@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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