2-config") in R console helped me successfully compile XML.

The cause of this problem might be that I did not install Xcode in my computer, which seems to come with a proper version of libxml2 to replace the one coming with the system, and according to the installation message of libxml2, libxml2 from homebrew is keg-only, which means it was not symlinked into/usr/local, because macOS already provides this software and installing another version in parallel can cause all kinds of trouble. Consequently , the compiler turned to the system copy of libxml2, causing failed compilation.

Of course, this problem could also be fixed by choosing to install from binary.

R version 3.4.4 (2018-03-15)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_3.4.4 tools_3.4.4    yaml_2.2.0
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Yen-Chung Chen
PhD Student

Yen is a graduate student interested in developmental biology, neurobiology and bioinformatics.

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