<div dir="ltr">@Dirk <br><br>> <span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">Could you possibly construct a smaller, self-contained example exhibiting the</span><br style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">same problem? That may be more efficient than requiring volunteer helpers to</span><br style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">install four other libraries.<br><br>Apologies, this is on the to-do list. <br><br>@Keith<br><br>Thanks for trying this out. This is interesting. <br><br>> <span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">Worked for me, after I modified the install name of libbamdb (from a runtime path to the installation directory, /usr/local/lib/libbamdb.dylib)</span><wbr style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">.<br></span><br>I want to be sure I understand---Could you clarify this? Which changes did you make? </span><div><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><br></span></div><div><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">That is created with `sudo make install`, i.e. from above<br><br><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">```</span><br style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"></span><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"></span><p class="gmail-m_8799637192103445667gmail-p1" style="font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="gmail-m_8799637192103445667gmail-s1" style="font-variant-ligatures:no-common-ligatures">$ sudo make install</span></p><p class="gmail-m_8799637192103445667gmail-p1" style="font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="gmail-m_8799637192103445667gmail-s1" style="font-variant-ligatures:no-common-ligatures">Password:</span></p><p class="gmail-m_8799637192103445667gmail-p1" style="font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="gmail-m_8799637192103445667gmail-s1" style="font-variant-ligatures:no-common-ligatures">[ 50%] Built target bamdb</span></p><p class="gmail-m_8799637192103445667gmail-p1" style="font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="gmail-m_8799637192103445667gmail-s1" style="font-variant-ligatures:no-common-ligatures">[100%] Built target libbamdb</span></p><p class="gmail-m_8799637192103445667gmail-p2" style="font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(51,187,200);background-color:rgb(255,255,255)"><span class="gmail-m_8799637192103445667gmail-s1" style="font-variant-ligatures:no-common-ligatures">Install the project...</span></p><p class="gmail-m_8799637192103445667gmail-p1" style="font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="gmail-m_8799637192103445667gmail-s1" style="font-variant-ligatures:no-common-ligatures">-- Install configuration: ""</span></p><p class="gmail-m_8799637192103445667gmail-p1" style="font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="gmail-m_8799637192103445667gmail-s1" style="font-variant-ligatures:no-common-ligatures">-- Installing: /usr/local/bin/bamdb</span></p><p class="gmail-m_8799637192103445667gmail-p1" style="font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="gmail-m_8799637192103445667gmail-s1" style="font-variant-ligatures:no-common-ligatures">-- Up-to-date: /usr/local/include/bamdb</span></p><p class="gmail-m_8799637192103445667gmail-p1" style="font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="gmail-m_8799637192103445667gmail-s1" style="font-variant-ligatures:no-common-ligatures">-- Up-to-date: /usr/local/include/bamdb/bam_<wbr>api.h</span></p><p class="gmail-m_8799637192103445667gmail-p1" style="font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="gmail-m_8799637192103445667gmail-s1" style="font-variant-ligatures:no-common-ligatures">-- Up-to-date: /usr/local/include/bamdb/bam_<wbr>lmdb.h</span></p><p class="gmail-m_8799637192103445667gmail-p1" style="font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="gmail-m_8799637192103445667gmail-s1" style="font-variant-ligatures:no-common-ligatures">-- Up-to-date: /usr/local/include/bamdb/<wbr>bamdb.h</span></p><p class="gmail-m_8799637192103445667gmail-p1" style="font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="gmail-m_8799637192103445667gmail-s1" style="font-variant-ligatures:no-common-ligatures">-- Installing: /usr/local/lib/libbamdb.dylib</span></p><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">```</span><br><br><br><br><br></span></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, May 1, 2018 at 11:42 AM, Keith O'Hara <span dir="ltr"><<a href="mailto:kth.ohr@gmail.com" target="_blank">kth.ohr@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Worked for me, after I modified the install name of libbamdb (from a runtime path to the installation directory, /usr/local/lib/libbamdb.dylib)<wbr>.<br>
<br>
* installing to library ‘/Users/<blah blah>/R-devel/lib/R/library’<br>
<span class="">* installing *source* package ‘bambi’ ...<br>
** libs<br>
</span>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/<wbr>Rcpp/include" -I/usr/local/include -fPIC -Wall -march=native -g -O3 -ffp-contract=fast -c RcppExports.cpp -o RcppExports.o<br>
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/<wbr>Rcpp/include" -I/usr/local/include -fPIC -Wall -march=native -g -O3 -ffp-contract=fast -c bambi.cpp -o bambi.o<br>
clang++-mp-6.0 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_<wbr>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<br>
installing to /Users/<blah blah>/R-devel/lib/R/library/<wbr>bambi/libs<br>
** R<br>
** byte-compile and prepare package for lazy loading<br>
<span class="">** help<br>
*** installing help indices<br>
** building package indices<br>
</span><span class="">** testing if installed package can be loaded<br>
</span>* DONE (bambi)<br>
<br>
Try building from a new, clean directory. <br>
<span class="HOEnZb"><font color="#888888"><br>
Keith<br>
</font></span><div class="HOEnZb"><div class="h5"><br>
> On May 1, 2018, at 10:24 AM, Evan Biederstedt <<a href="mailto:evan.biederstedt@gmail.com">evan.biederstedt@gmail.com</a>> wrote:<br>
> <br>
> @Keith<br>
> <br>
> > Unless I'm mistaken, neither are required to install binary packages. Can you check your *source* build setup; try:<br>
> <br>
> > curl -O <a href="https://cran.r-project.org/src/contrib/RcppArmadillo_0.8.500.0.tar.gz" rel="noreferrer" target="_blank">https://cran.r-project.org/<wbr>src/contrib/RcppArmadillo_0.8.<wbr>500.0.tar.gz</a><br>
> > R CMD INSTALL RcppArmadillo_0.8.500.0.tar.gz<br>
> <br>
> This looks successful<br>
> <br>
> ```<br>
> $ R CMD INSTALL RcppArmadillo_0.8.500.0.tar.gz<br>
> <br>
> * installing to library ‘/Library/Frameworks/R.<wbr>framework/Versions/3.4/<wbr>Resources/library’<br>
> * installing *source* package ‘RcppArmadillo’ ...<br>
> ** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked<br>
> checking whether the C++ compiler works... yes<br>
> checking for C++ compiler default output file name... a.out<br>
> checking for suffix of executables... <br>
> checking whether we are cross compiling... no<br>
> checking for suffix of object files... o<br>
> checking whether we are using the GNU C++ compiler... yes<br>
> checking whether clang++ accepts -g... yes<br>
> checking how to run the C++ preprocessor... clang++ -E<br>
> checking whether we are using the GNU C++ compiler... (cached) yes<br>
> checking whether clang++ accepts -g... (cached) yes<br>
> checking whether g++ version is sufficient... almost<br>
> configure: WARNING: Compiler self-identifies as being compliant with GNUC extensions but is not g++.<br>
> checking for macOS... found<br>
> checking for macOS Apple compiler... found<br>
> configure: WARNING: OpenMP unavailable and turned off.<br>
> checking LAPACK_LIBS... R-supplied partial LAPACK found<br>
> configure: WARNING: Some complex-valued LAPACK functions may not be available<br>
> configure: creating ./config.status<br>
> config.status: creating inst/include/<wbr>RcppArmadilloConfigGenerated.h<br>
> config.status: creating src/Makevars<br>
> ** libs<br>
> clang++ -std=gnu++11 -I/Library/Frameworks/R.<wbr>framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.<wbr>framework/Versions/3.4/<wbr>Resources/library/Rcpp/<wbr>include" -I/usr/local/include -I../inst/include -fPIC -Wall -g -O2 -c RcppArmadillo.cpp -o RcppArmadillo.o<br>
> clang++ -std=gnu++11 -I/Library/Frameworks/R.<wbr>framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.<wbr>framework/Versions/3.4/<wbr>Resources/library/Rcpp/<wbr>include" -I/usr/local/include -I../inst/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o<br>
> clang++ -std=gnu++11 -I/Library/Frameworks/R.<wbr>framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.<wbr>framework/Versions/3.4/<wbr>Resources/library/Rcpp/<wbr>include" -I/usr/local/include -I../inst/include -fPIC -Wall -g -O2 -c fastLm.cpp -o fastLm.o<br>
> clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_<wbr>names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.<wbr>framework/Resources/lib -L/usr/local/lib -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -L/Library/Frameworks/R.<wbr>framework/Resources/lib -lRlapack -L/Library/Frameworks/R.<wbr>framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/<wbr>x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.<wbr>framework/.. -framework R -Wl,-framework -Wl,CoreFoundation<br>
> ld: warning: directory not found for option '-L/usr/local/gfortran/lib/<wbr>gcc/x86_64-apple-darwin15/6.1.<wbr>0'<br>
> ld: warning: directory not found for option '-L/usr/local/gfortran/lib'<br>
> installing to /Library/Frameworks/R.<wbr>framework/Versions/3.4/<wbr>Resources/library/<wbr>RcppArmadillo/libs<br>
> ** R<br>
> ** inst<br>
> ** preparing package for lazy loading<br>
> ** help<br>
> *** installing help indices<br>
> ** building package indices<br>
> ** installing vignettes<br>
> ** testing if installed package can be loaded<br>
> * DONE (RcppArmadillo)<br>
> <br>
> ```<br>
> <br>
> > Check your build directory for any .Rprofile or .Renviron files, and also check ~/.R/Makevars for errors.<br>
> <br>
> 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?<br>
> <br>
> <br>
> > 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 :-))<br>
> <br>
> There are four dependencies:<br>
> <br>
> htslib/1.5 or higher: <a href="https://github.com/samtools/htslib" rel="noreferrer" target="_blank">https://github.com/samtools/<wbr>htslib</a><br>
> <br>
> LMDB key-value store: <a href="https://github.com/LMDB/lmdb" rel="noreferrer" target="_blank">https://github.com/LMDB/lmdb</a><br>
> <br>
> Concurreny-Ck: <a href="https://github.com/concurrencykit/ck" rel="noreferrer" target="_blank">https://github.com/<wbr>concurrencykit/ck</a><br>
> <br>
> zlib: Standard compression library <a href="https://github.com/madler/zlib" rel="noreferrer" target="_blank">https://github.com/madler/zlib</a> (probably already installed)<br>
> <br>
> Mac OS:<br>
> ```<br>
> brew install lmdb<br>
> brew install concurrencykit<br>
> brew install zlib // mac OS already provides this software<br>
> brew install htslib // I *think* this is the latest htslib, but I would double-check<br>
> ```<br>
> <br>
> Linux (for the record):<br>
> ```<br>
> yum install libhts-dev ## dev branch of latest htslib<br>
> yum install liblmdb-dev ## LMDB dev<br>
> yum install libck-dev ## Concurrency-ck<br>
> yum install libz-dev ## zlib compresssion<br>
> ```<br>
> <br>
> On Tue, May 1, 2018 at 3:45 AM, Keith O'Hara <<a href="mailto:kth.ohr@gmail.com">kth.ohr@gmail.com</a>> wrote:<br>
> Unless I'm mistaken, neither are required to install binary packages. Can you check your *source* build setup; try:<br>
> <br>
> curl -O <a href="https://cran.r-project.org/src/contrib/RcppArmadillo_0.8.500.0.tar.gz" rel="noreferrer" target="_blank">https://cran.r-project.org/<wbr>src/contrib/RcppArmadillo_0.8.<wbr>500.0.tar.gz</a><br>
> R CMD INSTALL RcppArmadillo_0.8.500.0.tar.gz<br>
> <br>
> 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.<br>
> <br>
> 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 :-))<br>
> <br>
> Keith<br>
> <br>
> > On May 1, 2018, at 3:07 AM, Evan Biederstedt <<a href="mailto:evan.biederstedt@gmail.com">evan.biederstedt@gmail.com</a>> wrote:<br>
> > <br>
> > I would add, I think clang and gfortran are working correctly, as these are required for `install.packages('<wbr>RcppArmadillo')` to install properly.<br>
> > <br>
> > On Tue, May 1, 2018 at 3:06 AM, Evan Biederstedt <<a href="mailto:evan.biederstedt@gmail.com">evan.biederstedt@gmail.com</a>> wrote:<br>
> > Maybe my Mac OS needs updating...possibly something with XCode, but it's not clear how...<br>
> > <br>
> > --- mac OS Sierra 10.12.6<br>
> > --- CRAN R 3.4.3<br>
> > ---clang & gfortran<br>
> > <br>
> > $ clang --version<br>
> > Apple LLVM version 9.0.0 (clang-900.0.39.2)<br>
> > Target: x86_64-apple-darwin16.7.0<br>
> > Thread model: posix<br>
> > InstalledDir: /Library/Developer/<wbr>CommandLineTools/usr/bin<br>
> > <br>
> > $ gfortran --version<br>
> > GNU Fortran (GCC) 7.1.0<br>
> > Copyright (C) 2017 Free Software Foundation, Inc.<br>
> > This is free software; see the source for copying conditions. There is NO<br>
> > warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.<br>
> > <br>
> > I will update once I have access to and try this on several other mac boxes with different specs..<br>
> > <br>
> > Thank you to everyone for the help. <br>
> > <br>
> > <br>
> > On Tue, May 1, 2018 at 1:44 AM, Ralf Stubner <<a href="mailto:ralf.stubner@r-institute.com">ralf.stubner@r-institute.com</a>> wrote:<br>
> > <br>
> > Am 30.04.2018 um 23:42 schrieb Evan Biederstedt <<a href="mailto:evan.biederstedt@gmail.com">evan.biederstedt@gmail.com</a>>:<br>
> > <br>
> >> @Ralf<br>
> >> <br>
> >> > 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 …<br>
> >> <br>
> >> 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....<br>
> > <br>
> > On my side that would be<br>
> > • macOS high Sierra<br>
> > • CRAN R 3.4.4<br>
> > • clang and gfortran as recommended by CRAN<br>
> > • brew is installed but I do not see how it enters the picture <br>
> > <br>
> > Greetings <br>
> > Ralf <br>
> > <br>
> > <br>
> > ______________________________<wbr>_________________<br>
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> > <a href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel" rel="noreferrer" target="_blank">https://lists.r-forge.r-<wbr>project.org/cgi-bin/mailman/<wbr>listinfo/rcpp-devel</a><br>
> <br>
> <br>
<br>
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