[R-SIG-Mac] OS X builds for R-devel

David Winsemius dwinsemius at comcast.net
Fri Feb 23 18:01:58 CET 2018

> On Feb 19, 2018, at 12:27 PM, Alexey Sergushichev <alsergbox at gmail.com> wrote:
> Dear all,
> Are there any plans on having package build for r-devel on CRAN? I
> understand it's far from the highest priority but it would be good to have
> any estimates. I'm aware of several packages on Bioconoductor-devel that
> fail builds due to absence of binary versions of some packages (
> http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineR/merida2-buildsrc.html
> http://bioconductor.org/checkResults/devel/bioc-LATEST/cbaf/merida2-buildsrc.html
> ).
> Thanks,
> Alexey Sergushichev
> 	[[alternative HTML version deleted]]

The fact that you post in HTML and make no effort to describe your setup makes me suspect you may also have missed the instructions about installing XCode and configuring R for compiling source packages. This can still be done with the binary distribution versions of R and R.app, and do not require that you build R from sources. See the CRAN-Mac-tools page:


It used to be the case that one needed Xcode and Command Line Tools installed. (I do have them.) I cannot tell from the current Mac-devel page whether that is still the case. I have a current version of R running in El Capitan. This is my ~/.R/Makevars file:

# created by rstan at Thu Mar 19 11:26:15 2015 
CXXFLAGS = -mtune=core2 -O3 $(LTO)  #set_by_rstan
R_XTRA_CPPFLAGS =  -I$(R_INCLUDE_DIR)   #set_by_rstan

I just executed the following commands in the R.app environment.

# declined the offer to update packages
 biocLite(c("ChemmineR"), type="source", dependencies=TRUE)

It then tried to install all the dependencies (failing for ChemmineOB because the OpenBabel system requirement was not met) and got a  report of success with ChemmineR and the package was capable of loading. So I've successfully tested my theory that the only barriers to successful compilation of ChemmineR from source are lack of knowledge of the R and Bioconductor ecosystem (and lack of one external package.) I'm not that interested in getting a full package installed, so haven't taken the time to install OpenBabel and recompile ChemmineOB.

Hope this helps;

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David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   -Gehm's Corollary to Clarke's Third Law

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