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ck-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpmat.c -o glpk/glpmat.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpmpl01.c -o glpk/glpmpl01.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpmpl02.c -o glpk/glpmpl02.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpmpl03.c -o glpk/glpmpl03.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpmpl04.c -o glpk/glpmpl04.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpmpl05.c -o glpk/glpmpl05.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpmpl06.c -o glpk/glpmpl06.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpmps.c -o glpk/glpmps.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpnet01.c -o glpk/glpnet01.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpnet02.c -o glpk/glpnet02.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpnet03.c -o glpk/glpnet03.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpnet04.c -o glpk/glpnet04.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpnet05.c -o glpk/glpnet05.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpnet06.c -o glpk/glpnet06.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpnet07.c -o glpk/glpnet07.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpnet08.c -o glpk/glpnet08.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpnet09.c -o glpk/glpnet09.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpnpp01.c -o glpk/glpnpp01.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpnpp02.c -o glpk/glpnpp02.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpnpp03.c -o glpk/glpnpp03.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpnpp04.c -o glpk/glpnpp04.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpnpp05.c -o glpk/glpnpp05.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpqmd.c -o glpk/glpqmd.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glprgr.c -o glpk/glprgr.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glprng01.c -o glpk/glprng01.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glprng02.c -o glpk/glprng02.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpscf.c -o glpk/glpscf.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpscl.c -o glpk/glpscl.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpsdf.c -o glpk/glpsdf.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpspm.c -o glpk/glpspm.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpspx01.c -o glpk/glpspx01.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpspx02.c -o glpk/glpspx02.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpsql.c -o glpk/glpsql.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpssx01.c -o glpk/glpssx01.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glpssx02.c -o glpk/glpssx02.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glpk/glptsp.c -o glpk/glptsp.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c simpleraytracer/Color.cpp -o simpleraytracer/Color.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c simpleraytracer/Light.cpp -o simpleraytracer/Light.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c simpleraytracer/Point.cpp -o simpleraytracer/Point.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c simpleraytracer/RIgraphRay.cpp -o simpleraytracer/RIgraphRay.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c simpleraytracer/Ray.cpp -o simpleraytracer/Ray.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c simpleraytracer/RayTracer.cpp -o simpleraytracer/RayTracer.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c simpleraytracer/RayVector.cpp -o simpleraytracer/RayVector.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c simpleraytracer/Shape.cpp -o simpleraytracer/Shape.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c simpleraytracer/Sphere.cpp -o simpleraytracer/Sphere.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c simpleraytracer/Triangle.cpp -o simpleraytracer/Triangle.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c simpleraytracer/unit_limiter.cpp -o simpleraytracer/unit_limiter.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c uuid/R.c -o uuid/R.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c uuid/clear.c -o uuid/clear.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c uuid/compare.c -o uuid/compare.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c uuid/copy.c -o uuid/copy.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c uuid/gen_uuid.c -o uuid/gen_uuid.o
In file included from /usr/include/stdio.h:27:0,
                 from uuid/gen_uuid.c:48:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
 # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
   ^~~~~~~
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c uuid/isnull.c -o uuid/isnull.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c uuid/pack.c -o uuid/pack.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c uuid/parse.c -o uuid/parse.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c uuid/unpack.c -o uuid/unpack.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c uuid/unparse.c -o uuid/unparse.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rinterface.c -o rinterface.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rinterface_extra.c -o rinterface_extra.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c lazyeval.c -o lazyeval.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o igraph.so AMD/Source/amd.o AMD/Source/amd_1.o AMD/Source/amd_2.o AMD/Source/amd_aat.o AMD/Source/amd_control.o AMD/Source/amd_defaults.o AMD/Source/amd_dump.o AMD/Source/amd_global.o AMD/Source/amd_info.o AMD/Source/amd_order.o AMD/Source/amd_post_tree.o AMD/Source/amd_postorder.o AMD/Source/amd_preprocess.o AMD/Source/amd_valid.o AMD/Source/amdbar.o CHOLMOD/Check/cholmod_check.o CHOLMOD/Check/cholmod_read.o CHOLMOD/Check/cholmod_write.o CHOLMOD/Cholesky/cholmod_amd.o CHOLMOD/Cholesky/cholmod_analyze.o CHOLMOD/Cholesky/cholmod_colamd.o CHOLMOD/Cholesky/cholmod_etree.o CHOLMOD/Cholesky/cholmod_factorize.o CHOLMOD/Cholesky/cholmod_postorder.o CHOLMOD/Cholesky/cholmod_rcond.o CHOLMOD/Cholesky/cholmod_resymbol.o CHOLMOD/Cholesky/cholmod_rowcolcounts.o CHOLMOD/Cholesky/cholmod_rowfac.o CHOLMOD/Cholesky/cholmod_solve.o CHOLMOD/Cholesky/cholmod_spsolve.o CHOLMOD/Core/cholmod_aat.o CHOLMOD/Core/cholmod_add.o CHOLMOD/Core/cholmod_band.o CHOLMOD/Core/cholmod_change_factor.o CHOLMOD/Core/cholmod_common.o CHOLMOD/Core/cholmod_complex.o CHOLMOD/Core/cholmod_copy.o CHOLMOD/Core/cholmod_dense.o CHOLMOD/Core/cholmod_error.o CHOLMOD/Core/cholmod_factor.o CHOLMOD/Core/cholmod_memory.o CHOLMOD/Core/cholmod_sparse.o CHOLMOD/Core/cholmod_transpose.o CHOLMOD/Core/cholmod_triplet.o CHOLMOD/Core/cholmod_version.o CHOLMOD/MatrixOps/cholmod_drop.o CHOLMOD/MatrixOps/cholmod_horzcat.o CHOLMOD/MatrixOps/cholmod_norm.o CHOLMOD/MatrixOps/cholmod_scale.o CHOLMOD/MatrixOps/cholmod_sdmult.o CHOLMOD/MatrixOps/cholmod_ssmult.o CHOLMOD/MatrixOps/cholmod_submatrix.o CHOLMOD/MatrixOps/cholmod_symmetry.o CHOLMOD/MatrixOps/cholmod_vertcat.o CHOLMOD/Modify/cholmod_rowadd.o CHOLMOD/Modify/cholmod_rowdel.o CHOLMOD/Modify/cholmod_updown.o CHOLMOD/Partition/cholmod_camd.o CHOLMOD/Partition/cholmod_ccolamd.o CHOLMOD/Partition/cholmod_csymamd.o CHOLMOD/Partition/cholmod_metis.o CHOLMOD/Partition/cholmod_nesdis.o CHOLMOD/Supernodal/cholmod_super_numeric.o CHOLMOD/Supernodal/cholmod_super_solve.o CHOLMOD/Supernodal/cholmod_super_symbolic.o COLAMD/Source/colamd.o COLAMD/Source/colamd_global.o DensityGrid.o DensityGrid_3d.o NetDataTypes.o NetRoutines.o SuiteSparse_config/SuiteSparse_config.o adjlist.o arpack.o array.o atlas.o attributes.o basic_query.o bfgs.o bigint.o bignum.o bipartite.o blas.o bliss.o bliss_eqrefhash.o bliss_graph.o bliss_heap.o bliss_orbit.o bliss_partition.o bliss_timer.o bliss_utils.o cattributes.o centrality.o cliques.o clustertool.o cocitation.o cohesive_blocks.o community.o complex.o components.o conversion.o cores.o cs/cs_add.o cs/cs_amd.o cs/cs_chol.o cs/cs_cholsol.o cs/cs_compress.o cs/cs_counts.o cs/cs_cumsum.o cs/cs_dfs.o cs/cs_dmperm.o cs/cs_droptol.o cs/cs_dropzeros.o cs/cs_dupl.o cs/cs_entry.o cs/cs_ereach.o cs/cs_etree.o cs/cs_fkeep.o cs/cs_gaxpy.o cs/cs_happly.o cs/cs_house.o cs/cs_ipvec.o cs/cs_leaf.o cs/cs_load.o cs/cs_lsolve.o cs/cs_ltsolve.o cs/cs_lu.o cs/cs_lusol.o cs/cs_malloc.o cs/cs_maxtrans.o cs/cs_multiply.o cs/cs_norm.o cs/cs_permute.o cs/cs_pinv.o cs/cs_post.o cs/cs_print.o cs/cs_pvec.o cs/cs_qr.o cs/cs_qrsol.o cs/cs_randperm.o cs/cs_reach.o cs/cs_scatter.o cs/cs_scc.o cs/cs_schol.o cs/cs_spsolve.o cs/cs_sqr.o cs/cs_symperm.o cs/cs_tdfs.o cs/cs_transpose.o cs/cs_updown.o cs/cs_usolve.o cs/cs_util.o cs/cs_utsolve.o decomposition.o distances.o dotproduct.o dqueue.o drl_graph.o drl_graph_3d.o drl_layout.o drl_layout_3d.o drl_parse.o eigen.o embedding.o fast_community.o feedback_arc_set.o flow.o foreign-dl-lexer.o foreign-dl-parser.o foreign-gml-lexer.o foreign-gml-parser.o foreign-graphml.o foreign-lgl-lexer.o foreign-lgl-parser.o foreign-ncol-lexer.o foreign-ncol-parser.o foreign-pajek-lexer.o foreign-pajek-parser.o foreign.o forestfire.o fortran_intrinsics.o games.o gengraph_box_list.o gengraph_degree_sequence.o gengraph_graph_molloy_hash.o gengraph_graph_molloy_optimized.o gengraph_mr-connected.o gengraph_powerlaw.o gengraph_random.o glet.o glpk_support.o gml_tree.o hacks.o heap.o igraph_buckets.o igraph_error.o igraph_estack.o igraph_fixed_vectorlist.o igraph_grid.o igraph_hashtable.o igraph_heap.o igraph_hrg.o igraph_hrg_types.o igraph_marked_queue.o igraph_psumtree.o igraph_set.o igraph_stack.o igraph_strvector.o igraph_trie.o infomap.o infomap_FlowGraph.o infomap_Greedy.o infomap_Node.o interrupt.o iterators.o lad.o lapack.o layout.o layout_dh.o layout_fr.o layout_gem.o layout_kk.o lsap.o matching.o math.o matrix.o maximal_cliques.o memory.o microscopic_update.o mixing.o motifs.o operators.o optimal_modularity.o other.o paths.o plfit/error.o plfit/gss.o plfit/kolmogorov.o plfit/lbfgs.o plfit/options.o plfit/plfit.o plfit/zeta.o pottsmodel_2.o progress.o prpack.o prpack/prpack_base_graph.o prpack/prpack_igraph_graph.o prpack/prpack_preprocessed_ge_graph.o prpack/prpack_preprocessed_gs_graph.o prpack/prpack_preprocessed_scc_graph.o prpack/prpack_preprocessed_schur_graph.o prpack/prpack_result.o prpack/prpack_solver.o prpack/prpack_utils.o qsort.o qsort_r.o random.o random_walk.o sbm.o scan.o scg.o scg_approximate_methods.o scg_exact_scg.o scg_kmeans.o scg_optimal_method.o scg_utils.o separators.o sir.o spanning_trees.o sparsemat.o spectral_properties.o spmatrix.o st-cuts.o statusbar.o structural_properties.o structure_generators.o sugiyama.o topology.o triangles.o type_indexededgelist.o types.o vector.o vector_ptr.o version.o visitors.o walktrap.o walktrap_communities.o walktrap_graph.o walktrap_heap.o zeroin.o dgetv0.o dlaqrb.o dmout.o dnaitr.o dnapps.o dnaup2.o dnaupd.o dnconv.o dneigh.o dneupd.o dngets.o dsaitr.o dsapps.o dsaup2.o dsaupd.o dsconv.o dseigt.o dsesrt.o dseupd.o dsgets.o dsortc.o dsortr.o dstatn.o dstats.o dstqrb.o dvout.o ivout.o second.o glpk/amd/amd_1.o glpk/amd/amd_2.o glpk/amd/amd_aat.o glpk/amd/amd_control.o glpk/amd/amd_defaults.o glpk/amd/amd_dump.o glpk/amd/amd_info.o glpk/amd/amd_order.o glpk/amd/amd_post_tree.o glpk/amd/amd_postorder.o glpk/amd/amd_preprocess.o glpk/amd/amd_valid.o glpk/colamd/colamd.o glpk/glpapi01.o glpk/glpapi02.o glpk/glpapi03.o glpk/glpapi04.o glpk/glpapi05.o glpk/glpapi06.o glpk/glpapi07.o glpk/glpapi08.o glpk/glpapi09.o glpk/glpapi10.o glpk/glpapi11.o glpk/glpapi12.o glpk/glpapi13.o glpk/glpapi14.o glpk/glpapi15.o glpk/glpapi16.o glpk/glpapi17.o glpk/glpapi18.o glpk/glpapi19.o glpk/glpavl.o glpk/glpbfd.o glpk/glpbfx.o glpk/glpcpx.o glpk/glpdmp.o glpk/glpdmx.o glpk/glpenv01.o glpk/glpenv02.o glpk/glpenv03.o glpk/glpenv04.o glpk/glpenv05.o glpk/glpenv06.o glpk/glpenv07.o glpk/glpenv08.o glpk/glpfhv.o glpk/glpgmp.o glpk/glphbm.o glpk/glpini01.o glpk/glpini02.o glpk/glpios01.o glpk/glpios02.o glpk/glpios03.o glpk/glpios04.o glpk/glpios05.o glpk/glpios06.o glpk/glpios07.o glpk/glpios08.o glpk/glpios09.o glpk/glpios10.o glpk/glpios11.o glpk/glpios12.o glpk/glpipm.o glpk/glplib01.o glpk/glplib02.o glpk/glplib03.o glpk/glplpf.o glpk/glplpx01.o glpk/glplpx02.o glpk/glplpx03.o glpk/glpluf.o glpk/glplux.o glpk/glpmat.o glpk/glpmpl01.o glpk/glpmpl02.o glpk/glpmpl03.o glpk/glpmpl04.o glpk/glpmpl05.o glpk/glpmpl06.o glpk/glpmps.o glpk/glpnet01.o glpk/glpnet02.o glpk/glpnet03.o glpk/glpnet04.o glpk/glpnet05.o glpk/glpnet06.o glpk/glpnet07.o glpk/glpnet08.o glpk/glpnet09.o glpk/glpnpp01.o glpk/glpnpp02.o glpk/glpnpp03.o glpk/glpnpp04.o glpk/glpnpp05.o glpk/glpqmd.o glpk/glprgr.o glpk/glprng01.o glpk/glprng02.o glpk/glpscf.o glpk/glpscl.o glpk/glpsdf.o glpk/glpspm.o glpk/glpspx01.o glpk/glpspx02.o glpk/glpsql.o glpk/glpssx01.o glpk/glpssx02.o glpk/glptsp.o simpleraytracer/Color.o simpleraytracer/Light.o simpleraytracer/Point.o simpleraytracer/RIgraphRay.o simpleraytracer/Ray.o simpleraytracer/RayTracer.o simpleraytracer/RayVector.o simpleraytracer/Shape.o simpleraytracer/Sphere.o simpleraytracer/Triangle.o simpleraytracer/unit_limiter.o uuid/R.o uuid/clear.o uuid/compare.o uuid/copy.o uuid/gen_uuid.o uuid/isnull.o uuid/pack.o uuid/parse.o uuid/unpack.o uuid/unparse.o rinterface.o rinterface_extra.o lazyeval.o -lxml2 -lgmp -lgfortran -lm -lquadmath -L/usr/local/lib/R/lib -lRlapack -L/usr/local/lib/R/lib -lRblas -lgfortran -lm -lquadmath -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/igraph/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (igraph)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘agricolae’ ...
** package ‘agricolae’ successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (agricolae)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘sapa’ ...
** package ‘sapa’ successfully unpacked and MD5 sums checked
** libs
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sapa_lapack.c -o sapa_lapack.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o sapa.so sapa_lapack.o -L/usr/local/lib/R/lib -lRlapack -L/usr/local/lib/R/lib -lRblas -lgfortran -lm -lquadmath -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/sapa/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (sapa)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘rcdk’ ...
** package ‘rcdk’ successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (rcdk)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘rrcov’ ...
** package ‘rrcov’ successfully unpacked and MD5 sums checked
** libs
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R-rng4ftn.c -o R-rng4ftn.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c covOPW.c -o covOPW.o
f95   -fpic  -g -O2  -c ds11.f -o ds11.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fast-mve.c -o fast-mve.o
f95   -fpic  -g -O2  -c fsada.f -o fsada.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sest.c -o sest.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o rrcov.so R-rng4ftn.o covOPW.o ds11.o fast-mve.o fsada.o sest.o -L/usr/local/lib/R/lib -lRlapack -L/usr/local/lib/R/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/rrcov/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (rrcov)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘Metab’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (Metab)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘MetCirc’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (MetCirc)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘mQTL.NMR’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (mQTL.NMR)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘PAPi’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (PAPi)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘yamss’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (yamss)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘assertive.strings’ ...
** package ‘assertive.strings’ successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (assertive.strings)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘assertive.datetimes’ ...
** package ‘assertive.datetimes’ successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (assertive.datetimes)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘assertive.code’ ...
** package ‘assertive.code’ successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (assertive.code)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘rsm’ ...
** package ‘rsm’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (rsm)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘optimx’ ...
** package ‘optimx’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (optimx)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘car’ ...
** package ‘car’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (car)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘BiGGR’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (BiGGR)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘CAMERA’ ...
** libs
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fastMatch.c -o fastMatch.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o CAMERA.so fastMatch.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/CAMERA/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (CAMERA)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘msPurity’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (msPurity)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘RMassBank’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (RMassBank)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘statTarget’ ...
** R
** inst
** preparing package for lazy loading
R session is headless; GTK+ not initialized.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
R session is headless; GTK+ not initialized.
* DONE (statTarget)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘assertive.data’ ...
** package ‘assertive.data’ successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (assertive.data)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘assertive.data.uk’ ...
** package ‘assertive.data.uk’ successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (assertive.data.uk)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘assertive.data.us’ ...
** package ‘assertive.data.us’ successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (assertive.data.us)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘caret’ ...
** package ‘caret’ successfully unpacked and MD5 sums checked
** libs
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c caret.c -o caret.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o caret.so caret.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/caret/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (caret)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘IPO’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (IPO)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘LOBSTAHS’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (LOBSTAHS)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘metabomxtr’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (metabomxtr)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘metaMS’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (metaMS)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘MWASTools’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (MWASTools)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘assertive’ ...
** package ‘assertive’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (assertive)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘MAIT’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘scores’ in package ‘MAIT’
Creating a new generic function for ‘loadings’ in package ‘MAIT’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (MAIT)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘OmicsMarkeR’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (OmicsMarkeR)

The downloaded source packages are in
	‘/tmp/RtmpwPBy1K/downloaded_packages’
Old packages: 'Biostrings', 'curl', 'KEGGREST', 'kohonen', 'lattice', 'proFIA',
  'rmarkdown', 'stringi', 'viridis'
> 
> # just in case there were warnings, we want to see them
> # without having to scroll up:
> warnings()
NULL
> 
> if (!is.null(warnings()))
+ {
+     w <- capture.output(warnings())
+     if (length(grep("is not available|had non-zero exit status", w)))
+         quit("no", 1L)
+ }
> 
> suppressWarnings(BiocInstaller::biocValid(fix=TRUE, ask=FALSE))

* sessionInfo()

R Under development (unstable) (2017-03-19 r72368)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default
BLAS: /usr/local/lib/R/lib/libRblas.so
LAPACK: /usr/local/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.25.3

loaded via a namespace (and not attached):
[1] compiler_3.4.0 tools_3.4.0   

* Out-of-date packages
           Package      LibPath                         Installed Built  
Biostrings "Biostrings" "/usr/local/lib/R/site-library" "2.43.5"  "3.4.0"
curl       "curl"       "/usr/local/lib/R/site-library" "2.3"     "3.4.0"
KEGGREST   "KEGGREST"   "/usr/local/lib/R/site-library" "1.15.0"  "3.4.0"
kohonen    "kohonen"    "/usr/local/lib/R/site-library" "3.0.0"   "3.4.0"
proFIA     "proFIA"     "/usr/local/lib/R/site-library" "1.1.3"   "3.4.0"
rmarkdown  "rmarkdown"  "/usr/local/lib/R/site-library" "1.3"     "3.4.0"
stringi    "stringi"    "/usr/local/lib/R/site-library" "1.1.2"   "3.4.0"
viridis    "viridis"    "/usr/local/lib/R/site-library" "0.3.4"   "3.4.0"
           ReposVer Repository                                              
Biostrings "2.43.6" "https://bioconductor.org/packages/3.5/bioc/src/contrib"
curl       "2.4"    "https://cran.rstudio.com/src/contrib"                  
KEGGREST   "1.15.1" "https://bioconductor.org/packages/3.5/bioc/src/contrib"
kohonen    "3.0.2"  "https://cran.rstudio.com/src/contrib"                  
proFIA     "1.1.9"  "https://bioconductor.org/packages/3.5/bioc/src/contrib"
rmarkdown  "1.4"    "https://cran.rstudio.com/src/contrib"                  
stringi    "1.1.3"  "https://cran.rstudio.com/src/contrib"                  
viridis    "0.4.0"  "https://cran.rstudio.com/src/contrib"                  

update with biocLite()

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.25.3), R Under development (unstable)
  (2017-03-19 r72368).
Installing package(s) ‘Biostrings’, ‘curl’, ‘KEGGREST’, ‘kohonen’, ‘proFIA’,
  ‘rmarkdown’, ‘stringi’, ‘viridis’
also installing the dependency ‘viridisLite’

trying URL 'https://cran.rstudio.com/src/contrib/viridisLite_0.2.0.tar.gz'
Content type 'application/x-gzip' length 48073 bytes (46 KB)
==================================================
downloaded 46 KB

trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/Biostrings_2.43.6.tar.gz'
Content type 'application/x-gzip' length 12699079 bytes (12.1 MB)
==================================================
downloaded 12.1 MB

trying URL 'https://cran.rstudio.com/src/contrib/curl_2.4.tar.gz'
Content type 'application/x-gzip' length 403058 bytes (393 KB)
==================================================
downloaded 393 KB

trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/KEGGREST_1.15.1.tar.gz'
Content type 'application/x-gzip' length 24432 bytes (23 KB)
==================================================
downloaded 23 KB

trying URL 'https://cran.rstudio.com/src/contrib/kohonen_3.0.2.tar.gz'
Content type 'application/x-gzip' length 1097852 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/proFIA_1.1.9.tar.gz'
Content type 'application/x-gzip' length 412778 bytes (403 KB)
==================================================
downloaded 403 KB

trying URL 'https://cran.rstudio.com/src/contrib/rmarkdown_1.4.tar.gz'
Content type 'application/x-gzip' length 2077472 bytes (2.0 MB)
==================================================
downloaded 2.0 MB

trying URL 'https://cran.rstudio.com/src/contrib/stringi_1.1.3.tar.gz'
Content type 'application/x-gzip' length 3644529 bytes (3.5 MB)
==================================================
downloaded 3.5 MB

trying URL 'https://cran.rstudio.com/src/contrib/viridis_0.4.0.tar.gz'
Content type 'application/x-gzip' length 1787731 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘viridisLite’ ...
** package ‘viridisLite’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** preparing package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (viridisLite)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘Biostrings’ ...
** libs
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c BAB_class.c -o BAB_class.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c BitMatrix.c -o BitMatrix.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c MIndex_class.c -o MIndex_class.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SparseList_utils.c -o SparseList_utils.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XStringSetList_class.c -o XStringSetList_class.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XStringSet_class.c -o XStringSet_class.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XStringSet_io.c -o XStringSet_io.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XString_class.c -o XString_class.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XVector_stubs.c -o XVector_stubs.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c align_needwunsQS.c -o align_needwunsQS.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c align_utils.c -o align_utils.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c find_palindromes.c -o find_palindromes.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gtestsim.c -o gtestsim.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c inject_code.c -o inject_code.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c letter_frequency.c -o letter_frequency.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c lowlevel_matching.c -o lowlevel_matching.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_PWM.c -o match_PWM.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pattern.c -o match_pattern.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pattern_indels.c -o match_pattern_indels.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pdict.c -o match_pdict.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pdict_Twobit.c -o match_pdict_Twobit.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pdict_utils.c -o match_pdict_utils.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_reporting.c -o match_reporting.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c matchprobes.c -o matchprobes.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pmatchPattern.c -o pmatchPattern.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c replaceAt.c -o replaceAt.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c replace_letter_at.c -o replace_letter_at.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c strutils.c -o strutils.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c translate.c -o translate.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utils.c -o utils.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c xscat.c -o xscat.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XStringSet_io.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/Biostrings/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘ls’ from package ‘base’ in package ‘Biostrings’
Creating a new generic function for ‘offset’ in package ‘Biostrings’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (Biostrings)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-I/usr/include/x86_64-linux-gnu
Using PKG_LIBS=-lcurl
** libs
rm -f curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o reflist.o utils.o version.o
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu  -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c callbacks.c -o callbacks.o
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu  -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c curl.c -o curl.o
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu  -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c download.c -o download.o
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu  -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c escape.c -o escape.o
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu  -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fetch.c -o fetch.o
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu  -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c form.c -o form.o
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu  -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c getdate.c -o getdate.o
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu  -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c handle.c -o handle.o
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu  -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ieproxy.c -o ieproxy.o
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu  -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu  -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c interrupt.c -o interrupt.o
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu  -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c multi.c -o multi.o
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu  -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nslookup.c -o nslookup.o
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu  -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c reflist.c -o reflist.o
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu  -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utils.c -o utils.o
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu  -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c version.c -o version.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o reflist.o utils.o version.o -lcurl -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/curl/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (curl)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘kohonen’ ...
** package ‘kohonen’ successfully unpacked and MD5 sums checked
** libs
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c batch-supersom.cpp -o batch-supersom.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c distance-functions.cpp -o distance-functions.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c kohonen_init.c -o kohonen_init.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c map.cpp -o map.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c neighbourhood-functions.cpp -o neighbourhood-functions.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pbatch-supersom.cpp -o pbatch-supersom.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c supersom.cpp -o supersom.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o kohonen.so RcppExports.o batch-supersom.o distance-functions.o kohonen_init.o map.o neighbourhood-functions.o pbatch-supersom.o supersom.o -fopenmp -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/kohonen/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (kohonen)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘proFIA’ ...
** libs
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c FIABandsExtractionCentroid.c -o FIABandsExtractionCentroid.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c UtilFunc.c -o UtilFunc.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fastMatchPpm.c -o fastMatchPpm.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o proFIA.so FIABandsExtractionCentroid.o UtilFunc.o fastMatchPpm.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/proFIA/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (proFIA)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘rmarkdown’ ...
** package ‘rmarkdown’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (rmarkdown)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘stringi’ ...
** package ‘stringi’ successfully unpacked and MD5 sums checked
checking for local ICUDT_DIR... icu55/data
checking for R_HOME... /usr/local/lib/R
checking for R... /usr/local/lib/R/bin/R
checking for R >= 3.1.0... yes
checking for cat... /usr/bin/cat
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... g++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking elf.h usability... yes
checking elf.h presence... yes
checking for elf.h... yes
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++11 accepts -g... yes
checking whether the C++ compiler supports the long long type... yes
checking whether the compiler implements namespaces... yes
checking whether the compiler supports Standard Template Library... yes
checking whether std::map is available... yes
checking for pkg-config... /usr/bin/pkg-config
checking with pkg-config for ICU4C installed... 57.1
checking for ICU4C >= 50... yes
checking for proper CPPFLAGS, LDFLAGS, and LIBS... done
checking whether we may build an ICU-based project... yes
checking for available ICU data library (ucnv, uloc, utrans)... yes
checking for available ICU data library (ucol)... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/uconfig_local.h
config.status: creating src/install.libs.R

*** stringi configure summary:
    ICU_FOUND=1
    ICUDT_DIR=icu55/data
    STRINGI_CXXSTD=CXX_STD=CXX11
    STRINGI_CFLAGS=   -fpic
    STRINGI_CPPFLAGS=-I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H
    STRINGI_CXXFLAGS=   -fpic
    STRINGI_LDFLAGS=-L/usr/lib/x86_64-linux-gnu  
    STRINGI_LIBS=-licui18n -licuuc -licudata  

*** compiler settings used:
    CC=gcc
    CPP=g++ -E
    LD=g++
    CFLAGS=-g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic  
    CPPFLAGS=-I/usr/local/include   -UDEBUG -DNDEBUG
    CXX=g++ -std=gnu++11
    CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic  
    LDFLAGS=  
    LIBS=  

** libs
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_brkiter.cpp -o stri_brkiter.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_collator.cpp -o stri_collator.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_common.cpp -o stri_common.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_compare.cpp -o stri_compare.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_base.cpp -o stri_container_base.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_bytesearch.cpp -o stri_container_bytesearch.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_listint.cpp -o stri_container_listint.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_listraw.cpp -o stri_container_listraw.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_listutf8.cpp -o stri_container_listutf8.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_regex.cpp -o stri_container_regex.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_usearch.cpp -o stri_container_usearch.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_utf16.cpp -o stri_container_utf16.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_utf8.cpp -o stri_container_utf8.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_utf8_indexable.cpp -o stri_container_utf8_indexable.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_encoding_conversion.cpp -o stri_encoding_conversion.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_encoding_detection.cpp -o stri_encoding_detection.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_encoding_management.cpp -o stri_encoding_management.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_escape.cpp -o stri_escape.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_exception.cpp -o stri_exception.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_ICU_settings.cpp -o stri_ICU_settings.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_join.cpp -o stri_join.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_length.cpp -o stri_length.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_pad.cpp -o stri_pad.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_prepare_arg.cpp -o stri_prepare_arg.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_random.cpp -o stri_random.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_reverse.cpp -o stri_reverse.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_class_count.cpp -o stri_search_class_count.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_class_detect.cpp -o stri_search_class_detect.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_class_extract.cpp -o stri_search_class_extract.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_class_locate.cpp -o stri_search_class_locate.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_class_replace.cpp -o stri_search_class_replace.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_class_split.cpp -o stri_search_class_split.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_class_startsendswith.cpp -o stri_search_class_startsendswith.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_class_subset.cpp -o stri_search_class_subset.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_class_trim.cpp -o stri_search_class_trim.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_common.cpp -o stri_search_common.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_coll_count.cpp -o stri_search_coll_count.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_coll_detect.cpp -o stri_search_coll_detect.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_coll_extract.cpp -o stri_search_coll_extract.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_coll_locate.cpp -o stri_search_coll_locate.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_coll_replace.cpp -o stri_search_coll_replace.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_coll_split.cpp -o stri_search_coll_split.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_coll_startsendswith.cpp -o stri_search_coll_startsendswith.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_coll_subset.cpp -o stri_search_coll_subset.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_boundaries_count.cpp -o stri_search_boundaries_count.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_boundaries_extract.cpp -o stri_search_boundaries_extract.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_boundaries_locate.cpp -o stri_search_boundaries_locate.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_boundaries_split.cpp -o stri_search_boundaries_split.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_fixed_count.cpp -o stri_search_fixed_count.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_fixed_detect.cpp -o stri_search_fixed_detect.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_fixed_extract.cpp -o stri_search_fixed_extract.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_fixed_locate.cpp -o stri_search_fixed_locate.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_fixed_replace.cpp -o stri_search_fixed_replace.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_fixed_split.cpp -o stri_search_fixed_split.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_fixed_subset.cpp -o stri_search_fixed_subset.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_fixed_startsendswith.cpp -o stri_search_fixed_startsendswith.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_in.cpp -o stri_search_in.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_other_replace.cpp -o stri_search_other_replace.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_other_split.cpp -o stri_search_other_split.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_regex_count.cpp -o stri_search_regex_count.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_regex_detect.cpp -o stri_search_regex_detect.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_regex_extract.cpp -o stri_search_regex_extract.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_regex_locate.cpp -o stri_search_regex_locate.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_regex_match.cpp -o stri_search_regex_match.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_regex_replace.cpp -o stri_search_regex_replace.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_regex_split.cpp -o stri_search_regex_split.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_regex_subset.cpp -o stri_search_regex_subset.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_sort.cpp -o stri_sort.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_stats.cpp -o stri_stats.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_stringi.cpp -o stri_stringi.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_sub.cpp -o stri_sub.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_test.cpp -o stri_test.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_time_zone.cpp -o stri_time_zone.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_time_calendar.cpp -o stri_time_calendar.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_time_symbols.cpp -o stri_time_symbols.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_time_format.cpp -o stri_time_format.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_trans_casemap.cpp -o stri_trans_casemap.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_trans_other.cpp -o stri_trans_other.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_trans_normalization.cpp -o stri_trans_normalization.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_trans_transliterate.cpp -o stri_trans_transliterate.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_ucnv.cpp -o stri_ucnv.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_uloc.cpp -o stri_uloc.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_utils.cpp -o stri_utils.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I.    -UDEBUG -DNDEBUG -DU_HAVE_ELF_H  -I/usr/local/include  -fpic -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_wrap.cpp -o stri_wrap.o
g++ -std=gnu++11 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o stringi.so stri_brkiter.o stri_collator.o stri_common.o stri_compare.o stri_container_base.o stri_container_bytesearch.o stri_container_listint.o stri_container_listraw.o stri_container_listutf8.o stri_container_regex.o stri_container_usearch.o stri_container_utf16.o stri_container_utf8.o stri_container_utf8_indexable.o stri_encoding_conversion.o stri_encoding_detection.o stri_encoding_management.o stri_escape.o stri_exception.o stri_ICU_settings.o stri_join.o stri_length.o stri_pad.o stri_prepare_arg.o stri_random.o stri_reverse.o stri_search_class_count.o stri_search_class_detect.o stri_search_class_extract.o stri_search_class_locate.o stri_search_class_replace.o stri_search_class_split.o stri_search_class_startsendswith.o stri_search_class_subset.o stri_search_class_trim.o stri_search_common.o stri_search_coll_count.o stri_search_coll_detect.o stri_search_coll_extract.o stri_search_coll_locate.o stri_search_coll_replace.o stri_search_coll_split.o stri_search_coll_startsendswith.o stri_search_coll_subset.o stri_search_boundaries_count.o stri_search_boundaries_extract.o stri_search_boundaries_locate.o stri_search_boundaries_split.o stri_search_fixed_count.o stri_search_fixed_detect.o stri_search_fixed_extract.o stri_search_fixed_locate.o stri_search_fixed_replace.o stri_search_fixed_split.o stri_search_fixed_subset.o stri_search_fixed_startsendswith.o stri_search_in.o stri_search_other_replace.o stri_search_other_split.o stri_search_regex_count.o stri_search_regex_detect.o stri_search_regex_extract.o stri_search_regex_locate.o stri_search_regex_match.o stri_search_regex_replace.o stri_search_regex_split.o stri_search_regex_subset.o stri_sort.o stri_stats.o stri_stringi.o stri_sub.o stri_test.o stri_time_zone.o stri_time_calendar.o stri_time_symbols.o stri_time_format.o stri_trans_casemap.o stri_trans_other.o stri_trans_normalization.o stri_trans_transliterate.o stri_ucnv.o stri_uloc.o stri_utils.o stri_wrap.o -L/usr/lib/x86_64-linux-gnu -licui18n -licuuc -licudata -L/usr/local/lib/R/lib -lR
installing via 'install.libs.R' to /usr/local/lib/R/site-library/stringi
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Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (stringi)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘KEGGREST’ ...
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* DONE (KEGGREST)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘viridis’ ...
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* DONE (viridis)

The downloaded source packages are in
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Updating packages 'lattice'
trying URL 'https://cran.rstudio.com/src/contrib/lattice_0.20-35.tar.gz'
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==================================================
downloaded 351 KB

Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘lattice’ ...
** package ‘lattice’ successfully unpacked and MD5 sums checked
** libs
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c threeDplot.c -o threeDplot.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o lattice.so init.o threeDplot.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/lattice/libs
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Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (lattice)

The downloaded source packages are in
	‘/tmp/RtmpwPBy1K/downloaded_packages’
> 
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Removing intermediate container e7ada23f88a3
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[container-bioc_devel_metabolomics] $ docker tag 0ba158da4a8f docker-registry-v2.local:30750/bioconductor/devel_metabolomics2:latest
[container-bioc_devel_metabolomics] $ docker inspect 0ba158da4a8f
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