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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL msa
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘msa’ ...
** this is package ‘msa’ version ‘1.39.1’
** 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'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -I"./gc-8.2.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fpic  -g -O2  -DR_NO_REMAP -c R_init_msa.cpp -o R_init_msa.o
In file included from ./Muscle/RMuscle.h:4,
                 from R_init_msa.cpp:3:
./Muscle/muscle.h:54: warning: "assert" redefined
   54 | #define assert(exp)     ((void)0)
      | 
In file included from /usr/include/c++/13/cassert:44,
                 from /home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include/Rcpp/utils/tinyformat/tinyformat.h:137,
                 from /home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include/Rcpp/utils/tinyformat.h:40,
                 from /home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include/RcppCommon.h:74,
                 from /home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include/Rcpp.h:27,
                 from ./ClustalOmega/src/RClustalOmega.h:4,
                 from R_init_msa.cpp:1:
/usr/include/assert.h:50: note: this is the location of the previous definition
   50 | # define assert(expr)           (__ASSERT_VOID_CAST (0))
      | 
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -I"./gc-8.2.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fpic  -g -O2  -DR_NO_REMAP -c SplitCharVector2List.cpp -o SplitCharVector2List.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -I"./gc-8.2.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fpic  -g -O2  -DR_NO_REMAP -c SplitCharVector2Matrix.cpp -o SplitCharVector2Matrix.o
make --file=msaMakefile --directory=gc-8.2.2
make[1]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/msa/src/gc-8.2.2'
./configure --enable-cplusplus --enable-threads=pthreads --enable-shared=no --with-pic
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking GC version numbers... major=8 minor=2                 micro=2
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking whether make supports the include directive... yes (GNU style)
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
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 whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking dependency style of gcc... gcc3
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for emscripten... no
checking for inline... inline
configure: WARNING: "Explicit GC_INIT() calls may be required."
checking for pthread_self in -lpthread... yes
checking for clock_gettime without additional libraries... yes
checking whether compiler supports -Wextra... yes
checking whether compiler supports -Wpedantic... yes
checking for xlc... no
checking whether compiler supports -fno-strict-aliasing... yes
checking for getcontext... yes
checking for dl_iterate_phdr... yes
checking for dlopen in -ldl... yes
checking execinfo.h usability... yes
checking execinfo.h presence... yes
checking for execinfo.h... yes
checking whether to build shared libraries... no
checking which machine-dependent code should be used... 
checking whether AIX gcc optimization fix is necessary... no
checking whether -Wno-frame-address works... yes
checking for dladdr... yes
checking for sigsetjmp... yes
checking for pthread_setname_np... yes (with tid)
checking sys/dg_sys_info.h usability... no
checking sys/dg_sys_info.h presence... no
checking for sys/dg_sys_info.h... no
checking for compiler intrinsics support... yes
checking which libatomic_ops to use... none
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating bdw-gc.pc
config.status: creating include/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
config.status: executing default commands
make
make[2]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/msa/src/gc-8.2.2'
make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/msa/src/gc-8.2.2'
depbase=`echo allchblk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./libtool  --tag=CC   --mode=compile  -DHAVE_CONFIG_H   -I./include -I./include      -fexceptions  -MT allchblk.lo -MD -MP -MF $depbase.Tpo -c -o allchblk.lo allchblk.c &&\
mv -f $depbase.Tpo $depbase.Plo
Usage: /home/biocbuild/bbs-3.21-bioc/meat/msa/src/gc-8.2.2/libtool [OPTION]... [MODE-ARG]...
Try 'libtool --help' for more information.
libtool:   error: unrecognised option: '-DHAVE_CONFIG_H'
make[3]: *** [Makefile:1709: allchblk.lo] Error 1
make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/msa/src/gc-8.2.2'
make[2]: *** [Makefile:1933: all-recursive] Error 1
make[2]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/msa/src/gc-8.2.2'
make[1]: *** [msaMakefile:7: build_gc] Error 2
make[1]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/msa/src/gc-8.2.2'
make: *** [Makevars:13: build_gc] Error 2
ERROR: compilation failed for package ‘msa’
* removing ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/msa’
* restoring previous ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/msa’