############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL bgx ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘bgx’ ... ** using staged installation checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for C compiler vendor... gnu checking whether C compiler accepts -ffast-math... yes checking whether C compiler accepts -O3... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for gcc architecture flag... checking for x86 cpuid 0 output... 16:756e6547:6c65746e:49656e69 checking for x86 cpuid 1 output... 50657:4400800:7ffefbff:bfebfbff checking whether C compiler accepts -march=pentium2... no checking whether C compiler accepts -mcpu=pentium2... no checking whether C compiler accepts -mpentium2... no checking whether C compiler accepts -march=pentiumpro... no checking whether C compiler accepts -mcpu=pentiumpro... no checking whether C compiler accepts -mpentiumpro... no checking for gcc architecture flag... unknown checking for gcc option to accept ISO C99... none needed checking for main in -lm... yes Untarring Boost header files... tar: Ignoring unknown extended header keyword 'SCHILY.fflags' checking for an ANSI C-conforming const... yes checking for inline... inline configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I ../boostIncl -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -g -O2 -Wall -ffast-math -O3 -DUSING_R -c bgx.cc -o bgx.o In file included from bgx.cc:32: rand.hh: In member function ‘RealType Rand::Normal()’: rand.hh:399:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 399 | if(u0<.5) return y; return -y; | ^~ rand.hh:399:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 399 | if(u0<.5) return y; return -y; | ^~~~~~ rand.hh:406:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 406 | if(u0<.5) return y; return -y; | ^~ rand.hh:406:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 406 | if(u0<.5) return y; return -y; | ^~~~~~ rand.hh:413:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 413 | if(u0<.5) return y; return -y; | ^~ rand.hh:413:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 413 | if(u0<.5) return y; return -y; | ^~~~~~ rand.hh:420:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 420 | if(u0<.5) return y; return -y; | ^~ rand.hh:420:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 420 | if(u0<.5) return y; return -y; | ^~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I ../boostIncl -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -g -O2 -Wall -ffast-math -O3 -DUSING_R -c bgx_frontend.cc -o bgx_frontend.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I ../boostIncl -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -g -O2 -Wall -ffast-math -O3 -c qnorm.c -o qnorm.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I ../boostIncl -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -g -O2 -Wall -ffast-math -O3 -DUSING_R -c rundir.cc -o rundir.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I ../boostIncl -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -g -O2 -Wall -ffast-math -O3 -DUSING_R -c sokal.cc -o sokal.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o bgx.so bgx.o bgx_frontend.o qnorm.o rundir.o sokal.o -lm -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR rm -r ../boostIncl installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-bgx/00new/bgx/libs ** R ** 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 (bgx)