Error(s) in re-building vignettes:
--- re-building ‘ALA4R.Rmd’ using rmarkdown
Installing package into '/tmp/RtmpXT4Yq0/RLIBS_3e488b49ef8b39'
(as 'lib' is unspecified)
also installing the dependencies 'tmvnsim', 'fastmatch', 'igraph', 'quadprog', 'clusterGeneration', 'coda', 'combinat', 'expm', 'mnormt', 'numDeriv', 'phangorn', 'plotrix', 'scatterplot3d'

trying URL 'http://cran.us.r-project.org/src/contrib/tmvnsim_1.0-2.tar.gz'
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downloaded 6052 bytes

trying URL 'http://cran.us.r-project.org/src/contrib/fastmatch_1.1-0.tar.gz'
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trying URL 'http://cran.us.r-project.org/src/contrib/igraph_1.2.6.tar.gz'
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trying URL 'http://cran.us.r-project.org/src/contrib/quadprog_1.5-8.tar.gz'
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trying URL 'http://cran.us.r-project.org/src/contrib/clusterGeneration_1.3.7.tar.gz'
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trying URL 'http://cran.us.r-project.org/src/contrib/coda_0.19-4.tar.gz'
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trying URL 'http://cran.us.r-project.org/src/contrib/combinat_0.0-8.tar.gz'
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trying URL 'http://cran.us.r-project.org/src/contrib/expm_0.999-6.tar.gz'
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trying URL 'http://cran.us.r-project.org/src/contrib/mnormt_2.0.2.tar.gz'
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trying URL 'http://cran.us.r-project.org/src/contrib/numDeriv_2016.8-1.1.tar.gz'
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trying URL 'http://cran.us.r-project.org/src/contrib/phangorn_2.7.1.tar.gz'
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trying URL 'http://cran.us.r-project.org/src/contrib/plotrix_3.8-1.tar.gz'
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trying URL 'http://cran.us.r-project.org/src/contrib/scatterplot3d_0.3-41.tar.gz'
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trying URL 'http://cran.us.r-project.org/src/contrib/phytools_0.7-80.tar.gz'
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* installing *source* package ‘tmvnsim’ ...
** package ‘tmvnsim’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
make[1]: Entering directory '/tmp/RtmpXT4Yq0/working_dir/RtmpoObvZg/R.INSTALL3e834bbc773b/tmvnsim/src'
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c Fortran2CWrapper.c -o Fortran2CWrapper.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  tmvnghk.f90 -o tmvnghk.o
clang -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o tmvnsim.so Fortran2CWrapper.o tmvnghk.o -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath
make[1]: Leaving directory '/tmp/RtmpXT4Yq0/working_dir/RtmpoObvZg/R.INSTALL3e834bbc773b/tmvnsim/src'
make[1]: Entering directory '/tmp/RtmpXT4Yq0/working_dir/RtmpoObvZg/R.INSTALL3e834bbc773b/tmvnsim/src'
make[1]: Leaving directory '/tmp/RtmpXT4Yq0/working_dir/RtmpoObvZg/R.INSTALL3e834bbc773b/tmvnsim/src'
installing to /tmp/RtmpXT4Yq0/RLIBS_3e488b49ef8b39/00LOCK-tmvnsim/00new/tmvnsim/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (tmvnsim)
* installing *source* package ‘fastmatch’ ...
** package ‘fastmatch’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
make[1]: Entering directory '/tmp/RtmpXT4Yq0/working_dir/RtmpQ0KTLY/R.INSTALL3e862c74d9f103/fastmatch/src'
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c ctapply.c -o ctapply.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c fasthash.c -o fasthash.o
In file included from fasthash.c:19:
./common.h:13:17: error: typedef redefinition with different types ('R_len_t' (aka 'int') vs 'ptrdiff_t' (aka 'long'))
typedef R_len_t R_xlen_t;
                ^
/data/gannet/ripley/R/R-clang/include/Rinternals.h:72:23: note: previous definition is here
    typedef ptrdiff_t R_xlen_t;
                      ^
1 error generated.
make[1]: *** [/data/gannet/ripley/R/R-clang/etc/Makeconf:168: fasthash.o] Error 1
make[1]: Leaving directory '/tmp/RtmpXT4Yq0/working_dir/RtmpQ0KTLY/R.INSTALL3e862c74d9f103/fastmatch/src'
ERROR: compilation failed for package ‘fastmatch’
* removing ‘/tmp/RtmpXT4Yq0/RLIBS_3e488b49ef8b39/fastmatch’
* installing *source* package ‘igraph’ ...
** package ‘igraph’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... clang
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 clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -std=gnu++14 accepts -g... yes
checking how to run the C++ preprocessor... clang++ -std=gnu++14 -E
checking for rintf... yes
checking for finite... yes
checking for expm1... yes
checking for rint... yes
checking for log2... yes
checking for logbl... yes
checking for snprintf... yes
checking for log1p... yes
checking for round... yes
checking for fmin... yes
checking for stpcpy... yes
checking how to run the C preprocessor... clang -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 whether stpcpy is declared... yes
checking sys/times.h usability... yes
checking sys/times.h presence... yes
checking for sys/times.h... yes
checking net/if.h usability... yes
checking net/if.h presence... yes
checking for net/if.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking net/if_dl.h usability... no
checking net/if_dl.h presence... no
checking for net/if_dl.h... no
checking sys/sockio.h usability... no
checking sys/sockio.h presence... no
checking for sys/sockio.h... no
checking sys/un.h usability... yes
checking sys/un.h presence... yes
checking for sys/un.h... yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
checking for sys/ioctl.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/file.h usability... yes
checking sys/file.h presence... yes
checking for sys/file.h... yes
checking for struct sockaddr.sa_len... no
checking for xml2-config... /usr/bin/xml2-config
checking for xmlSAXUserParseFile in -lxml2... yes
checking libxml/parser.h usability... yes
checking libxml/parser.h presence... yes
checking for libxml/parser.h... yes
checking for __gmpz_add in -lgmp... yes
checking gmp.h usability... yes
checking gmp.h presence... yes
checking for gmp.h... yes
checking for glp_read_mps in -lglpk... yes
checking glpk.h usability... yes
checking glpk.h presence... yes
checking for glpk.h... yes
configure: creating ./config.status
config.status: creating src/Makevars.tmp
config.status: creating src/Makevars
config.status: creating src/config.h
** libs
make[1]: Entering directory '/tmp/RtmpXT4Yq0/working_dir/RtmplbK7Jb/R.INSTALL3e870279b670b7/igraph/src'
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c AMD/Source/amd.f -o AMD/Source/amd.o
f951: Warning: Nonconforming tab character in column 1 of line 422 [-Wtabs]
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c AMD/Source/amd_1.c -o AMD/Source/amd_1.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c AMD/Source/amd_2.c -o AMD/Source/amd_2.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c AMD/Source/amd_aat.c -o AMD/Source/amd_aat.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c AMD/Source/amd_control.c -o AMD/Source/amd_control.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c AMD/Source/amd_defaults.c -o AMD/Source/amd_defaults.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c AMD/Source/amd_dump.c -o AMD/Source/amd_dump.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c AMD/Source/amd_global.c -o AMD/Source/amd_global.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c AMD/Source/amd_info.c -o AMD/Source/amd_info.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c AMD/Source/amd_order.c -o AMD/Source/amd_order.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c AMD/Source/amd_post_tree.c -o AMD/Source/amd_post_tree.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c AMD/Source/amd_postorder.c -o AMD/Source/amd_postorder.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c AMD/Source/amd_preprocess.c -o AMD/Source/amd_preprocess.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c AMD/Source/amd_valid.c -o AMD/Source/amd_valid.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c AMD/Source/amdbar.f -o AMD/Source/amdbar.o
f951: Warning: Nonconforming tab character in column 1 of line 422 [-Wtabs]
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Check/cholmod_check.c -o CHOLMOD/Check/cholmod_check.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Check/cholmod_read.c -o CHOLMOD/Check/cholmod_read.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Check/cholmod_write.c -o CHOLMOD/Check/cholmod_write.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Cholesky/cholmod_amd.c -o CHOLMOD/Cholesky/cholmod_amd.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Cholesky/cholmod_analyze.c -o CHOLMOD/Cholesky/cholmod_analyze.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Cholesky/cholmod_colamd.c -o CHOLMOD/Cholesky/cholmod_colamd.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Cholesky/cholmod_etree.c -o CHOLMOD/Cholesky/cholmod_etree.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Cholesky/cholmod_factorize.c -o CHOLMOD/Cholesky/cholmod_factorize.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Cholesky/cholmod_postorder.c -o CHOLMOD/Cholesky/cholmod_postorder.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Cholesky/cholmod_rcond.c -o CHOLMOD/Cholesky/cholmod_rcond.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Cholesky/cholmod_resymbol.c -o CHOLMOD/Cholesky/cholmod_resymbol.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Cholesky/cholmod_rowcolcounts.c -o CHOLMOD/Cholesky/cholmod_rowcolcounts.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Cholesky/cholmod_rowfac.c -o CHOLMOD/Cholesky/cholmod_rowfac.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Cholesky/cholmod_solve.c -o CHOLMOD/Cholesky/cholmod_solve.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Cholesky/cholmod_spsolve.c -o CHOLMOD/Cholesky/cholmod_spsolve.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Core/cholmod_aat.c -o CHOLMOD/Core/cholmod_aat.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Core/cholmod_add.c -o CHOLMOD/Core/cholmod_add.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Core/cholmod_band.c -o CHOLMOD/Core/cholmod_band.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Core/cholmod_change_factor.c -o CHOLMOD/Core/cholmod_change_factor.o
CHOLMOD/Core/cholmod_change_factor.c:528:21: warning: implicit conversion from 'size_t' (aka 'unsigned long') to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-const-int-float-conversion]
                xlnz = MIN (xlnz, Size_max) ;
                       ~~~~~~~~~~~^~~~~~~~~
CHOLMOD/Include/cholmod_internal.h:210:19: note: expanded from macro 'Size_max'
#define Size_max ((size_t) (-1))
                  ^~~~~~~~~~~~~
CHOLMOD/Include/cholmod_internal.h:101:27: note: expanded from macro 'MIN'
#define MIN(a,b) (((a) < (b)) ? (a) : (b))
                       ~  ^
CHOLMOD/Core/cholmod_change_factor.c:528:21: warning: implicit conversion from 'size_t' (aka 'unsigned long') to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-const-int-float-conversion]
                xlnz = MIN (xlnz, Size_max) ;
                     ~            ^~~~~~~~
CHOLMOD/Include/cholmod_internal.h:210:19: note: expanded from macro 'Size_max'
#define Size_max ((size_t) (-1))
                  ^~~~~~~~~~~~~
CHOLMOD/Include/cholmod_internal.h:101:40: note: expanded from macro 'MIN'
#define MIN(a,b) (((a) < (b)) ? (a) : (b))
                                       ^
CHOLMOD/Core/cholmod_change_factor.c:760:24: warning: implicit conversion from 'size_t' (aka 'unsigned long') to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-const-int-float-conversion]
            xlnz = MIN (xlnz, Size_max) ;
                   ~~~~~~~~~~~^~~~~~~~~
CHOLMOD/Include/cholmod_internal.h:210:19: note: expanded from macro 'Size_max'
#define Size_max ((size_t) (-1))
                  ^~~~~~~~~~~~~
CHOLMOD/Include/cholmod_internal.h:101:27: note: expanded from macro 'MIN'
#define MIN(a,b) (((a) < (b)) ? (a) : (b))
                       ~  ^
CHOLMOD/Core/cholmod_change_factor.c:760:24: warning: implicit conversion from 'size_t' (aka 'unsigned long') to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-const-int-float-conversion]
            xlnz = MIN (xlnz, Size_max) ;
                 ~            ^~~~~~~~
CHOLMOD/Include/cholmod_internal.h:210:19: note: expanded from macro 'Size_max'
#define Size_max ((size_t) (-1))
                  ^~~~~~~~~~~~~
CHOLMOD/Include/cholmod_internal.h:101:40: note: expanded from macro 'MIN'
#define MIN(a,b) (((a) < (b)) ? (a) : (b))
                                       ^
4 warnings generated.
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Core/cholmod_common.c -o CHOLMOD/Core/cholmod_common.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Core/cholmod_complex.c -o CHOLMOD/Core/cholmod_complex.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Core/cholmod_copy.c -o CHOLMOD/Core/cholmod_copy.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Core/cholmod_dense.c -o CHOLMOD/Core/cholmod_dense.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Core/cholmod_error.c -o CHOLMOD/Core/cholmod_error.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Core/cholmod_factor.c -o CHOLMOD/Core/cholmod_factor.o
CHOLMOD/Core/cholmod_factor.c:387:14: warning: implicit conversion from 'size_t' (aka 'unsigned long') to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-const-int-float-conversion]
        if (xneed > Size_max ||
                  ~ ^~~~~~~~
CHOLMOD/Include/cholmod_internal.h:210:19: note: expanded from macro 'Size_max'
#define Size_max ((size_t) (-1))
                  ^~~~~~~~~~~~~
1 warning generated.
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Core/cholmod_memory.c -o CHOLMOD/Core/cholmod_memory.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Core/cholmod_sparse.c -o CHOLMOD/Core/cholmod_sparse.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Core/cholmod_transpose.c -o CHOLMOD/Core/cholmod_transpose.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Core/cholmod_triplet.c -o CHOLMOD/Core/cholmod_triplet.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Core/cholmod_version.c -o CHOLMOD/Core/cholmod_version.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/MatrixOps/cholmod_drop.c -o CHOLMOD/MatrixOps/cholmod_drop.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/MatrixOps/cholmod_horzcat.c -o CHOLMOD/MatrixOps/cholmod_horzcat.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/MatrixOps/cholmod_norm.c -o CHOLMOD/MatrixOps/cholmod_norm.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/MatrixOps/cholmod_scale.c -o CHOLMOD/MatrixOps/cholmod_scale.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/MatrixOps/cholmod_sdmult.c -o CHOLMOD/MatrixOps/cholmod_sdmult.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/MatrixOps/cholmod_ssmult.c -o CHOLMOD/MatrixOps/cholmod_ssmult.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/MatrixOps/cholmod_submatrix.c -o CHOLMOD/MatrixOps/cholmod_submatrix.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/MatrixOps/cholmod_symmetry.c -o CHOLMOD/MatrixOps/cholmod_symmetry.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/MatrixOps/cholmod_vertcat.c -o CHOLMOD/MatrixOps/cholmod_vertcat.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Modify/cholmod_rowadd.c -o CHOLMOD/Modify/cholmod_rowadd.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Modify/cholmod_rowdel.c -o CHOLMOD/Modify/cholmod_rowdel.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Modify/cholmod_updown.c -o CHOLMOD/Modify/cholmod_updown.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Partition/cholmod_camd.c -o CHOLMOD/Partition/cholmod_camd.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Partition/cholmod_ccolamd.c -o CHOLMOD/Partition/cholmod_ccolamd.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Partition/cholmod_csymamd.c -o CHOLMOD/Partition/cholmod_csymamd.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Partition/cholmod_metis.c -o CHOLMOD/Partition/cholmod_metis.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Partition/cholmod_nesdis.c -o CHOLMOD/Partition/cholmod_nesdis.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Supernodal/cholmod_super_numeric.c -o CHOLMOD/Supernodal/cholmod_super_numeric.o
In file included from CHOLMOD/Supernodal/cholmod_super_numeric.c:80:
CHOLMOD/Supernodal/t_cholmod_super_numeric.c:141:40: warning: unused variable 'tstart' [-Wunused-variable]
    double one [2], zero [2], fjk [2], tstart ;
                                       ^
1 warning generated.
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Supernodal/cholmod_super_solve.c -o CHOLMOD/Supernodal/cholmod_super_solve.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c CHOLMOD/Supernodal/cholmod_super_symbolic.c -o CHOLMOD/Supernodal/cholmod_super_symbolic.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c COLAMD/Source/colamd.c -o COLAMD/Source/colamd.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c COLAMD/Source/colamd_global.c -o COLAMD/Source/colamd_global.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c DensityGrid.cpp -o DensityGrid.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c DensityGrid_3d.cpp -o DensityGrid_3d.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c NetDataTypes.cpp -o NetDataTypes.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c NetRoutines.cpp -o NetRoutines.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c SuiteSparse_config/SuiteSparse_config.c -o SuiteSparse_config/SuiteSparse_config.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c adjlist.c -o adjlist.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c arpack.c -o arpack.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c array.c -o array.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c atlas.c -o atlas.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c attributes.c -o attributes.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c basic_query.c -o basic_query.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c bfgs.c -o bfgs.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c bigint.c -o bigint.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c bignum.c -o bignum.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c bipartite.c -o bipartite.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c blas.c -o blas.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c bliss.cc -o bliss.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c bliss/bliss_heap.cc -o bliss/bliss_heap.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c bliss/defs.cc -o bliss/defs.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c bliss/graph.cc -o bliss/graph.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c bliss/orbit.cc -o bliss/orbit.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c bliss/partition.cc -o bliss/partition.o
bliss/partition.cc:984:15: warning: unused variable 'sorted' [-Wunused-variable]
          const bool sorted = shellsort_cell(cell);
                     ^
1 warning generated.
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c bliss/uintseqhash.cc -o bliss/uintseqhash.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c bliss/utils.cc -o bliss/utils.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cattributes.c -o cattributes.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c centrality.c -o centrality.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cliquer/cliquer.c -o cliquer/cliquer.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cliquer/cliquer_graph.c -o cliquer/cliquer_graph.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cliquer/reorder.c -o cliquer/reorder.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cliques.c -o cliques.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c clustertool.cpp -o clustertool.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cocitation.c -o cocitation.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cohesive_blocks.c -o cohesive_blocks.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c coloring.c -o coloring.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c community.c -o community.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c complex.c -o complex.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c components.c -o components.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c conversion.c -o conversion.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cores.c -o cores.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_add.c -o cs/cs_add.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_amd.c -o cs/cs_amd.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_chol.c -o cs/cs_chol.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_cholsol.c -o cs/cs_cholsol.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_compress.c -o cs/cs_compress.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_counts.c -o cs/cs_counts.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_cumsum.c -o cs/cs_cumsum.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_dfs.c -o cs/cs_dfs.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_dmperm.c -o cs/cs_dmperm.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_droptol.c -o cs/cs_droptol.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_dropzeros.c -o cs/cs_dropzeros.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_dupl.c -o cs/cs_dupl.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_entry.c -o cs/cs_entry.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_ereach.c -o cs/cs_ereach.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_etree.c -o cs/cs_etree.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_fkeep.c -o cs/cs_fkeep.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_gaxpy.c -o cs/cs_gaxpy.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_happly.c -o cs/cs_happly.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_house.c -o cs/cs_house.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_ipvec.c -o cs/cs_ipvec.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_leaf.c -o cs/cs_leaf.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_load.c -o cs/cs_load.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_lsolve.c -o cs/cs_lsolve.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_ltsolve.c -o cs/cs_ltsolve.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_lu.c -o cs/cs_lu.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_lusol.c -o cs/cs_lusol.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_malloc.c -o cs/cs_malloc.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_maxtrans.c -o cs/cs_maxtrans.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_multiply.c -o cs/cs_multiply.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_norm.c -o cs/cs_norm.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_permute.c -o cs/cs_permute.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_pinv.c -o cs/cs_pinv.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_post.c -o cs/cs_post.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_print.c -o cs/cs_print.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_pvec.c -o cs/cs_pvec.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_qr.c -o cs/cs_qr.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_qrsol.c -o cs/cs_qrsol.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_randperm.c -o cs/cs_randperm.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_reach.c -o cs/cs_reach.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_scatter.c -o cs/cs_scatter.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_scc.c -o cs/cs_scc.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_schol.c -o cs/cs_schol.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_spsolve.c -o cs/cs_spsolve.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_sqr.c -o cs/cs_sqr.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_symperm.c -o cs/cs_symperm.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_tdfs.c -o cs/cs_tdfs.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_transpose.c -o cs/cs_transpose.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_updown.c -o cs/cs_updown.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_usolve.c -o cs/cs_usolve.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_util.c -o cs/cs_util.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c cs/cs_utsolve.c -o cs/cs_utsolve.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c decomposition.c -o decomposition.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c distances.c -o distances.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c dotproduct.c -o dotproduct.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c dqueue.c -o dqueue.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c drl_graph.cpp -o drl_graph.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c drl_graph_3d.cpp -o drl_graph_3d.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c drl_layout.cpp -o drl_layout.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c drl_layout_3d.cpp -o drl_layout_3d.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c drl_parse.cpp -o drl_parse.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c eigen.c -o eigen.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c embedding.c -o embedding.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c fast_community.c -o fast_community.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c feedback_arc_set.c -o feedback_arc_set.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c flow.c -o flow.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c foreign-dl-lexer.c -o foreign-dl-lexer.o
lex.yy.c:2108:24: warning: unused function 'yy_fatal_error' [-Wunused-function]
static void yynoreturn yy_fatal_error (const char* msg , yyscan_t yyscanner)
                       ^
1 warning generated.
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c foreign-dl-parser.c -o foreign-dl-parser.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c foreign-gml-lexer.c -o foreign-gml-lexer.o
lex.yy.c:1927:24: warning: unused function 'yy_fatal_error' [-Wunused-function]
static void yynoreturn yy_fatal_error (const char* msg , yyscan_t yyscanner)
                       ^
1 warning generated.
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c foreign-gml-parser.c -o foreign-gml-parser.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c foreign-graphml.c -o foreign-graphml.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c foreign-lgl-lexer.c -o foreign-lgl-lexer.o
lex.yy.c:1887:24: warning: unused function 'yy_fatal_error' [-Wunused-function]
static void yynoreturn yy_fatal_error (const char* msg , yyscan_t yyscanner)
                       ^
1 warning generated.
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c foreign-lgl-parser.c -o foreign-lgl-parser.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c foreign-ncol-lexer.c -o foreign-ncol-lexer.o
lex.yy.c:1882:24: warning: unused function 'yy_fatal_error' [-Wunused-function]
static void yynoreturn yy_fatal_error (const char* msg , yyscan_t yyscanner)
                       ^
1 warning generated.
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c foreign-ncol-parser.c -o foreign-ncol-parser.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c foreign-pajek-lexer.c -o foreign-pajek-lexer.o
lex.yy.c:2372:24: warning: unused function 'yy_fatal_error' [-Wunused-function]
static void yynoreturn yy_fatal_error (const char* msg , yyscan_t yyscanner)
                       ^
1 warning generated.
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c foreign-pajek-parser.c -o foreign-pajek-parser.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c foreign.c -o foreign.o
foreign.c:243:17: warning: address of array 'context.errmsg' will always evaluate to 'true' [-Wpointer-bool-conversion]
    if (context.errmsg) {
    ~~  ~~~~~~~~^~~~~~
foreign.c:399:17: warning: address of array 'context.errmsg' will always evaluate to 'true' [-Wpointer-bool-conversion]
    if (context.errmsg) {
    ~~  ~~~~~~~~^~~~~~
foreign.c:585:17: warning: address of array 'context.errmsg' will always evaluate to 'true' [-Wpointer-bool-conversion]
    if (context.errmsg) {
    ~~  ~~~~~~~~^~~~~~
foreign.c:1126:17: warning: address of array 'context.errmsg' will always evaluate to 'true' [-Wpointer-bool-conversion]
    if (context.errmsg) {
    ~~  ~~~~~~~~^~~~~~
foreign.c:3049:17: warning: address of array 'context.errmsg' will always evaluate to 'true' [-Wpointer-bool-conversion]
    if (context.errmsg) { 
    ~~  ~~~~~~~~^~~~~~
5 warnings generated.
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c forestfire.c -o forestfire.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c fortran_intrinsics.c -o fortran_intrinsics.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c games.c -o games.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c gengraph_box_list.cpp -o gengraph_box_list.o
In file included from gengraph_box_list.cpp:21:
./gengraph_box_list.h:33:9: warning: keyword is hidden by macro definition [-Wkeyword-macro]
#define register
        ^
1 warning generated.
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c gengraph_degree_sequence.cpp -o gengraph_degree_sequence.o
In file included from gengraph_degree_sequence.cpp:21:
./gengraph_definitions.h:26:9: warning: keyword is hidden by macro definition [-Wkeyword-macro]
#define register
        ^
1 warning generated.
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c gengraph_graph_molloy_hash.cpp -o gengraph_graph_molloy_hash.o
In file included from gengraph_graph_molloy_hash.cpp:21:
./gengraph_definitions.h:26:9: warning: keyword is hidden by macro definition [-Wkeyword-macro]
#define register
        ^
1 warning generated.
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c gengraph_graph_molloy_optimized.cpp -o gengraph_graph_molloy_optimized.o
In file included from gengraph_graph_molloy_optimized.cpp:21:
./gengraph_definitions.h:26:9: warning: keyword is hidden by macro definition [-Wkeyword-macro]
#define register
        ^
1 warning generated.
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c gengraph_mr-connected.cpp -o gengraph_mr-connected.o
In file included from gengraph_mr-connected.cpp:21:
In file included from ./gengraph_header.h:21:
./gengraph_definitions.h:26:9: warning: keyword is hidden by macro definition [-Wkeyword-macro]
#define register
        ^
gengraph_mr-connected.cpp:37:19: warning: unused variable 'MONITOR_TIME' [-Wunused-const-variable]
static const bool MONITOR_TIME = false;
                  ^
gengraph_mr-connected.cpp:39:19: warning: unused variable 'RAW_DEGREES' [-Wunused-const-variable]
static const bool RAW_DEGREES  = false;
                  ^
gengraph_mr-connected.cpp:40:20: warning: unused variable 'Fdeg' [-Wunused-variable]
static const FILE *Fdeg = stdin;
                   ^
4 warnings generated.
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c gengraph_powerlaw.cpp -o gengraph_powerlaw.o
In file included from gengraph_powerlaw.cpp:26:
./gengraph_definitions.h:26:9: warning: keyword is hidden by macro definition [-Wkeyword-macro]
#define register
        ^
1 warning generated.
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c gengraph_random.cpp -o gengraph_random.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c glet.c -o glet.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c glpk_support.c -o glpk_support.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c gml_tree.c -o gml_tree.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c hacks.c -o hacks.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c heap.c -o heap.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c igraph_buckets.c -o igraph_buckets.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c igraph_cliquer.c -o igraph_cliquer.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c igraph_error.c -o igraph_error.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c igraph_estack.c -o igraph_estack.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c igraph_fixed_vectorlist.c -o igraph_fixed_vectorlist.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c igraph_grid.c -o igraph_grid.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c igraph_hashtable.c -o igraph_hashtable.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c igraph_heap.c -o igraph_heap.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c igraph_hrg.cc -o igraph_hrg.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c igraph_hrg_types.cc -o igraph_hrg_types.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c igraph_marked_queue.c -o igraph_marked_queue.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c igraph_psumtree.c -o igraph_psumtree.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c igraph_set.c -o igraph_set.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c igraph_stack.c -o igraph_stack.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c igraph_strvector.c -o igraph_strvector.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c igraph_trie.c -o igraph_trie.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c infomap.cc -o infomap.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c infomap_FlowGraph.cc -o infomap_FlowGraph.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c infomap_Greedy.cc -o infomap_Greedy.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c infomap_Node.cc -o infomap_Node.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c interrupt.c -o interrupt.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c iterators.c -o iterators.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c lad.c -o lad.o
lad.c:499:20: warning: unused variable 'Gp_uneis' [-Wunused-variable]
  igraph_vector_t *Gp_uneis;
                   ^
lad.c:500:20: warning: unused variable 'Gt_vneis' [-Wunused-variable]
  igraph_vector_t *Gt_vneis;
                   ^
2 warnings generated.
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c lapack.c -o lapack.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c layout.c -o layout.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c layout_dh.c -o layout_dh.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c layout_fr.c -o layout_fr.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c layout_gem.c -o layout_gem.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c layout_kk.c -o layout_kk.o
layout_kk.c:256:37: warning: unused variable 'old_mi' [-Wunused-variable]
      igraph_real_t old_dx, old_dy, old_mi, new_dx, new_dy, new_mi_dist, old_mi_dist;
                                    ^
1 warning generated.
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c lsap.c -o lsap.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c matching.c -o matching.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c math.c -o math.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c matrix.c -o matrix.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c maximal_cliques.c -o maximal_cliques.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c memory.c -o memory.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c microscopic_update.c -o microscopic_update.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c mixing.c -o mixing.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c motifs.c -o motifs.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c operators.c -o operators.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c optimal_modularity.c -o optimal_modularity.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c other.c -o other.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c paths.c -o paths.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c plfit/error.c -o plfit/error.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c plfit/gss.c -o plfit/gss.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c plfit/kolmogorov.c -o plfit/kolmogorov.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c plfit/lbfgs.c -o plfit/lbfgs.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c plfit/options.c -o plfit/options.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c plfit/plfit.c -o plfit/plfit.o
plfit/plfit.c:334:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation]
        if (options->xmin_method == PLFIT_GSS_OR_LINEAR && num_uniques > 5) {
        ^
plfit/plfit.c:327:5: note: previous statement is here
    if (opt_data.uniques == 0)
    ^
plfit/plfit.c:447:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation]
        if (x[0] <= 1.0) {
        ^
plfit/plfit.c:443:5: note: previous statement is here
    else if (dx < -0.001)
    ^
2 warnings generated.
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c plfit/zeta.c -o plfit/zeta.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c pottsmodel_2.cpp -o pottsmodel_2.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c progress.c -o progress.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c prpack.cpp -o prpack.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c prpack/prpack_base_graph.cpp -o prpack/prpack_base_graph.o
prpack/prpack_base_graph.cpp:170:12: warning: unused variable 'ignore' [-Wunused-variable]
    double ignore = 0.0;
           ^
1 warning generated.
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c prpack/prpack_igraph_graph.cpp -o prpack/prpack_igraph_graph.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c prpack/prpack_preprocessed_ge_graph.cpp -o prpack/prpack_preprocessed_ge_graph.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c prpack/prpack_preprocessed_gs_graph.cpp -o prpack/prpack_preprocessed_gs_graph.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c prpack/prpack_preprocessed_scc_graph.cpp -o prpack/prpack_preprocessed_scc_graph.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c prpack/prpack_preprocessed_schur_graph.cpp -o prpack/prpack_preprocessed_schur_graph.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c prpack/prpack_result.cpp -o prpack/prpack_result.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c prpack/prpack_solver.cpp -o prpack/prpack_solver.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c prpack/prpack_utils.cpp -o prpack/prpack_utils.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c qsort.c -o qsort.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c qsort_r.c -o qsort_r.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c random.c -o random.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c random_walk.c -o random_walk.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c sbm.c -o sbm.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c scan.c -o scan.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c scg.c -o scg.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c scg_approximate_methods.c -o scg_approximate_methods.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c scg_exact_scg.c -o scg_exact_scg.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c scg_kmeans.c -o scg_kmeans.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c scg_optimal_method.c -o scg_optimal_method.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c scg_utils.c -o scg_utils.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c separators.c -o separators.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c sir.c -o sir.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c spanning_trees.c -o spanning_trees.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c sparsemat.c -o sparsemat.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c spectral_properties.c -o spectral_properties.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c spmatrix.c -o spmatrix.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c st-cuts.c -o st-cuts.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c statusbar.c -o statusbar.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c structural_properties.c -o structural_properties.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c structure_generators.c -o structure_generators.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c sugiyama.c -o sugiyama.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c topology.c -o topology.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c triangles.c -o triangles.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c type_indexededgelist.c -o type_indexededgelist.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c types.c -o types.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c vector.c -o vector.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c vector_ptr.c -o vector_ptr.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c version.c -o version.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c visitors.c -o visitors.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c walktrap.cpp -o walktrap.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c walktrap_communities.cpp -o walktrap_communities.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c walktrap_graph.cpp -o walktrap_graph.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c walktrap_heap.cpp -o walktrap_heap.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c zeroin.c -o zeroin.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c dgetv0.f -o dgetv0.o
dgetv0.f:120:26:

  120 |      &   ( ido, bmat, itry, initv, n, j, v, ldv, resid, rnorm,
      |                          1
Warning: Unused dummy argument ‘itry’ at (1) [-Wunused-dummy-argument]
stat.h:8:35:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
dgetv0.f:269:72:

  269 |          tmvopx = tmvopx + (t3 - t2)
      |                                                                        ^
Warning: ‘t2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c dlaqrb.f -o dlaqrb.o
dlaqrb.f:497:72:

  497 |      &                    cs, sn )
      |                                                                        ^
Warning: ‘i2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c dmout.f -o dmout.o
dmout.f:34:19:

   34 |       CHARACTER*80       LINE
      |                   1
Warning: Obsolescent feature: Old-style character length at (1)
dmout.f:21:43:

   21 |       SUBROUTINE IGRAPHDMOUT( LOUT, M, N, A, LDA, IDIGIT, IFMT )
      |                                           1
Warning: Unused dummy argument ‘a’ at (1) [-Wunused-dummy-argument]
dmout.f:35:26:

   35 |       INTEGER            I, J, K1, K2, LLL, NDIGIT
      |                          1
Warning: Unused variable ‘i’ declared at (1) [-Wunused-variable]
dmout.f:21:56:

   21 |       SUBROUTINE IGRAPHDMOUT( LOUT, M, N, A, LDA, IDIGIT, IFMT )
      |                                                        1
Warning: Unused dummy argument ‘idigit’ at (1) [-Wunused-dummy-argument]
dmout.f:21:62:

   21 |       SUBROUTINE IGRAPHDMOUT( LOUT, M, N, A, LDA, IDIGIT, IFMT )
      |                                                              1
Warning: Unused dummy argument ‘ifmt’ at (1) [-Wunused-dummy-argument]
dmout.f:35:29:

   35 |       INTEGER            I, J, K1, K2, LLL, NDIGIT
      |                             1
Warning: Unused variable ‘j’ declared at (1) [-Wunused-variable]
dmout.f:35:33:

   35 |       INTEGER            I, J, K1, K2, LLL, NDIGIT
      |                                 1
Warning: Unused variable ‘k1’ declared at (1) [-Wunused-variable]
dmout.f:35:37:

   35 |       INTEGER            I, J, K1, K2, LLL, NDIGIT
      |                                     1
Warning: Unused variable ‘k2’ declared at (1) [-Wunused-variable]
dmout.f:34:29:

   34 |       CHARACTER*80       LINE
      |                             1
Warning: Unused variable ‘line’ declared at (1) [-Wunused-variable]
dmout.f:35:42:

   35 |       INTEGER            I, J, K1, K2, LLL, NDIGIT
      |                                          1
Warning: Unused variable ‘lll’ declared at (1) [-Wunused-variable]
dmout.f:21:34:

   21 |       SUBROUTINE IGRAPHDMOUT( LOUT, M, N, A, LDA, IDIGIT, IFMT )
      |                                  1
Warning: Unused dummy argument ‘lout’ at (1) [-Wunused-dummy-argument]
dmout.f:21:37:

   21 |       SUBROUTINE IGRAPHDMOUT( LOUT, M, N, A, LDA, IDIGIT, IFMT )
      |                                     1
Warning: Unused dummy argument ‘m’ at (1) [-Wunused-dummy-argument]
dmout.f:21:40:

   21 |       SUBROUTINE IGRAPHDMOUT( LOUT, M, N, A, LDA, IDIGIT, IFMT )
      |                                        1
Warning: Unused dummy argument ‘n’ at (1) [-Wunused-dummy-argument]
dmout.f:35:50:

   35 |       INTEGER            I, J, K1, K2, LLL, NDIGIT
      |                                                  1
Warning: Unused variable ‘ndigit’ declared at (1) [-Wunused-variable]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c dnaitr.f -o dnaitr.o
dnaitr.f:210:33:

  210 |      &   (ido, bmat, n, k, np, nb, resid, rnorm, v, ldv, h, ldh,
      |                                 1
Warning: Unused dummy argument ‘nb’ at (1) [-Wunused-dummy-argument]
dnaitr.f:494:72:

  494 |          tmvopx = tmvopx + (t3 - t2)
      |                                                                        ^
Warning: ‘t2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c dnapps.f -o dnapps.o
stat.h:8:27:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c dnaup2.f -o dnaup2.o
dnaup2.f:315:5:

  315 |    10 continue
      |     1
Warning: Label 10 at (1) defined but not used [-Wunused-label]
dnaup2.f:175:63:

  175 |      &   ( ido, bmat, n, which, nev, np, tol, resid, mode, iupd,
      |                                                               1
Warning: Unused dummy argument ‘iupd’ at (1) [-Wunused-dummy-argument]
stat.h:8:35:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c dnaupd.f -o dnaupd.o
dnaupd.f:541:25:

  541 |          if (nb .le. 0)    nb = 1
      |                         1
Warning: Nonconforming tab character at (1) [-Wtabs]
dnaupd.f:542:29:

  542 |          if (tol .le. zero)   tol = dlamch('EpsMach')
      |                             1
Warning: Nonconforming tab character at (1) [-Wtabs]
stat.h:8:27:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c dnconv.f -o dnconv.o
stat.h:8:27:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c dneigh.f -o dneigh.o
stat.h:8:27:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c dneupd.f -o dneupd.o
stat.h:8:19:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                   1
Warning: Unused variable ‘t0’ declared at (1) [-Wunused-variable]
stat.h:8:23:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                       1
Warning: Unused variable ‘t1’ declared at (1) [-Wunused-variable]
stat.h:8:27:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
dneupd.f:537:72:

  537 |      &           '_neupd: Threshold eigenvalue used for re-ordering')
      |                                                                        ^
Warning: ‘thres’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c dngets.f -o dngets.o
dngets.f:109:18:

  109 |       character*2 which
      |                  1
Warning: Obsolescent feature: Old-style character length at (1)
dngets.f:96:33:

   96 |      &     bounds, shiftr, shifti )
      |                                 1
Warning: Unused dummy argument ‘shifti’ at (1) [-Wunused-dummy-argument]
dngets.f:96:25:

   96 |      &     bounds, shiftr, shifti )
      |                         1
Warning: Unused dummy argument ‘shiftr’ at (1) [-Wunused-dummy-argument]
stat.h:8:27:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c dsaitr.f -o dsaitr.o
dsaitr.f:484:72:

  484 |          tmvopx = tmvopx + (t3 - t2)
      |                                                                        ^
Warning: ‘t2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c dsapps.f -o dsapps.o
stat.h:8:27:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c dsaup2.f -o dsaup2.o
dsaup2.f:812:5:

  812 |   130    continue
      |     1
Warning: Label 130 at (1) defined but not used [-Wunused-label]
dsaup2.f:326:5:

  326 |    10 continue
      |     1
Warning: Label 10 at (1) defined but not used [-Wunused-label]
dsaup2.f:180:63:

  180 |      &   ( ido, bmat, n, which, nev, np, tol, resid, mode, iupd,
      |                                                               1
Warning: Unused dummy argument ‘iupd’ at (1) [-Wunused-dummy-argument]
stat.h:8:35:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c dsaupd.f -o dsaupd.o
stat.h:8:27:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c dsconv.f -o dsconv.o
stat.h:8:27:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c dseigt.f -o dseigt.o
dseigt.f:124:18:

  124 |       integer    i, k, msglvl
      |                  1
Warning: Unused variable ‘i’ declared at (1) [-Wunused-variable]
stat.h:8:27:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c dsesrt.f -o dsesrt.o
dsesrt.f:74:18:

   74 |       character*2 which
      |                  1
Warning: Obsolescent feature: Old-style character length at (1)
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c dseupd.f -o dseupd.o
stat.h:8:19:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                   1
Warning: Unused variable ‘t0’ declared at (1) [-Wunused-variable]
stat.h:8:23:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                       1
Warning: Unused variable ‘t1’ declared at (1) [-Wunused-variable]
stat.h:8:27:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
dseupd.f:557:49:

  557 |                if ( workl(irz+j) .le. thres1 .or.
      |                                                 ^
Warning: ‘thres2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
dseupd.f:529:19:

  529 |                if (abs(workl(irz+j)) .ge. abs(thres1)) then
      |                   ^
Warning: ‘thres1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c dsgets.f -o dsgets.o
dsgets.f:107:18:

  107 |       character*2 which
      |                  1
Warning: Obsolescent feature: Old-style character length at (1)
stat.h:8:27:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c dsortc.f -o dsortc.o
dsortc.f:72:18:

   72 |       character*2 which
      |                  1
Warning: Obsolescent feature: Old-style character length at (1)
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c dsortr.f -o dsortr.o
dsortr.f:65:18:

   65 |       character*2 which
      |                  1
Warning: Obsolescent feature: Old-style character length at (1)
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c dstatn.f -o dstatn.o
stat.h:8:19:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                   1
Warning: Unused variable ‘t0’ declared at (1) [-Wunused-variable]
stat.h:8:23:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                       1
Warning: Unused variable ‘t1’ declared at (1) [-Wunused-variable]
stat.h:8:27:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c dstats.f -o dstats.o
stat.h:8:19:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                   1
Warning: Unused variable ‘t0’ declared at (1) [-Wunused-variable]
stat.h:8:23:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                       1
Warning: Unused variable ‘t1’ declared at (1) [-Wunused-variable]
stat.h:8:27:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

    8 |       real       t0, t1, t2, t3, t4, t5
      |                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c dstqrb.f -o dstqrb.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c dvout.f -o dvout.o
dvout.f:31:19:

   31 |       CHARACTER*80       LINE
      |                   1
Warning: Obsolescent feature: Old-style character length at (1)
dvout.f:32:26:

   32 |       INTEGER            I, K1, K2, LLL, NDIGIT
      |                          1
Warning: Unused variable ‘i’ declared at (1) [-Wunused-variable]
dvout.f:18:49:

   18 |       SUBROUTINE IGRAPHDVOUT( LOUT, N, SX, IDIGIT, IFMT )
      |                                                 1
Warning: Unused dummy argument ‘idigit’ at (1) [-Wunused-dummy-argument]
dvout.f:18:55:

   18 |       SUBROUTINE IGRAPHDVOUT( LOUT, N, SX, IDIGIT, IFMT )
      |                                                       1
Warning: Unused dummy argument ‘ifmt’ at (1) [-Wunused-dummy-argument]
dvout.f:32:30:

   32 |       INTEGER            I, K1, K2, LLL, NDIGIT
      |                              1
Warning: Unused variable ‘k1’ declared at (1) [-Wunused-variable]
dvout.f:32:34:

   32 |       INTEGER            I, K1, K2, LLL, NDIGIT
      |                                  1
Warning: Unused variable ‘k2’ declared at (1) [-Wunused-variable]
dvout.f:31:29:

   31 |       CHARACTER*80       LINE
      |                             1
Warning: Unused variable ‘line’ declared at (1) [-Wunused-variable]
dvout.f:32:39:

   32 |       INTEGER            I, K1, K2, LLL, NDIGIT
      |                                       1
Warning: Unused variable ‘lll’ declared at (1) [-Wunused-variable]
dvout.f:18:34:

   18 |       SUBROUTINE IGRAPHDVOUT( LOUT, N, SX, IDIGIT, IFMT )
      |                                  1
Warning: Unused dummy argument ‘lout’ at (1) [-Wunused-dummy-argument]
dvout.f:18:37:

   18 |       SUBROUTINE IGRAPHDVOUT( LOUT, N, SX, IDIGIT, IFMT )
      |                                     1
Warning: Unused dummy argument ‘n’ at (1) [-Wunused-dummy-argument]
dvout.f:32:47:

   32 |       INTEGER            I, K1, K2, LLL, NDIGIT
      |                                               1
Warning: Unused variable ‘ndigit’ declared at (1) [-Wunused-variable]
dvout.f:18:41:

   18 |       SUBROUTINE IGRAPHDVOUT( LOUT, N, SX, IDIGIT, IFMT )
      |                                         1
Warning: Unused dummy argument ‘sx’ at (1) [-Wunused-dummy-argument]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c ivout.f -o ivout.o
ivout.f:26:19:

   26 |       CHARACTER*80 LINE
      |                   1
Warning: Obsolescent feature: Old-style character length at (1)
ivout.f:25:18:

   25 |       INTEGER    I, NDIGIT, K1, K2, LLL
      |                  1
Warning: Unused variable ‘i’ declared at (1) [-Wunused-variable]
ivout.f:18:49:

   18 |       SUBROUTINE IGRAPHIVOUT (LOUT, N, IX, IDIGIT, IFMT)
      |                                                 1
Warning: Unused dummy argument ‘idigit’ at (1) [-Wunused-dummy-argument]
ivout.f:18:55:

   18 |       SUBROUTINE IGRAPHIVOUT (LOUT, N, IX, IDIGIT, IFMT)
      |                                                       1
Warning: Unused dummy argument ‘ifmt’ at (1) [-Wunused-dummy-argument]
ivout.f:18:41:

   18 |       SUBROUTINE IGRAPHIVOUT (LOUT, N, IX, IDIGIT, IFMT)
      |                                         1
Warning: Unused dummy argument ‘ix’ at (1) [-Wunused-dummy-argument]
ivout.f:25:30:

   25 |       INTEGER    I, NDIGIT, K1, K2, LLL
      |                              1
Warning: Unused variable ‘k1’ declared at (1) [-Wunused-variable]
ivout.f:25:34:

   25 |       INTEGER    I, NDIGIT, K1, K2, LLL
      |                                  1
Warning: Unused variable ‘k2’ declared at (1) [-Wunused-variable]
ivout.f:26:23:

   26 |       CHARACTER*80 LINE
      |                       1
Warning: Unused variable ‘line’ declared at (1) [-Wunused-variable]
ivout.f:25:39:

   25 |       INTEGER    I, NDIGIT, K1, K2, LLL
      |                                       1
Warning: Unused variable ‘lll’ declared at (1) [-Wunused-variable]
ivout.f:18:34:

   18 |       SUBROUTINE IGRAPHIVOUT (LOUT, N, IX, IDIGIT, IFMT)
      |                                  1
Warning: Unused dummy argument ‘lout’ at (1) [-Wunused-dummy-argument]
ivout.f:18:37:

   18 |       SUBROUTINE IGRAPHIVOUT (LOUT, N, IX, IDIGIT, IFMT)
      |                                     1
Warning: Unused dummy argument ‘n’ at (1) [-Wunused-dummy-argument]
ivout.f:25:26:

   25 |       INTEGER    I, NDIGIT, K1, K2, LLL
      |                          1
Warning: Unused variable ‘ndigit’ declared at (1) [-Wunused-variable]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c second.f -o second.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c wrap.f -o wrap.o
wrap.f:9:18:

    9 |       character*2 which
      |                  1
Warning: Obsolescent feature: Old-style character length at (1)
wrap.f:33:18:

   33 |       character*2 which
      |                  1
Warning: Obsolescent feature: Old-style character length at (1)
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c simpleraytracer/Color.cpp -o simpleraytracer/Color.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c simpleraytracer/Light.cpp -o simpleraytracer/Light.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c simpleraytracer/Point.cpp -o simpleraytracer/Point.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c simpleraytracer/RIgraphRay.cpp -o simpleraytracer/RIgraphRay.o
simpleraytracer/RIgraphRay.cpp:49:11: warning: unused variable 'svgcolor' [-Wunused-variable]
  double *svgcolor=REAL(bgcolor);
          ^
1 warning generated.
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c simpleraytracer/Ray.cpp -o simpleraytracer/Ray.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c simpleraytracer/RayTracer.cpp -o simpleraytracer/RayTracer.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c simpleraytracer/RayVector.cpp -o simpleraytracer/RayVector.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c simpleraytracer/Shape.cpp -o simpleraytracer/Shape.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c simpleraytracer/Sphere.cpp -o simpleraytracer/Sphere.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c simpleraytracer/Triangle.cpp -o simpleraytracer/Triangle.o
clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -g -O3 -Wall -pedantic -frtti  -c simpleraytracer/unit_limiter.cpp -o simpleraytracer/unit_limiter.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c uuid/R.c -o uuid/R.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c uuid/clear.c -o uuid/clear.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c uuid/compare.c -o uuid/compare.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c uuid/copy.c -o uuid/copy.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c uuid/gen_uuid.c -o uuid/gen_uuid.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c uuid/isnull.c -o uuid/isnull.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c uuid/pack.c -o uuid/pack.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c uuid/parse.c -o uuid/parse.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c uuid/unpack.c -o uuid/unpack.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c uuid/unparse.c -o uuid/unparse.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c rinterface.c -o rinterface.o
rinterface.c:189:53: warning: passing 'void *' to parameter of type 'igraph_function_pointer_t' (aka 'void (*)(void)') converts between void pointer and function pointer [-Wpedantic]
    igraph_attribute_combination_add(comb, n, type, func);
                                                    ^~~~
include/igraph_attributes.h:153:43: note: passing argument to parameter 'func' here
                igraph_function_pointer_t func);
                                          ^
rinterface.c:1952:11: warning: initializing 'void *' with an expression of type 'igraph_function_pointer_t' (aka 'void (*)(void)') converts between void pointer and function pointer [-Wpedantic]
    void *voidfunc=funcs[i];
          ^        ~~~~~~~~
rinterface.c:2127:11: warning: initializing 'void *' with an expression of type 'igraph_function_pointer_t' (aka 'void (*)(void)') converts between void pointer and function pointer [-Wpedantic]
    void *voidfunc=funcs[i];
          ^        ~~~~~~~~
3 warnings generated.
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c rinterface_extra.c -o rinterface_extra.o
rinterface_extra.c:232:25: warning: format specifies type 'void *' but the argument has type 'SEXP' (aka 'struct SEXPREC *') [-Wformat-pedantic]
  snprintf(s, 64, "%p", object);
                   ~~   ^~~~~~
1 warning generated.
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O3 -Wall -pedantic -I/usr/include/libxml2 -g -O3 -Wall -pedantic -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O3 -Wall -pedantic  -c lazyeval.c -o lazyeval.o
clang++ -std=gnu++14 -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -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/bliss_heap.o bliss/defs.o bliss/graph.o bliss/orbit.o bliss/partition.o bliss/uintseqhash.o bliss/utils.o cattributes.o centrality.o cliquer/cliquer.o cliquer/cliquer_graph.o cliquer/reorder.o cliques.o clustertool.o cocitation.o cohesive_blocks.o coloring.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_cliquer.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 wrap.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 -lz -llzma -lm -ldl -lgmp -lglpk -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath
make[1]: Leaving directory '/tmp/RtmpXT4Yq0/working_dir/RtmplbK7Jb/R.INSTALL3e870279b670b7/igraph/src'
make[1]: Entering directory '/tmp/RtmpXT4Yq0/working_dir/RtmplbK7Jb/R.INSTALL3e870279b670b7/igraph/src'
make[1]: Leaving directory '/tmp/RtmpXT4Yq0/working_dir/RtmplbK7Jb/R.INSTALL3e870279b670b7/igraph/src'
installing to /tmp/RtmpXT4Yq0/RLIBS_3e488b49ef8b39/00LOCK-igraph/00new/igraph/libs
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (igraph)
* installing *source* package ‘quadprog’ ...
** package ‘quadprog’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
make[1]: Entering directory '/tmp/RtmpXT4Yq0/working_dir/RtmpOfnr6M/R.INSTALL3f7313712a2e15/quadprog/src'
gfortran -fno-optimize-sibling-calls  -fvisibility=hidden -fpic -g -O2 -mtune=native -Wall -pedantic -msse2 -mfpmath=sse   -fpic  -g -O2 -mtune=native -Wall -pedantic  -c aind.f -o aind.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c init.c -o init.o
gfortran -fno-optimize-sibling-calls  -fvisibility=hidden -fpic -g -O2 -mtune=native -Wall -pedantic -msse2 -mfpmath=sse   -fpic  -g -O2 -mtune=native -Wall -pedantic  -c solve.QP.compact.f -o solve.QP.compact.o
solve.QP.compact.f:254:3:

  254 |  72   if (nvl .EQ. 0) then
      |   1
Warning: Label 72 at (1) defined but not used [-Wunused-label]
solve.QP.compact.f:302:2:

  302 |  7       t1inf = .FALSE.
      |  1
Warning: Label 7 at (1) defined but not used [-Wunused-label]
gfortran -fno-optimize-sibling-calls  -fvisibility=hidden -fpic -g -O2 -mtune=native -Wall -pedantic -msse2 -mfpmath=sse   -fpic  -g -O2 -mtune=native -Wall -pedantic  -c solve.QP.f -o solve.QP.o
solve.QP.f:245:3:

  245 |  72   if (nvl .EQ. 0) then
      |   1
Warning: Label 72 at (1) defined but not used [-Wunused-label]
solve.QP.f:293:2:

  293 |  7       t1inf = .FALSE.
      |  1
Warning: Label 7 at (1) defined but not used [-Wunused-label]
gfortran -fno-optimize-sibling-calls  -fvisibility=hidden -fpic -g -O2 -mtune=native -Wall -pedantic -msse2 -mfpmath=sse   -fpic  -g -O2 -mtune=native -Wall -pedantic  -c util.f -o util.o
clang -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o quadprog.so aind.o init.o solve.QP.compact.o solve.QP.o util.o -L/data/gannet/ripley/R/R-clang/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath
make[1]: Leaving directory '/tmp/RtmpXT4Yq0/working_dir/RtmpOfnr6M/R.INSTALL3f7313712a2e15/quadprog/src'
make[1]: Entering directory '/tmp/RtmpXT4Yq0/working_dir/RtmpOfnr6M/R.INSTALL3f7313712a2e15/quadprog/src'
make[1]: Leaving directory '/tmp/RtmpXT4Yq0/working_dir/RtmpOfnr6M/R.INSTALL3f7313712a2e15/quadprog/src'
installing to /tmp/RtmpXT4Yq0/RLIBS_3e488b49ef8b39/00LOCK-quadprog/00new/quadprog/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (quadprog)
* installing *source* package ‘clusterGeneration’ ...
** package ‘clusterGeneration’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (clusterGeneration)
* installing *source* package ‘coda’ ...
** package ‘coda’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (coda)
* installing *source* package ‘combinat’ ...
** package ‘combinat’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (combinat)
* installing *source* package ‘expm’ ...
** package ‘expm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
make[1]: Entering directory '/tmp/RtmpXT4Yq0/working_dir/RtmpQAW2HW/R.INSTALL3f7e5856ddd5c7/expm/src'
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c R_dgebal.c -o R_dgebal.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c expm-eigen.c -o expm-eigen.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c expm.c -o expm.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c init.c -o init.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c logm-eigen.c -o logm-eigen.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c matexp.f -o matexp.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c matexp_MH09.c -o matexp_MH09.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c matpow.c -o matpow.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c matrexp.f -o matrexp.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c matrexpO.f -o matrexpO.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c mexp-common.f -o mexp-common.o
clang -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o expm.so R_dgebal.o expm-eigen.o expm.o init.o logm-eigen.o matexp.o matexp_MH09.o matpow.o matrexp.o matrexpO.o mexp-common.o -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath
make[1]: Leaving directory '/tmp/RtmpXT4Yq0/working_dir/RtmpQAW2HW/R.INSTALL3f7e5856ddd5c7/expm/src'
make[1]: Entering directory '/tmp/RtmpXT4Yq0/working_dir/RtmpQAW2HW/R.INSTALL3f7e5856ddd5c7/expm/src'
make[1]: Leaving directory '/tmp/RtmpXT4Yq0/working_dir/RtmpQAW2HW/R.INSTALL3f7e5856ddd5c7/expm/src'
installing to /tmp/RtmpXT4Yq0/RLIBS_3e488b49ef8b39/00LOCK-expm/00new/expm/libs
** R
** data
** demo
** 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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (expm)
* installing *source* package ‘numDeriv’ ...
** package ‘numDeriv’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (numDeriv)
* installing *source* package ‘plotrix’ ...
** package ‘plotrix’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (plotrix)
* installing *source* package ‘scatterplot3d’ ...
** package ‘scatterplot3d’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scatterplot3d)
* installing *source* package ‘mnormt’ ...
** package ‘mnormt’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
make[1]: Entering directory '/tmp/RtmpXT4Yq0/working_dir/Rtmp2ws8SX/R.INSTALL3f85511bf3401b/mnormt/src'
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c biv-nt.f -o biv-nt.o
biv-nt.f:371:11:

  371 |       hs = sign( one, dh - r*dk )
      |           1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
biv-nt.f:372:11:

  372 |       ks = sign( one, dk - r*dh )
      |           1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c mnormt_init.c -o mnormt_init.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c sadmvnt.f -o sadmvnt.o
sadmvnt.f:977:3:

  977 |  10      END DO
      |   1
Warning: Label 10 at (1) defined but not used [-Wunused-label]
sadmvnt.f:81:15:

   81 |       INFORM = MVNNIT( N, CORREL, LOWER, UPPER, INFIN, INFIS, D, E )
      |               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
sadmvnt.f:218:38:

  218 |         IF ( MINCLS .LT. 0 ) SBRGNS = WORK(LENWRK)
      |                                      1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
sadmvnt.f:276:21:

  276 |             RGNCLS = RGNCLS*(MESH(DIVAXN)+1)/MESH(DIVAXN)
      |                     1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
sadmvnt.f:277:21:

  277 |             NWRGNS = NWRGNS*(MESH(DIVAXN)+1)/MESH(DIVAXN)
      |                     1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
sadmvnt.f:1275:24:

 1275 |                POINTS = PONTRS(SUBTMP)
      |                        1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
sadmvnt.f:1276:24:

 1276 |                POINTP = PONTRS(SUBTMP+1)
      |                        1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
sadmvnt.f:1284:21:

 1284 |             POINTS = PONTRS(SUBTMP)
      |                     1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
sadmvnt.f:1304:21:

 1304 |             POINTS = PONTRS(SUBTMP)
      |                     1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
sadmvnt.f:325:15:

  325 |          TOP = PONTRS(1)
      |               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
sadmvnt.f:332:21:

  332 |             RGNCLS = RGNCLS*MESH(I)
      |                     1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
sadmvnt.f:337:18:

  337 |          RGNCLS = RGNCLS*(MESH(DIVAXN)+1)/MESH(DIVAXN)
      |                  1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
sadmvnt.f:1586:3:

 1586 |  10      END DO
      |   1
Warning: Label 10 at (1) defined but not used [-Wunused-label]
sadmvnt.f:1433:15:

 1433 |       INFORM = MVTNIT( N, NU, CORREL, LOWER, UPPER, INFIN, INFIS, D, E )
      |               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
sadmvnt.f:1662:72:

 1662 |      &              /( 1 + BMIN**2/(NU+I-1) )**( (NU+I-2)/TWO )
      |                                                                        ^
Warning: ‘bmin’ may be used uninitialized in this function [-Wmaybe-uninitialized]
sadmvnt.f:1659:72:

 1659 |      &              /( 1 + AMIN**2/(NU+I-1) )**( (NU+I-2)/TWO )
      |                                                                        ^
Warning: ‘amin’ may be used uninitialized in this function [-Wmaybe-uninitialized]
sadmvnt.f:1128:31:

 1128 |       INTEGER S, IXCHNG, LXCHNG, I, L
      |                               ^
Warning: ‘lxchng’ may be used uninitialized in this function [-Wmaybe-uninitialized]
sadmvnt.f:805:72:

  805 |       END
      |                                                                        ^
Warning: ‘__result_bvn’ may be used uninitialized in this function [-Wmaybe-uninitialized]
sadmvnt.f:763:35:

  763 |       DOUBLE PRECISION FUNCTION BVN ( LOWER, UPPER, INFIN, CORREL )
      |                                   ^
note: ‘__result_bvn’ was declared here
sadmvnt.f:1045:72:

 1045 |                   IF ( INFI(I) .EQ. 0 ) Y(I) = BMIN
      |                                                                        ^
Warning: ‘bmin’ may be used uninitialized in this function [-Wmaybe-uninitialized]
sadmvnt.f:1046:72:

 1046 |                   IF ( INFI(I) .EQ. 1 ) Y(I) = AMIN
      |                                                                        ^
Warning: ‘amin’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c tvpack.f -o tvpack.o
tvpack.f:459:14:

  459 |          HS = SIGN( ONE, DH - R*DK )
      |              1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
tvpack.f:460:14:

  460 |          KS = SIGN( ONE, DK - R*DH )
      |              1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
tvpack.f:126:52:

  126 |       DOUBLE PRECISION ONE, ZRO, EPS, ZROS(3), HS(3), TVT
      |                                                    1
Warning: Unused variable ‘hs’ declared at (1) [-Wunused-variable]
tvpack.f:126:45:

  126 |       DOUBLE PRECISION ONE, ZRO, EPS, ZROS(3), HS(3), TVT
      |                                             1
Warning: Unused variable ‘zros’ declared at (1) [-Wunused-variable]
tvpack.f:286:72:

  286 |       END
      |                                                                        ^
Warning: ‘fin’ may be used uninitialized in this function [-Wmaybe-uninitialized]
tvpack.f:262:58:

  262 |       DOUBLE PRECISION EI(NL), AI(NL), BI(NL), FI(NL), FIN, ERR, KRNRDT
      |                                                          ^
note: ‘fin’ was declared here
clang -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o mnormt.so biv-nt.o mnormt_init.o sadmvnt.o tvpack.o -lgfortran -lm -lquadmath
make[1]: Leaving directory '/tmp/RtmpXT4Yq0/working_dir/Rtmp2ws8SX/R.INSTALL3f85511bf3401b/mnormt/src'
make[1]: Entering directory '/tmp/RtmpXT4Yq0/working_dir/Rtmp2ws8SX/R.INSTALL3f85511bf3401b/mnormt/src'
make[1]: Leaving directory '/tmp/RtmpXT4Yq0/working_dir/Rtmp2ws8SX/R.INSTALL3f85511bf3401b/mnormt/src'
installing to /tmp/RtmpXT4Yq0/RLIBS_3e488b49ef8b39/00LOCK-mnormt/00new/mnormt/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (mnormt)
ERROR: dependency ‘fastmatch’ is not available for package ‘phangorn’
* removing ‘/tmp/RtmpXT4Yq0/RLIBS_3e488b49ef8b39/phangorn’
ERROR: dependency ‘phangorn’ is not available for package ‘phytools’
* removing ‘/tmp/RtmpXT4Yq0/RLIBS_3e488b49ef8b39/phytools’

The downloaded source packages are in
	'/tmp/RtmpXT4Yq0/working_dir/RtmpOKUh2X/downloaded_packages'

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 153-155 (ALA4R.Rmd) 
Error: processing vignette 'ALA4R.Rmd' failed with diagnostics:
there is no package called 'phytools'
--- failed re-building ‘ALA4R.Rmd’

SUMMARY: processing the following file failed:
  ‘ALA4R.Rmd’

Error: Vignette re-building failed.
Execution halted