############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL SynExtend ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘SynExtend’ ... ** this is package ‘SynExtend’ version ‘1.20.0’ ** using staged installation ** libs using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ using Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c CDend.c -o CDend.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c CShuffle.c -o CShuffle.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c HungarianAlgo.c -o HungarianAlgo.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c LoserTree.c -o LoserTree.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c MoranI.c -o MoranI.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c NucleotideCounts.c -o NucleotideCounts.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c OnDiskLP.c -o OnDiskLP.o OnDiskLP.c: In function ‘compressEdgeValues’: OnDiskLP.c:393:47: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 393 | error("ExoLabel can only support up to %llu nodes.", MAX_NUM_NODES); | ~~~^ ~~~~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu OnDiskLP.c: In function ‘R_LPOOM_cluster’: OnDiskLP.c:2185:5: warning: ‘debug_weights’ may be used uninitialized [-Wmaybe-uninitialized] 2185 | SET_VECTOR_ELT(LIST_VAL, 1, debug_weights); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ OnDiskLP.c:2076:8: note: ‘debug_weights’ was declared here 2076 | SEXP debug_weights, debug_degrees; | ^~~~~~~~~~~~~ OnDiskLP.c:2186:5: warning: ‘debug_degrees’ may be used uninitialized [-Wmaybe-uninitialized] 2186 | SET_VECTOR_ELT(LIST_VAL, 2, debug_degrees); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ OnDiskLP.c:2076:23: note: ‘debug_degrees’ was declared here 2076 | SEXP debug_weights, debug_degrees; | ^~~~~~~~~~~~~ OnDiskLP.c:2187:5: warning: ‘debug_disjoint_sizes’ may be used uninitialized [-Wmaybe-uninitialized] 2187 | SET_VECTOR_ELT(LIST_VAL, 3, debug_disjoint_sizes); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ OnDiskLP.c:2125:8: note: ‘debug_disjoint_sizes’ was declared here 2125 | SEXP debug_disjoint_sizes; | ^~~~~~~~~~~~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c PrefixTrie.c -o PrefixTrie.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c R_init_synextend.c -o R_init_synextend.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c RandomForest.c -o RandomForest.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c SEutils.c -o SEutils.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c XORRand.c -o XORRand.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gfortran -fPIC -g -O2 -Wall -Werror=format-security -c _fortran_tabulate.f95 -o _fortran_tabulate.o f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gfortran -fPIC -g -O2 -Wall -Werror=format-security -c _fortran_utils.f95 -o _fortran_utils.o f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c calcMIR2C.c -o calcMIR2C.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gfortran -fPIC -g -O2 -Wall -Werror=format-security -c cart_fort.f95 -o cart_fort.o f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c dendrapply.c -o dendrapply.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o SynExtend.so CDend.o CShuffle.o HungarianAlgo.o LoserTree.o MoranI.o NucleotideCounts.o OnDiskLP.o PrefixTrie.o R_init_synextend.o RandomForest.o SEutils.o XORRand.o _fortran_tabulate.o _fortran_utils.o calcMIR2C.o cart_fort.o dendrapply.o -fopenmp -lgfortran -lm -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-SynExtend/00new/SynExtend/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded 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 (SynExtend)