As a part of the RcppDeepState project, which has been graciously funded by R Consortium, we are creating an easy way to use DeepState to fuzz test R packages with C++ code defined using Rcpp. DeepState requires the C++ programmer to define a “test harness” which is C++ source code without a main function, but with tests/expectations. The DeepState framework then compiles that test harness to an executable (with a main function) to which fuzz testing libraries can send input.

Usually R runs as main, so we need to instead compile another program and link it to the R shared library, as documented in Writing R Extensions, section Embedding R under Unix-alikes.

So I downloaded the R source code, R-3.6.3.tar.gz, and I looked for examples in the R-3.6.3/tests/Embedding directory:

tdhock@maude-MacBookPro:~/R/R-3.6.3/tests/Embedding$ls *.c embeddedRCall.c Rerror.c Rpackage.c Rplot.c Rshutdown.c tryEval.c Rcpp.c RNamedCall.c RParseEval.c Rpostscript.c Rtest.c tdhock@maude-MacBookPro:~/R/R-3.6.3/tests/Embedding$


There is also a Makefile that can be used to compile the simplest test program:

tdhock@maude-MacBookPro:~/R/R-3.6.3/tests/Embedding$rm -f Rtest *.o && make Rtest gcc -I"../../include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Rtest.c -o Rtest.o gcc -I"../../include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c embeddedRCall.c -o embeddedRCall.o ../../bin/R CMD gcc -Wl,--export-dynamic -fopenmp -L/usr/local/lib -o Rtest Rtest.o embeddedRCall.o -L"../../lib" -lR  However when I ran that program as usual it seems there is some problem with the environment: tdhock@maude-MacBookPro:~/R/R-3.6.3/tests/Embedding$ ./Rtest
Fatal error: R home directory is not defined


The error message suggests that the problem may be fixed by setting R_HOME, but:

tdhock@maude-MacBookPro:~/R/R-3.6.3/tests/Embedding$R_HOME=~/lib/R ./Rtest Error in readRDS(mapfile) : cannot read workspace version 3 written by R 3.6.3; need R 3.5.0 or newer Error in attach(NULL, name = "Autoloads") : could not find function "attach" R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. Error in options(repos = "http://cloud.r-project.org") : could not find function "options" Error: object '.ArgsEnv' not found Fatal error: unable to initialize the JIT tdhock@maude-MacBookPro:~/R/R-3.6.3/tests/Embedding$


There still seems to be some problem above. It is definitely a problem with the environment, because running it via the code below (as found in the Makefile) works fine:

tdhock@maude-MacBookPro:~/R/R-3.6.3/tests/Embedding$R CMD ./Rtest R version 3.6.3 (2020-02-29) -- "Holding the Windsock" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. Loading required package: grDevices [1] 1 2 3 4 5 6 7 8 9 10 tdhock@maude-MacBookPro:~/R/R-3.6.3/tests/Embedding$


Looking at the ldd output below, it is clear that the problem is that the system/ubuntu/apt R is being used, rather than the more recent R-3.6.3,

tdhock@maude-MacBookPro:~/R/R-3.6.3/tests/Embedding$ldd Rtest|grep libR libR.so => /usr/lib/libR.so (0x00007fca1e951000) tdhock@maude-MacBookPro:~/R/R-3.6.3/tests/Embedding$


So I wrote my own Makefile (code below). First I start by defining some paths/flags to tell the compiler/linker where to find my R (under my home directory).

R_HOME=${HOME}/lib/R R_LIB=${R_HOME}/lib
R_INCLUDE=${R_HOME}/include CPPFLAGS=-I${R_INCLUDE}


After that, the key to getting it to work is to specify the non-standard library directory using two command line arguments, as explained in a previous blog post.

# R_LIB must be specified both using -L and via -Wl,-rpath=
Rtest: Rtest.o embeddedRCall.o
gcc -o Rtest Rtest.o embeddedRCall.o -L${R_LIB} -Wl,-rpath=${R_LIB} -lR
R_HOME=${R_HOME} ./Rtest  Finally the recipes below compile the two C source code files to object files. # -c option means to not link. Rtest.o: Rtest.c gcc${CPPFLAGS} Rtest.c -o Rtest.o -c
embeddedRCall.o: embeddedRCall.c
gcc ${CPPFLAGS} embeddedRCall.c -o embeddedRCall.o -c  I saved this code to Makefile.mine and I get the following output when running it: tdhock@maude-MacBookPro:~/R/R-3.6.3/tests/Embedding$ rm -f *.o Rtest && make -f Makefile.mine
gcc -I/home/tdhock/lib/R/include Rtest.c -o Rtest.o -c
gcc -I/home/tdhock/lib/R/include embeddedRCall.c -o embeddedRCall.o -c
gcc -o Rtest Rtest.o embeddedRCall.o -L/home/tdhock/lib/R/lib -Wl,-rpath=/home/tdhock/lib/R/lib -lR
R_HOME=/home/tdhock/lib/R ./Rtest

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

tdhock@maude-MacBookPro:~/R/R-3.6.3/tests/Embedding$ Note that the R_HOME environment variable must be specified, as in the code above. If not, we get an error, as in the code below: tdhock@maude-MacBookPro:~/R/R-3.6.3/tests/Embedding$ ./Rtest