############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data muscle ### ############################################################################## ############################################################################## * checking for file ‘muscle/DESCRIPTION’ ... OK * preparing ‘muscle’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes ----------------------------------- * installing *source* package ‘muscle’ ... ** this is package ‘muscle’ version ‘3.49.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c aligngivenpath.cpp -o aligngivenpath.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c aligngivenpathsw.cpp -o aligngivenpathsw.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c aligntwomsas.cpp -o aligntwomsas.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c aligntwoprofs.cpp -o aligntwoprofs.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c aln.cpp -o aln.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c alpha.cpp -o alpha.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c anchors.cpp -o anchors.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c bittraceback.cpp -o bittraceback.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c blosum62.cpp -o blosum62.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c blosumla.cpp -o blosumla.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c clust.cpp -o clust.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c cluster.cpp -o cluster.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c clwwt.cpp -o clwwt.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c color.cpp -o color.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c cons.cpp -o cons.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c diaglist.cpp -o diaglist.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c diffobjscore.cpp -o diffobjscore.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c diffpaths.cpp -o diffpaths.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c difftrees.cpp -o difftrees.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c difftreese.cpp -o difftreese.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c distcalc.cpp -o distcalc.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c distfunc.cpp -o distfunc.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c distpwkimura.cpp -o distpwkimura.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c domuscle.cpp -o domuscle.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c dosp.cpp -o dosp.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c dpreglist.cpp -o dpreglist.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c drawtree.cpp -o drawtree.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c edgelist.cpp -o edgelist.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c enumopts.cpp -o enumopts.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c enumtostr.cpp -o enumtostr.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c estring.cpp -o estring.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c fasta.cpp -o fasta.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c fasta2.cpp -o fasta2.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c fastclust.cpp -o fastclust.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c fastdist.cpp -o fastdist.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c fastdistjones.cpp -o fastdistjones.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c fastdistkbit.cpp -o fastdistkbit.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c fastdistkmer.cpp -o fastdistkmer.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c fastdistmafft.cpp -o fastdistmafft.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c fastdistnuc.cpp -o fastdistnuc.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c fastscorepath2.cpp -o fastscorepath2.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c finddiags.cpp -o finddiags.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c finddiagsn.cpp -o finddiagsn.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c glbalign.cpp -o glbalign.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c glbalign352.cpp -o glbalign352.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c glbaligndiag.cpp -o glbaligndiag.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c glbalignla.cpp -o glbalignla.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c glbalignle.cpp -o glbalignle.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c glbalignns.cpp -o glbalignns.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c glbalignsimple.cpp -o glbalignsimple.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c glbalignsp.cpp -o glbalignsp.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c glbalignspn.cpp -o glbalignspn.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c glbalignss.cpp -o glbalignss.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c glbalndimer.cpp -o glbalndimer.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c globals.cpp -o globals.o globals.cpp: In function ‘void Quit(const char*, ...)’: globals.cpp:107:9: error: ‘error’ was not declared in this scope; did you mean ‘perror’? 107 | error("error in muscle\n"); | ^~~~~ | perror make: *** [/home/biocbuild/bbs-3.21-bioc/R/etc/Makeconf:202: globals.o] Error 1 ERROR: compilation failed for package ‘muscle’ * removing ‘/tmp/RtmpztLb1W/Rinst3d044d6fddb418/muscle’ ----------------------------------- ERROR: package installation failed