I encountered a problem when I installed Bioconductor in Ubuntu 14.04. Here is the error information I have.
Any comment or suggestion will be highly appreciated.
> biocLite() BioC_mirror: http://bioconductor.org Using Bioconductor version 3.0 (BiocInstaller 1.16.5), R version 3.2.3. Old packages: 'RcppArmadillo', 'mgcv' Update all/some/none? [a/s/n]: a trying URL 'http://cran.fhcrc.org/src/contrib/RcppArmadillo_0.6.400.2.2.tar.gz' Content type 'application/x-gzip' length 986451 bytes (963 KB) ================================================== downloaded 963 KB * installing *source* package ‘RcppArmadillo’ ... ** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked * checking LAPACK_LIBS: system LAPACK found ** libs g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I../inst/include -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppArmadillo.cpp -o RcppArmadillo.o g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I../inst/include -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I../inst/include -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c fastLm.cpp -o fastLm.o g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR /usr/bin/ld: cannot find -llapack /usr/bin/ld: cannot find -lblas /usr/bin/ld: cannot find -lgfortran collect2: error: ld returned 1 exit status make: *** [RcppArmadillo.so] Error 1 ERROR: compilation failed for package ‘RcppArmadillo’ * removing ‘/usr/local/lib/R/site-library/RcppArmadillo’ * restoring previous ‘/usr/local/lib/R/site-library/RcppArmadillo’ The downloaded source packages are in ‘/tmp/RtmpO6UNRp/downloaded_packages’ trying URL 'http://cran.fhcrc.org/src/contrib/mgcv_1.8-10.tar.gz' Content type 'application/x-gzip' length 802060 bytes (783 KB) ================================================== downloaded 783 KB * installing *source* package ‘mgcv’ ... ** package ‘mgcv’ successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c coxph.c -o coxph.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c discrete.c -o discrete.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c gdi.c -o gdi.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c magic.c -o magic.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c mat.c -o mat.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c matrix.c -o matrix.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c mgcv.c -o mgcv.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c misc.c -o misc.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c mvn.c -o mvn.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c qp.c -o qp.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c soap.c -o soap.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c sparse-smooth.c -o sparse-smooth.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c tprs.c -o tprs.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o mgcv.so coxph.o discrete.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o mvn.o qp.o soap.o sparse-smooth.o tprs.o -llapack -lblas -lgfortran -lm -lquadmath -fopenmp -L/usr/lib/R/lib -lR /usr/bin/ld: cannot find -llapack /usr/bin/ld: cannot find -lblas /usr/bin/ld: cannot find -lgfortran collect2: error: ld returned 1 exit status make: *** [mgcv.so] Error 1 ERROR: compilation failed for package ‘mgcv’ * removing ‘/usr/lib/R/library/mgcv’ * restoring previous ‘/usr/lib/R/library/mgcv’ The downloaded source packages are in ‘/tmp/RtmpO6UNRp/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done Warning messages: 1: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘RcppArmadillo’ had non-zero exit status 2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘mgcv’ had non-zero exit status