The majority of Mac OS machines do not provide basic developer tools, e.g., the GNU Compiler Collection (gcc), a Fortran compiler, a TeX distribution, etc., to compile R source code. To identify and obtain these developer tools, please refer to the section entitled "Building R from sources" in the R for Mac OS X FAQ.
Please note that different Mac OS versions might require different sets of developer tools. Also, note that the same developer tools used to compile R from source are also required to compile R library packages. Once the appropriate set of developer tools are installed, instructions for modifying, compiling, and installing the modified BiasedUrn package are identical to those described in the Linux section of this document.
We will use shell commands within a terminal to edit, recompile, and install the package. First, change directories to that which contains the BiasedUrn package source code. Here, we assume this directory is called Downloads and is found under our home directory (i.e. ~/Downloads/).
John-Does-MacBook-Pro:~ jdoe$ cd ~/Downloads
Next, use the tar command to extract the BiasedUrn source code.
John-Does-MacBook-Pro:Downloads jdoe$ tar -zxf BiasedUrn_1.04.tar.gz
The default contents of the Makevars file within the package src directory is displayed here:
John-Does-MacBook-Pro:Downloads jdoe$ cat BiasedUrn/src/Makevars # Makevars for BiasedUrn # The value of MAXCOLORS may be modified PKG_CPPFLAGS= -DR_BUILD=1 -DMAXCOLORS=32
Using any text editor, change the value of MAXCOLORS from 32 to 10000. After performing this edit and saving the changes, the file should look like this:
John-Does-MacBook-Pro:Downloads jdoe$ cat BiasedUrn/src/Makevars # Makevars for BiasedUrn # The value of MAXCOLORS may be modified PKG_CPPFLAGS= -DR_BUILD=1 -DMAXCOLORS=10000
Before building the package, one should execute the R check script to resolve any problems that may arise from compiling the package, e.g., missing developer tools. The command line execution of this step along with example output is shown here:
John-Does-MacBook-Pro:Downloads jdoe$ R CMD check BiasedUrn * using log directory '/Users/jdoe/Downloads/BiasedUrn.Rcheck' * using R version 2.15.0 (2012-03-30) * using platform: x86_64-apple-darwin9.8.0 (64-bit) * using session charset: UTF-8 ... * checking running R code from vignettes ... OK * checking re-building of vignette PDFs ... OK * checking PDF version of manual ... OK
The full output generated from the check command can be found in the log file BiasedUrn.Rcheck/00check.log.
Next we use the build command to compile the modified package and create an installable package file. This step will overwrite the original source file BiasedUrn_1.04.tar.gz with the installable modified package file.
John-Does-MacBook-Pro:Downloads jdoe$ R CMD build BiasedUrn * checking for file 'BiasedUrn/DESCRIPTION' ... OK * preparing 'BiasedUrn': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to re-build vignettes * creating vignettes ... OK * cleaning src * checking for LF line-endings in source and make files * checking for empty or unneeded directories * building 'BiasedUrn_1.04.tar.gz'
The final step is to install this modified package. If you have root privileges, a global install can be performed; otherwise, installation to a local directory tree can be performed. Next we describe these two cases.
If you have root or sudo privileges and wish to make the new package available system-wide, then perform this action as superuser. Here we demonstrate this using the sudo command. Similarly, one could also perform this action from a root shell.
John-Does-MacBook-Pro:Downloads jdoe$ sudo R CMD INSTALL BiasedUrn WARNING: Improper use of the sudo command could lead to data loss or the deletion of important system files. Please double-check your typing when using sudo. Type "man sudo" for more information. To proceed, enter your password, or type Ctrl-C to abort. Password: * installing to library '/Library/Frameworks/R.framework/Versions/2.15/Resources/library' * installing *source* package 'BiasedUrn' ... file 'src/Makevars' has the wrong MD5 checksum ** libs *** arch - i386 g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c fnchyppr.cpp -o fnchyppr.o g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c stoc1.cpp -o stoc1.o g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c stoc3.cpp -o stoc3.o g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c stocR.cpp -o stocR.o g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c urn1.cpp -o urn1.o g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c urn2.cpp -o urn2.o g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c wnchyppr.cpp -o wnchyppr.o g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o BiasedUrn.so fnchyppr.o stoc1.o stoc3.o stocR.o urn1.o urn2.o wnchyppr.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/2.15/Resources/library/BiasedUrn/libs/i386 *** arch - x86_64 g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c fnchyppr.cpp -o fnchyppr.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c stoc1.cpp -o stoc1.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c stoc3.cpp -o stoc3.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c stocR.cpp -o stocR.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c urn1.cpp -o urn1.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c urn2.cpp -o urn2.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c wnchyppr.cpp -o wnchyppr.o g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o BiasedUrn.so fnchyppr.o stoc1.o stoc3.o stocR.o urn1.o urn2.o wnchyppr.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/2.15/Resources/library/BiasedUrn/libs/x86_64 ** R ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes 'UrnTheory.Rtex' ** testing if installed package can be loaded *** arch - i386 *** arch - x86_64 * DONE (BiasedUrn)
In the event one does not have root privileges, a local version of the package can be installed and used from the user account. Ensure that you have a directory set for local package installations; here we have created the directory ~/R/library/ for this purpose. In the output from this command you should see a line indicating installation to this local directory:
John-Does-MacBook-Pro:Downloads jdoe$ R CMD INSTALL BiasedUrn --library=~/R/library/ * installing *source* package 'BiasedUrn' ... file 'src/Makevars' has the wrong MD5 checksum ** libs *** arch - i386 g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c fnchyppr.cpp -o fnchyppr.o g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c stoc1.cpp -o stoc1.o g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c stoc3.cpp -o stoc3.o g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c stocR.cpp -o stocR.o g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c urn1.cpp -o urn1.o g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c urn2.cpp -o urn2.o g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c wnchyppr.cpp -o wnchyppr.o g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o BiasedUrn.so fnchyppr.o stoc1.o stoc3.o stocR.o urn1.o urn2.o wnchyppr.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/jdoe/R/library/BiasedUrn/libs/i386 *** arch - x86_64 g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c fnchyppr.cpp -o fnchyppr.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c stoc1.cpp -o stoc1.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c stoc3.cpp -o stoc3.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c stocR.cpp -o stocR.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c urn1.cpp -o urn1.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c urn2.cpp -o urn2.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fPIC -g -O2 -c wnchyppr.cpp -o wnchyppr.o g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o BiasedUrn.so fnchyppr.o stoc1.o stoc3.o stocR.o urn1.o urn2.o wnchyppr.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/jdoe/R/library/BiasedUrn/libs/x86_64 ** R ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes 'UrnTheory.Rtex' ** testing if installed package can be loaded *** arch - i386 *** arch - x86_64 * DONE (BiasedUrn)
Subsequent to either of these methods, the package should be ready to use.
Epstein software | Human Genetics | School of Medicine | Emory University