From my experience, R (on macOS) doesn't play well with libraries that have
install names containing runtime search paths. By changing the install name, I
mean changing the '@rpath' part here:
$ otool -L /usr/local/lib/libbamdb.dylib
/usr/local/lib/libbamdb.dylib:
@rpath/libbamdb.dylib (compatibility version 0.0.0, current version
0.0.0)
/usr/local/lib/libck.0.dylib (compatibility version 0.0.0, current
version 0.0.0)
/opt/local/lib/libhts.2.dylib (compatibility version 2.0.0, current
version 1.8.0)
/opt/local/lib/liblmdb.dylib (compatibility version 0.0.0, current
version 0.0.0)
...
using:
$ sudo install_name_tool -id /usr/local/lib/libbamdb.dylib
/usr/local/lib/libbamdb.dylib
$ otool -L /usr/local/lib/libbamdb.dylib
/usr/local/lib/libbamdb.dylib:
/usr/local/lib/libbamdb.dylib (compatibility version 0.0.0, current
version 0.0.0)
/usr/local/lib/libck.0.dylib (compatibility version 0.0.0, current
version 0.0.0)
/opt/local/lib/libhts.2.dylib (compatibility version 2.0.0, current
version 1.8.0)
/opt/local/lib/liblmdb.dylib (compatibility version 0.0.0, current
version 0.0.0)
...
Then build the R package (R CMD INSTALL …). Otherwise you could hit an 'image
not found' error. (But, to be clear, this error is not related to Rcpp.)
Keith
> On May 1, 2018, at 12:04 PM, Evan Biederstedt <evan.biederst...@gmail.com>
> wrote:
>
> @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
> >
> >
>
>
_______________________________________________
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
