<?xml version='1.0'?><rss version="2.0" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:georss="http://www.georss.org/georss" xmlns:atom="http://www.w3.org/2005/Atom" >
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	<title><![CDATA[BOL: How to fix the MacOS error for ‘ddalpha’ R package installation ?]]></title>
	<link>https://bioinformaticsonline.com/answers/view/35435/how-to-fix-the-macos-error-for-%E2%80%98ddalpha%E2%80%99-r-package-installation?</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/answers/view/35435/how-to-fix-the-macos-error-for-%E2%80%98ddalpha%E2%80%99-r-package-installation</guid>
	<pubDate>Sat, 03 Feb 2018 09:18:52 -0600</pubDate>
	<link>https://bioinformaticsonline.com/answers/view/35435/how-to-fix-the-macos-error-for-%E2%80%98ddalpha%E2%80%99-r-package-installation</link>
	<title><![CDATA[How to fix the MacOS error for ‘ddalpha’ R package installation ?]]></title>
	<description><![CDATA[<p>&gt; install.packages(c('ddalpha', 'recipes'))&nbsp;</p><p>&nbsp; There is a binary version available but the source version is later:</p><p>&nbsp; &nbsp; &nbsp; &nbsp; binary&nbsp; source needs_compilation</p><p>ddalpha&nbsp; 1.3.1 1.3.1.1&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; TRUE</p><p>&nbsp;</p><p><strong>Do you want to install from sources the package which needs compilation?</strong></p><p>y/n: y</p><p><strong>trying URL 'https://mirrors.nic.cz/R/bin/macosx/el-capitan/contrib/3.4/recipes_0.1.2.tgz'</strong></p><p><strong>Content type 'application/octet-stream' length 998818 bytes (975 KB)</strong></p><p><strong>==================================================</strong></p><p><strong>downloaded 975 KB</strong></p><p>&nbsp;</p><p>&nbsp;</p><p>The downloaded binary packages are in</p><p>/tmp/RtmpUg5Cs2/downloaded_packages</p><p><strong>installing the source package &lsquo;ddalpha&rsquo;</strong></p><p>&nbsp;</p><p><strong>trying URL 'https://mirrors.nic.cz/R/src/contrib/ddalpha_1.3.1.1.tar.gz'</strong></p><p><strong>Content type 'application/octet-stream' length 543279 bytes (530 KB)</strong></p><p><strong>==================================================</strong></p><p><strong>downloaded 530 KB</strong></p><p>&nbsp;</p><p>* installing *source* package &lsquo;ddalpha&rsquo; ...</p><p>** package &lsquo;ddalpha&rsquo; successfully unpacked and MD5 sums checked</p><p>** libs</p><p>clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG&nbsp; -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include &nbsp; -fPIC&nbsp; -Wall -g -O2 -c AlphaProcedure.cpp -o AlphaProcedure.o</p><p>clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG&nbsp; -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include &nbsp; -fPIC&nbsp; -Wall -g -O2 -c Common.cpp -o Common.o</p><p>clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG&nbsp; -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include &nbsp; -fPIC&nbsp; -Wall -g -O2 -c DKnn.cpp -o DKnn.o</p><p>clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG&nbsp; -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include &nbsp; -fPIC&nbsp; -Wall -g -O2 -c HD.cpp -o HD.o</p><p><strong>HD.cpp:25:14: </strong><strong>warning: </strong><strong>unused variable 'eps_Cmb1' [-Wunused-const-variable]</strong></p><p>const double eps_Cmb1 = 1e-8;</p><p><strong>&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ^</strong></p><p>1 warning generated.</p><p>clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG&nbsp; -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include &nbsp; -fPIC&nbsp; -Wall -g -O2 -c Knn.cpp -o Knn.o</p><p><strong>Knn.cpp:146:15: </strong><strong>warning: </strong><strong>unused variable 'd' [-Wunused-variable]</strong></p><p>&nbsp; &nbsp; &nbsp; &nbsp; unsigned int d = points[0].size();unsigned int n = points.size();</p><p><strong>&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ^</strong></p><p><strong>Knn.cpp:209:15: </strong><strong>warning: </strong><strong>unused variable 'd' [-Wunused-variable]</strong></p><p>&nbsp; &nbsp; &nbsp; &nbsp; unsigned int d = points[0].size();</p><p><strong>&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ^</strong></p><p>2 warnings generated.</p><p>clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG&nbsp; -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include &nbsp; -fPIC&nbsp; -Wall -g -O2 -c Mahalanobis.cpp -o Mahalanobis.o</p><p><strong>Mahalanobis.cpp:32:6: </strong><strong>warning: </strong><strong>unused variable 'res' [-Wunused-variable]</strong></p><p>&nbsp; &nbsp; &nbsp; &nbsp; int res = lu_factorize(A, pm);</p><p><strong>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ^</strong></p><p>1 warning generated.</p><p>clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG&nbsp; -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include &nbsp; -fPIC&nbsp; -Wall -g -O2 -c OjaDepth.cpp -o OjaDepth.o</p><p><strong>OjaDepth.cpp:44:8: </strong><strong>warning: </strong><strong>unused variable 'sc' [-Wunused-variable]</strong></p><p>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; bool sc = numSimplicesChecked == div0;</p><p><strong>&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ^</strong></p><p>1 warning generated.</p><p>clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG&nbsp; -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include &nbsp; -fPIC&nbsp; -Wall -g -O2 -c Polynomial.cpp -o Polynomial.o</p><p><strong>Polynomial.cpp:396:18: </strong><strong>warning: </strong><strong>unused variable 'tmp' [-Wunused-variable]</strong></p><p>&nbsp; &nbsp; &nbsp; &nbsp; for (int i = 0, tmp; i &lt; numPoints; i++){ input2[i][0] = input[i][1]; input2[i][1] = input[i][0]; } // swap columns</p><p><strong>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ^</strong></p><p>1 warning generated.</p><p>clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG&nbsp; -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include &nbsp; -fPIC&nbsp; -Wall -g -O2 -c PotentialDepth.cpp -o PotentialDepth.o</p><p>clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG&nbsp; -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include &nbsp; -fPIC&nbsp; -Wall -g -O2 -c ProjectionDepth.cpp -o ProjectionDepth.o</p><p><strong>ProjectionDepth.cpp:16:12: </strong><strong>warning: </strong><strong>unused function 'CompareAsc' [-Wunused-function]</strong></p><p>static int CompareAsc(OrderRec x, OrderRec y)</p><p><strong>&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ^</strong></p><p><strong>ProjectionDepth.cpp:21:12: </strong><strong>warning: </strong><strong>unused function 'CompareDec' [-Wunused-function]</strong></p><p>static int CompareDec(OrderRec x, OrderRec y)</p><p><strong>&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ^</strong></p><p>2 warnings generated.</p><p>clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG&nbsp; -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include &nbsp; -fPIC&nbsp; -Wall -g -O2 -c SimplicialDepth.cpp -o SimplicialDepth.o</p><p><strong>SimplicialDepth.cpp:46:8: </strong><strong>warning: </strong><strong>unused variable 'sc' [-Wunused-variable]</strong></p><p>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; bool sc = numSimplicesChecked == div0;</p><p><strong>&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ^</strong></p><p>1 warning generated.</p><p>clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG&nbsp; -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include &nbsp; -fPIC&nbsp; -Wall -g -O2 -c TukeyDepth.cpp -o TukeyDepth.o</p><p>clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG&nbsp; -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include &nbsp; -fPIC&nbsp; -Wall -g -O2 -c ZonoidDepth.cpp -o ZonoidDepth.o</p><p><strong>ZonoidDepth.cpp:63:25: </strong><strong>warning: </strong><strong>using the result of an assignment as a condition without parentheses [-Wparentheses]</strong></p><p>&nbsp; &nbsp; if ( RowInverted[j] = z[j] &lt; 0 ) {</p><p><strong>&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; ~~~~~~~~~~~~~~~^~~~~~~~~~</strong></p><p><strong>ZonoidDepth.cpp:63:25: note: </strong>place parentheses around the assignment to silence this warning</p><p>&nbsp; &nbsp; if ( RowInverted[j] = z[j] &lt; 0 ) {</p><p><strong>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ^</strong></p><p>&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; )</p><p><strong>ZonoidDepth.cpp:63:25: note: </strong>use '==' to turn this assignment into an equality comparison</p><p>&nbsp; &nbsp; if ( RowInverted[j] = z[j] &lt; 0 ) {</p><p><strong>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ^</strong></p><p>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ==</p><p>1 warning generated.</p><p>clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG&nbsp; -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include &nbsp; -fPIC&nbsp; -Wall -g -O2 -c asa047.cpp -o asa047.o</p><p>clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG&nbsp; -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include &nbsp; -fPIC&nbsp; -Wall -g -O2 -c ddalpha.cpp -o ddalpha.o</p><p>gfortran &nbsp; -fPIC&nbsp; -g -O2&nbsp; -c depth.fd.f -o depth.fd.o</p><p>make: gfortran: No such file or directory</p><p>make: *** [depth.fd.o] Error 1</p><p>ERROR: compilation failed for package &lsquo;ddalpha&rsquo;</p><p>* removing &lsquo;/Library/Frameworks/R.framework/Versions/3.4/Resources/library/ddalpha&rsquo;</p><p>&nbsp;</p><p><strong>The downloaded source packages are in</strong></p><p><strong> &lsquo;/private/tmp/RtmpUg5Cs2/downloaded_packages&rsquo;</strong></p><p><strong>Warning message:</strong></p><p><strong>In install.packages(c("ddalpha", "recipes")) :</strong></p><p><strong>&nbsp; installation of package &lsquo;ddalpha&rsquo; had non-zero exit status</strong></p><p>&gt;&nbsp;</p>]]></description>
	<dc:creator>Jit</dc:creator>
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