

## Compile the objects for R
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c linefile.c -o linefile.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c cheapcgi.c -o cheapcgi.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c common.c -o common.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c hash.c -o hash.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c localmem.c -o localmem.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c options.c -o options.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c dystring.c -o dystring.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c chain.c -o chain.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c memalloc.c -o memalloc.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c verbose.c -o verbose.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c portimpl.c -o portimpl.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c servcl.c -o servcl.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c servBrcMcw.c -o servBrcMcw.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c servpws.c -o servpws.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c servCrunx.c -o servCrunx.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c servmsII.c -o servmsII.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c servcis.c -o servcis.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c errabort.c -o errabort.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c pipeline.c -o pipeline.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c dlist.c -o dlist.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c bits.c -o bits.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c cirTree.c -o cirTree.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c udc.c -o udc.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c osunix.c -o osunix.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c wildcmp.c -o wildcmp.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c net.c -o net.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c sqlList.c -o sqlList.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c sqlNum.c -o sqlNum.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c internet.c -o internet.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c obscure.c -o obscure.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c dnautil.c -o dnautil.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c mime.c -o mime.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c base64.c -o base64.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c intExp.c -o intExp.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c kxTok.c -o kxTok.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c https.c -o https.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c axt.c -o axt.o
gcc -std=gnu99 -I/export/opt/radmin/R-2.15.2/lib64/R/include -DNDEBUG -I/mnt/biggley/home/gtan/Repos/CSC/CNEr/src -I/usr/local/include   -I/mnt/biggley/home/gtan/src/kent/src/inc -fpic  -g -O2  -c ceScanBranch1.c -o ceScanBranch1.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o ceScanBranch1.so ceScanBranch1.o linefile.o cheapcgi.o common.o hash.o localmem.o options.o dystring.o chain.o memalloc.o verbose.o portimpl.o servcl.o servBrcMcw.o servpws.o servCrunx.o servmsII.o servcis.o errabort.o pipeline.o dlist.o bits.o cirTree.o udc.o osunix.o wildcmp.o net.o sqlList.o sqlNum.o internet.o obscure.o dnautil.o mime.o base64.o intExp.o kxTok.o https.o axt.o -L/mnt/biggley/home/gtan/src/kent/src/lib  -L/export/opt/radmin/R-2.15.2/lib64/R/lib -lR

