@Dirk > Could you possibly construct a smaller, self-contained example exhibiting the same problem? That may be more efficient than requiring volunteer helpers to install four other libraries.
Apologies, this is on the to-do list. @Keith Thanks for trying this out. This is interesting. > Worked for me, after I modified the install name of libbamdb (from a runtime path to the installation directory, /usr/local/lib/libbamdb.dylib). I want to be sure I understand---Could you clarify this? Which changes did you make? That is created with `sudo make install`, i.e. from above ``` $ sudo make install Password: [ 50%] Built target bamdb [100%] Built target libbamdb Install the project... -- Install configuration: "" -- Installing: /usr/local/bin/bamdb -- Up-to-date: /usr/local/include/bamdb -- Up-to-date: /usr/local/include/bamdb/bam_api.h -- Up-to-date: /usr/local/include/bamdb/bam_lmdb.h -- Up-to-date: /usr/local/include/bamdb/bamdb.h -- Installing: /usr/local/lib/libbamdb.dylib ``` On Tue, May 1, 2018 at 11:42 AM, Keith O'Hara <kth....@gmail.com> wrote: > 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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