Worked for me, after I modified the install name of libbamdb (from a runtime 
path to the installation directory, /usr/local/lib/libbamdb.dylib).

* installing to library ‘/Users/<blah blah>/R-devel/lib/R/library’
* installing *source* package ‘bambi’ ...
** libs
clang++-mp-6.0 -std=gnu++11 -I"/Users/<blah blah>/R-devel/lib/R/include" 
-DNDEBUG -I../inst/include/ -I/usr/local/include/bamdb -I/opt/local/include 
-I"/Users/<blah blah>/R-devel/lib/R/library/Rcpp/include" -I/usr/local/include  
 -fPIC  -Wall -march=native -g -O3 -ffp-contract=fast -c RcppExports.cpp -o 
RcppExports.o
clang++-mp-6.0 -std=gnu++11 -I"/Users/<blah blah>/R-devel/lib/R/include" 
-DNDEBUG -I../inst/include/ -I/usr/local/include/bamdb -I/opt/local/include 
-I"/Users/<blah blah>/R-devel/lib/R/library/Rcpp/include" -I/usr/local/include  
 -fPIC  -Wall -march=native -g -O3 -ffp-contract=fast -c bambi.cpp -o bambi.o
clang++-mp-6.0 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names 
-undefined dynamic_lookup -single_module -multiply_defined suppress 
-L/Users/<blah blah>/R-devel/lib/R/lib -L/usr/local/lib -o bambi.so 
RcppExports.o bambi.o -lbamdb -L/opt/local/lib -llmdb -lhts -L/Users/<blah 
blah>/R-devel/lib/R/lib -lR -Wl,-framework -Wl,CoreFoundation
installing to /Users/<blah blah>/R-devel/lib/R/library/bambi/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (bambi)

Try building from a new, clean directory. 

Keith

> On May 1, 2018, at 10:24 AM, Evan Biederstedt <evan.biederst...@gmail.com> 
> wrote:
> 
> @Keith
> 
> > Unless I'm mistaken, neither are required to install binary packages. Can 
> > you check your *source* build setup; try:
> 
> > curl -O 
> > https://cran.r-project.org/src/contrib/RcppArmadillo_0.8.500.0.tar.gz
> > R CMD INSTALL RcppArmadillo_0.8.500.0.tar.gz
> 
> This looks successful
> 
> ```
> $ R CMD INSTALL RcppArmadillo_0.8.500.0.tar.gz
> 
> * installing to library 
> ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library’
> * installing *source* package ‘RcppArmadillo’ ...
> ** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
> checking whether the C++ compiler works... yes
> checking for C++ compiler default output file name... a.out
> checking for suffix of executables... 
> checking whether we are cross compiling... no
> checking for suffix of object files... o
> checking whether we are using the GNU C++ compiler... yes
> checking whether clang++ accepts -g... yes
> checking how to run the C++ preprocessor... clang++ -E
> checking whether we are using the GNU C++ compiler... (cached) yes
> checking whether clang++ accepts -g... (cached) yes
> checking whether g++ version is sufficient... almost
> configure: WARNING: Compiler self-identifies as being compliant with GNUC 
> extensions but is not g++.
> checking for macOS... found
> checking for macOS Apple compiler... found
> configure: WARNING: OpenMP unavailable and turned off.
> checking LAPACK_LIBS... R-supplied partial LAPACK found
> configure: WARNING: Some complex-valued LAPACK functions may not be available
> configure: creating ./config.status
> config.status: creating inst/include/RcppArmadilloConfigGenerated.h
> config.status: creating src/Makevars
> ** libs
> clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include 
> -DNDEBUG  
> -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include"
>  -I/usr/local/include  -I../inst/include  -fPIC  -Wall -g -O2 -c 
> RcppArmadillo.cpp -o RcppArmadillo.o
> clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include 
> -DNDEBUG  
> -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include"
>  -I/usr/local/include  -I../inst/include  -fPIC  -Wall -g -O2 -c 
> RcppExports.cpp -o RcppExports.o
> clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include 
> -DNDEBUG  
> -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include"
>  -I/usr/local/include  -I../inst/include  -fPIC  -Wall -g -O2 -c fastLm.cpp 
> -o fastLm.o
> clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined 
> dynamic_lookup -single_module -multiply_defined suppress 
> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o 
> RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o 
> -L/Library/Frameworks/R.framework/Resources/lib -lRlapack 
> -L/Library/Frameworks/R.framework/Resources/lib -lRblas 
> -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 
> -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm 
> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework 
> -Wl,CoreFoundation
> ld: warning: directory not found for option 
> '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
> ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
> installing to 
> /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/libs
> ** R
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded
> * DONE (RcppArmadillo)
> 
> ```
> 
> > Check your build directory for any .Rprofile or .Renviron files, and also 
> > check ~/.R/Makevars for errors.
> 
> I'm using the command line. I do not seem to have anything in `$ cat 
> ~/.R/Makevars` or `$cat ~/.Rprofile`. Perhaps this is the problem?
> 
> 
> > If you can list the required libraries for bamdb, I'm happy to try a build 
> > on my end. (I'm lazy to go through the CMake list :-))
> 
> There are four dependencies:
> 
> htslib/1.5 or higher: https://github.com/samtools/htslib
> 
> LMDB key-value store: https://github.com/LMDB/lmdb
> 
> Concurreny-Ck:  https://github.com/concurrencykit/ck
> 
> zlib: Standard compression library https://github.com/madler/zlib  (probably 
> already installed)
> 
> Mac OS:
> ```
> brew install lmdb
> brew install concurrencykit
> brew install zlib // mac OS already provides this software
> brew install htslib // I *think* this is the latest htslib, but I would 
> double-check
> ```
> 
> Linux (for the record):
> ```
> yum install libhts-dev    ## dev branch of latest htslib
> yum install liblmdb-dev   ## LMDB dev
> yum install libck-dev     ## Concurrency-ck
> yum install libz-dev      ## zlib compresssion
> ```
> 
> On Tue, May 1, 2018 at 3:45 AM, Keith O'Hara <kth....@gmail.com> wrote:
> Unless I'm mistaken, neither are required to install binary packages. Can you 
> check your *source* build setup; try:
> 
> curl -O https://cran.r-project.org/src/contrib/RcppArmadillo_0.8.500.0.tar.gz
> R CMD INSTALL RcppArmadillo_0.8.500.0.tar.gz
> 
> If that goes through without a hitch then it's probably a package issue. Are 
> you using RStudio? Check your build directory for any .Rprofile or .Renviron 
> files, and also check ~/.R/Makevars for errors.
> 
> If you can list the required libraries for bamdb, I'm happy to try a build on 
> my end. (I'm lazy to go through the CMake list :-))
> 
> Keith
> 
> > On May 1, 2018, at 3:07 AM, Evan Biederstedt <evan.biederst...@gmail.com> 
> > wrote:
> > 
> > I would add, I think clang and gfortran are working correctly, as these are 
> > required for `install.packages('RcppArmadillo')` to install properly.
> > 
> > On Tue, May 1, 2018 at 3:06 AM, Evan Biederstedt 
> > <evan.biederst...@gmail.com> wrote:
> > Maybe my Mac OS needs updating...possibly something with XCode, but it's 
> > not clear how...
> > 
> > --- mac OS Sierra 10.12.6
> > --- CRAN R 3.4.3
> > ---clang & gfortran
> > 
> > $ clang --version
> > Apple LLVM version 9.0.0 (clang-900.0.39.2)
> > Target: x86_64-apple-darwin16.7.0
> > Thread model: posix
> > InstalledDir: /Library/Developer/CommandLineTools/usr/bin
> > 
> > $ gfortran --version
> > GNU Fortran (GCC) 7.1.0
> > Copyright (C) 2017 Free Software Foundation, Inc.
> > This is free software; see the source for copying conditions.  There is NO
> > warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
> > 
> > I will update once I have access to and try this on several other mac boxes 
> > with different specs..
> > 
> > Thank you to everyone for the help. 
> > 
> > 
> > On Tue, May 1, 2018 at 1:44 AM, Ralf Stubner <ralf.stub...@r-institute.com> 
> > wrote:
> > 
> > Am 30.04.2018 um 23:42 schrieb Evan Biederstedt 
> > <evan.biederst...@gmail.com>:
> > 
> >> @Ralf
> >> 
> >> > I had not installed the necessary C library, so unsurprisingly the 
> >> > compilation step already failed. What I find interesting is that in my 
> >> > case "-std=gnu++11“ and "-I../inst/include/" are present in the command 
> >> > line options for clang++. These are also missing from what you quoted 
> >> > and are also a consequence of src/Makevars. It almost looks as if this 
> >> > file got lost on your macOS box …
> >> 
> >> Interesting....I'm not sure what to make of this of course, but it would 
> >> be interesting if it was only happening on this macbook. Perhaps OS 
> >> version or brew could be to blame? I'm not sure what else would be 
> >> "special" about this macbook....
> > 
> > On my side that would be
> > • macOS high Sierra
> > • CRAN R 3.4.4
> > • clang and gfortran as recommended by CRAN
> > • brew is installed but I do not see how it enters the picture 
> > 
> > Greetings 
> > Ralf 
> > 
> > 
> > _______________________________________________
> > Rcpp-devel mailing list
> > Rcpp-devel@lists.r-forge.r-project.org
> > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
> 
> 

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