############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data XNAString ### ############################################################################## ############################################################################## * checking for file ‘XNAString/DESCRIPTION’ ... OK * preparing ‘XNAString’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes ----------------------------------- * installing *source* package ‘XNAString’ ... ** this is package ‘XNAString’ version ‘1.15.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++11 gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ViennaRNA/utils/cpu.c -o ViennaRNA/utils/cpu.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ViennaRNA/utils/msa_utils.c -o ViennaRNA/utils/msa_utils.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ViennaRNA/utils/structure_tree.c -o ViennaRNA/utils/structure_tree.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ViennaRNA/utils/higher_order_functions.c -o ViennaRNA/utils/higher_order_functions.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ViennaRNA/utils/string_utils.c -o ViennaRNA/utils/string_utils.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ViennaRNA/utils/structure_utils.c -o ViennaRNA/utils/structure_utils.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ViennaRNA/utils/utils.c -o ViennaRNA/utils/utils.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ViennaRNA/constraints/SHAPE.c -o ViennaRNA/constraints/SHAPE.o ViennaRNA/constraints/SHAPE.c: In function ‘vrna_constraints_add_SHAPE’: ViennaRNA/constraints/SHAPE.c:202:10: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 202 | method = shape_method; | ^ ViennaRNA/constraints/SHAPE.c:206:51: warning: comparison between pointer and integer 206 | vrna_file_SHAPE_read(shape_file, length, method == 'W' ? 0 : -1, sequence, values); | ^~ ViennaRNA/constraints/SHAPE.c:208:14: warning: comparison between pointer and integer 208 | if (method == 'D') { | ^~ ViennaRNA/constraints/SHAPE.c:210:21: warning: comparison between pointer and integer 210 | } else if (method == 'Z') { | ^~ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ViennaRNA/constraints/constraints.c -o ViennaRNA/constraints/constraints.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ViennaRNA/constraints/soft.c -o ViennaRNA/constraints/soft.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ViennaRNA/constraints/hard.c -o ViennaRNA/constraints/hard.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ViennaRNA/constraints/ligand.c -o ViennaRNA/constraints/ligand.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ViennaRNA/datastructures/basic_datastructures.c -o ViennaRNA/datastructures/basic_datastructures.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ViennaRNA/datastructures/lists.c -o ViennaRNA/datastructures/lists.o ViennaRNA/datastructures/lists.c:97:1: error: conflicting types for ‘lst_kill’; have ‘void(LIST *, void (*)(void *))’ 97 | lst_kill (LIST * l, void (*freeNode) (void *node)) | ^~~~~~~~ In file included from ViennaRNA/datastructures/lists.c:33: ../src/ViennaRNA/datastructures/lists.h:58:6: note: previous declaration of ‘lst_kill’ with type ‘void(LIST *, void (*)(void))’ 58 | void lst_kill (LIST * l, void (*freeNode) ()); | ^~~~~~~~ ViennaRNA/datastructures/lists.c:284:1: error: conflicting types for ‘lst_mergesort’; have ‘void(LIST *, int (*)(void *, void *))’ 284 | lst_mergesort (LIST * l, int (*cmp_func) (void *, void *)) | ^~~~~~~~~~~~~ ../src/ViennaRNA/datastructures/lists.h:63:6: note: previous declaration of ‘lst_mergesort’ with type ‘void(LIST *, int (*)(void))’ 63 | void lst_mergesort (LIST * l, int (*cmp_func) ()); | ^~~~~~~~~~~~~ make: *** [/home/biocbuild/bbs-3.21-bioc/R/etc/Makeconf:201: ViennaRNA/datastructures/lists.o] Error 1 ERROR: compilation failed for package ‘XNAString’ * removing ‘/tmp/Rtmpp965RD/Rinst2830e93b266eba/XNAString’ ----------------------------------- ERROR: package installation failed