<div dir="ltr">@Keith<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">Unless I'm mistaken, neither are required to install binary packages. Can you check your *source* build setup; try:</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"><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">> curl -O<span> </span></span><a href="https://cran.r-project.org/src/contrib/RcppArmadillo_0.8.500.0.tar.gz" rel="noreferrer" target="_blank" style="color:rgb(17,85,204);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)">https://cran.r-project.org/<wbr>src/contrib/RcppArmadillo_0.8.<wbr>500.0.tar.gz</a><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">> R CMD INSTALL RcppArmadillo_0.8.500.0.tar.gz<br></span><br>This looks successful<br><br>```<br>




<span></span>





<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">$ R CMD INSTALL RcppArmadillo_0.8.500.0.tar.gz</span></p>
<p class="gmail-p2" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255);min-height:13px"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">* installing to library ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library’</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">* installing *source* package ‘RcppArmadillo’ ...</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">checking whether the C++ compiler works... yes</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">checking for C++ compiler default output file name... a.out</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">checking for suffix of executables...<span class="gmail-Apple-converted-space"> </span></span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">checking whether we are cross compiling... no</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">checking for suffix of object files... o</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">checking whether we are using the GNU C++ compiler... yes</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">checking whether clang++ accepts -g... yes</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">checking how to run the C++ preprocessor... clang++ -E</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">checking whether we are using the GNU C++ compiler... (cached) yes</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">checking whether clang++ accepts -g... (cached) yes</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">checking whether g++ version is sufficient... almost</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">configure: WARNING: Compiler self-identifies as being compliant with GNUC extensions but is not g++.</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">checking for macOS... found</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">checking for macOS Apple compiler... found</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">configure: WARNING: OpenMP unavailable and turned off.</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">checking LAPACK_LIBS... R-supplied partial LAPACK found</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">configure: WARNING: Some complex-valued LAPACK functions may not be available</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">configure: creating ./config.status</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">config.status: creating inst/include/RcppArmadilloConfigGenerated.h</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">config.status: creating src/Makevars</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">** libs</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG<span class="gmail-Apple-converted-space">  </span>-I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include<span class="gmail-Apple-converted-space">  </span>-I../inst/include<span class="gmail-Apple-converted-space">  </span>-fPIC<span class="gmail-Apple-converted-space">  </span>-Wall -g -O2 -c RcppArmadillo.cpp -o RcppArmadillo.o</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG<span class="gmail-Apple-converted-space">  </span>-I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include<span class="gmail-Apple-converted-space">  </span>-I../inst/include<span class="gmail-Apple-converted-space">  </span>-fPIC<span class="gmail-Apple-converted-space">  </span>-Wall -g -O2 -c RcppExports.cpp -o RcppExports.o</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG<span class="gmail-Apple-converted-space">  </span>-I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include<span class="gmail-Apple-converted-space">  </span>-I../inst/include<span class="gmail-Apple-converted-space">  </span>-fPIC<span class="gmail-Apple-converted-space">  </span>-Wall -g -O2 -c fastLm.cpp -o fastLm.o</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">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</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">ld: warning: directory not found for option '-L/usr/local/gfortran/lib'</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">installing to /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/libs</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">** R</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">** inst</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">** preparing package for lazy loading</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">** help</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">*** installing help indices</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">** building package indices</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">** installing vignettes</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">** testing if installed package can be loaded</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;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-s1" style="font-variant-ligatures:no-common-ligatures">* DONE (RcppArmadillo)</span></p><br>```<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"><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">Check your build directory for any .Rprofile or .Renviron files, and also check ~/.R/Makevars for errors.</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"><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>> <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">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 :-))</span><div><br><span style="font-size:12.8px">There are four dependencies:</span><br><br><span style="font-size:12.8px">htslib/1.5 or higher: </span><span style="font-size:12.8px"><a href="https://github.com/samtools/htslib">https://github.com/samtools/htslib</a><br></span><br>LMDB key-value store: <a href="https://github.com/LMDB/lmdb">https://github.com/LMDB/lmdb</a><br><br><div>Concurreny-Ck:  <a href="https://github.com/concurrencykit/ck">https://github.com/concurrencykit/ck</a></div><div><br></div><div>zlib: Standard compression library <a href="https://github.com/madler/zlib">https://github.com/madler/zlib</a>  (probably already installed)<br><br>Mac OS:<br>```<br><div>brew install lmdb</div><div>brew install concurrencykit</div><div>brew install zlib // mac OS already provides this software</div><div>brew install htslib // I *think* this is the latest htslib, but I would double-check<br>```</div><div><br>Linux (for the record):</div><div>```<br><div>yum install libhts-dev    ## dev branch of latest htslib</div><div>yum install liblmdb-dev   ## LMDB dev</div><div>yum install libck-dev     ## Concurrency-ck</div><div>yum install libz-dev      ## zlib compresssion</div></div></div>```</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, May 1, 2018 at 3:45 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">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>
<span class="HOEnZb"><font color="#888888"><br>
Keith<br>
</font></span><div class="HOEnZb"><div class="h5"><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>
</div></div><div class="HOEnZb"><div class="h5">> ______________________________<wbr>_________________<br>
> Rcpp-devel mailing list<br>
> <a href="mailto:Rcpp-devel@lists.r-forge.r-project.org">Rcpp-devel@lists.r-forge.r-<wbr>project.org</a><br>
> <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>
</div></div></blockquote></div><br></div>