############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SynExtend ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘SynExtend’ ... ** this is package ‘SynExtend’ version ‘1.21.2’ ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using Fortran compiler: ‘GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic -g -O2 -Wall -Werror=format-security -c calcMIR2C.c -o calcMIR2C.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic -g -O2 -Wall -Werror=format-security -c CDend.c -o CDend.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic -g -O2 -Wall -Werror=format-security -c CShuffle.c -o CShuffle.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic -g -O2 -Wall -Werror=format-security -c dendrapply.c -o dendrapply.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic -g -O2 -Wall -Werror=format-security -c HitConsensus.c -o HitConsensus.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic -g -O2 -Wall -Werror=format-security -c HungarianAlgo.c -o HungarianAlgo.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic -g -O2 -Wall -Werror=format-security -c MoranI.c -o MoranI.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic -g -O2 -Wall -Werror=format-security -c NucleotideCounts.c -o NucleotideCounts.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic -g -O2 -Wall -Werror=format-security -c R_init_synextend.c -o R_init_synextend.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic -g -O2 -Wall -Werror=format-security -c RandomForest.c -o RandomForest.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic -g -O2 -Wall -Werror=format-security -c SEutils.c -o SEutils.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic -g -O2 -Wall -Werror=format-security -c XORRand.c -o XORRand.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic -g -O2 -Wall -Werror=format-security -c ExoLabel/ExoLabel.c -o ExoLabel/ExoLabel.o ExoLabel/ExoLabel.c: In function ‘R_LPOOM_cluster’: ExoLabel/ExoLabel.c:1882:5: warning: ‘debug_weights’ may be used uninitialized [-Wmaybe-uninitialized] 1882 | SET_VECTOR_ELT(LIST_VAL, 1, debug_weights); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ExoLabel/ExoLabel.c:1777:8: note: ‘debug_weights’ was declared here 1777 | SEXP debug_weights, debug_degrees; | ^~~~~~~~~~~~~ ExoLabel/ExoLabel.c:1883:5: warning: ‘debug_degrees’ may be used uninitialized [-Wmaybe-uninitialized] 1883 | SET_VECTOR_ELT(LIST_VAL, 2, debug_degrees); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ExoLabel/ExoLabel.c:1777:23: note: ‘debug_degrees’ was declared here 1777 | SEXP debug_weights, debug_degrees; | ^~~~~~~~~~~~~ ExoLabel/ExoLabel.c:1884:5: warning: ‘debug_disjoint_sizes’ may be used uninitialized [-Wmaybe-uninitialized] 1884 | SET_VECTOR_ELT(LIST_VAL, 3, debug_disjoint_sizes); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ExoLabel/ExoLabel.c:1826:8: note: ‘debug_disjoint_sizes’ was declared here 1826 | SEXP debug_disjoint_sizes; | ^~~~~~~~~~~~~~~~~~~~ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic -g -O2 -Wall -Werror=format-security -c ExoLabel/FileHandlers.c -o ExoLabel/FileHandlers.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic -g -O2 -Wall -Werror=format-security -c ExoLabel/PrefixTrie.c -o ExoLabel/PrefixTrie.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic -g -O2 -Wall -Werror=format-security -c ExoLabel/LoserTree.c -o ExoLabel/LoserTree.o gfortran -fpic -g -O2 -Wall -Werror=format-security -c utilfuncs.f95 -o utilfuncs.o f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran gfortran -fpic -g -O2 -Wall -Werror=format-security -c tabulate_mod.f95 -o tabulate_mod.o f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran gfortran -fpic -g -O2 -Wall -Werror=format-security -c cart_methods.f95 -o cart_methods.o f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o SynExtend.so calcMIR2C.o CDend.o CShuffle.o dendrapply.o HitConsensus.o HungarianAlgo.o MoranI.o NucleotideCounts.o R_init_synextend.o RandomForest.o SEutils.o XORRand.o ExoLabel/ExoLabel.o ExoLabel/FileHandlers.o ExoLabel/PrefixTrie.o ExoLabel/LoserTree.o cart_methods.o tabulate_mod.o utilfuncs.o -fopenmp -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.22-bioc/R/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)