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###
### Running command:
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### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL msa
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* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘msa’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/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 -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++/10.3.1/cassert:44,
from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/Rcpp/utils/tinyformat/tinyformat.h:137,
from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/Rcpp/utils/tinyformat.h:40,
from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:73,
from /home/biocbuild/R/R-4.3.0/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/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/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 -c SplitCharVector2List.cpp -o SplitCharVector2List.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/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 -c SplitCharVector2Matrix.cpp -o SplitCharVector2Matrix.o
make --file=msaMakefile --directory=gc-8.2.2
make[1]: Entering directory '/home/biocbuild/bbs-3.18-bioc/meat/msa/src/gc-8.2.2'
./configure --enable-cplusplus --enable-threads=pthreads --enable-shared=no --with-pic
checking build system type... aarch64-unknown-linux-gnu
checking host system type... aarch64-unknown-linux-gnu
checking target system type... aarch64-unknown-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 aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert aarch64-unknown-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... no
checking if : 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) 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
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) 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... no
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) 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-3.18-bioc/meat/msa/src/gc-8.2.2'
make[3]: Entering directory '/home/biocbuild/bbs-3.18-bioc/meat/msa/src/gc-8.2.2'
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/bin/sh ./libtool --tag=CC --mode=link gcc -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -Wno-frame-address -version-info 6:1:5 -no-undefined -o libgc.la -rpath /usr/local/lib allchblk.lo alloc.lo blacklst.lo dbg_mlc.lo dyn_load.lo finalize.lo gc_dlopen.lo headers.lo mach_dep.lo malloc.lo mallocx.lo mark.lo mark_rts.lo misc.lo new_hblk.lo obj_map.lo os_dep.lo ptr_chck.lo reclaim.lo specific.lo typd_mlc.lo pthread_start.lo pthread_support.lo pthread_stop_world.lo thread_local_alloc.lo gcj_mlc.lo fnlz_mlc.lo -lpthread -ldl
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depbase=`echo gc_cpp.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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/bin/sh ./libtool --tag=CXX --mode=link g++ -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -version-info 6:0:5 -no-undefined -o libgccpp.la -rpath /usr/local/lib gc_badalc.lo gc_cpp.lo libgc.la
libtool: link: ar cru .libs/libgccpp.a gc_badalc.o gc_cpp.o
libtool: link: ranlib .libs/libgccpp.a
libtool: link: ( cd ".libs" && rm -f "libgccpp.la" && ln -s "../libgccpp.la" "libgccpp.la" )
/bin/sh ./libtool --tag=CXX --mode=link g++ -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -version-info 6:0:5 -no-undefined -o libgctba.la -rpath /usr/local/lib gc_badalc.lo libgc.la
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libtool: link: ( cd ".libs" && rm -f "libgctba.la" && ln -s "../libgctba.la" "libgctba.la" )
/bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -Wno-frame-address -MT cord/libcord_la-cordbscs.lo -MD -MP -MF cord/.deps/libcord_la-cordbscs.Tpo -c -o cord/libcord_la-cordbscs.lo `test -f 'cord/cordbscs.c' || echo './'`cord/cordbscs.c
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mv -f cord/.deps/libcord_la-cordbscs.Tpo cord/.deps/libcord_la-cordbscs.Plo
/bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -Wno-frame-address -MT cord/libcord_la-cordprnt.lo -MD -MP -MF cord/.deps/libcord_la-cordprnt.Tpo -c -o cord/libcord_la-cordprnt.lo `test -f 'cord/cordprnt.c' || echo './'`cord/cordprnt.c
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/bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -Wno-frame-address -MT cord/libcord_la-cordxtra.lo -MD -MP -MF cord/.deps/libcord_la-cordxtra.Tpo -c -o cord/libcord_la-cordxtra.lo `test -f 'cord/cordxtra.c' || echo './'`cord/cordxtra.c
libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -Wno-frame-address -MT cord/libcord_la-cordxtra.lo -MD -MP -MF cord/.deps/libcord_la-cordxtra.Tpo -c cord/cordxtra.c -fPIC -DPIC -o cord/libcord_la-cordxtra.o
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/bin/sh ./libtool --tag=CC --mode=link gcc -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -Wno-frame-address -version-info 6:0:5 -no-undefined -o libcord.la -rpath /usr/local/lib cord/libcord_la-cordbscs.lo cord/libcord_la-cordprnt.lo cord/libcord_la-cordxtra.lo libgc.la
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libtool: link: ranlib .libs/libcord.a
libtool: link: ( cd ".libs" && rm -f "libcord.la" && ln -s "../libcord.la" "libcord.la" )
make[3]: Leaving directory '/home/biocbuild/bbs-3.18-bioc/meat/msa/src/gc-8.2.2'
make[2]: Leaving directory '/home/biocbuild/bbs-3.18-bioc/meat/msa/src/gc-8.2.2'
cp .libs/libgc.a ../
cp .libs/libgccpp.a ../
make[1]: Leaving directory '/home/biocbuild/bbs-3.18-bioc/meat/msa/src/gc-8.2.2'
----------------------------------------
------------------ GC -----------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile --directory=Muscle
make[1]: Entering directory '/home/biocbuild/bbs-3.18-bioc/meat/msa/src/Muscle'
export PKG_CXXFLAGS=" -I../gc-8.2.2/include"
/home/biocbuild/R/R-4.3.0/bin/R CMD SHLIB -o libMuscle.so aligngivenpath.cpp aligngivenpathsw.cpp aligntwomsas.cpp aligntwoprofs.cpp aln.cpp alpha.cpp anchors.cpp bittraceback.cpp blosum62.cpp blosumla.cpp clust.cpp cluster.cpp clwwt.cpp color.cpp cons.cpp diaglist.cpp diffobjscore.cpp diffpaths.cpp difftrees.cpp difftreese.cpp distcalc.cpp distfunc.cpp distpwkimura.cpp domuscle.cpp dosp.cpp dpreglist.cpp drawtree.cpp edgelist.cpp enumopts.cpp enumtostr.cpp estring.cpp fasta.cpp fasta2.cpp fastclust.cpp fastdist.cpp fastdistjones.cpp fastdistkbit.cpp fastdistkmer.cpp fastdistmafft.cpp fastdistnuc.cpp fastscorepath2.cpp finddiags.cpp finddiagsn.cpp glbalign.cpp glbalign352.cpp glbaligndiag.cpp glbalignle.cpp glbalignsimple.cpp glbalignsp.cpp glbalignspn.cpp glbalignss.cpp glbalndimer.cpp globals.cpp globalslinux.cpp globalsosx.cpp globalsother.cpp globalswin32.cpp gonnet.cpp henikoffweight.cpp henikoffweightpb.cpp html.cpp hydro.cpp intmath.cpp local.cpp main.cpp makerootmsa.cpp makerootmsab.cpp maketree.cpp mhack.cpp mpam200.cpp msa.cpp msa2.cpp msadistkimura.cpp msf.cpp muscle.cpp muscleout.cpp nucmx.cpp nwdasimple.cpp nwdasimple2.cpp nwdasmall.cpp nwrec.cpp nwsmall.cpp objscore.cpp objscore2.cpp objscoreda.cpp onexception.cpp options.cpp outweights.cpp pam200mafft.cpp params.cpp phy.cpp phy2.cpp phy3.cpp phy4.cpp phyfromclust.cpp phyfromfile.cpp physeq.cpp phytofile.cpp posgap.cpp ppscore.cpp profdb.cpp profile.cpp profilefrommsa.cpp progalign.cpp progress.cpp progressivealign.cpp pwpath.cpp readmx.cpp realigndiffs.cpp realigndiffse.cpp refine.cpp refinehoriz.cpp refinesubfams.cpp refinetree.cpp refinetreee.cpp refinevert.cpp refinew.cpp savebest.cpp scoredist.cpp scoregaps.cpp scorehistory.cpp scorepp.cpp seq.cpp seqvect.cpp setblosumweights.cpp setgscweights.cpp setnewhandler.cpp spfast.cpp sptest.cpp stabilize.cpp subfam.cpp subfams.cpp sw.cpp termgaps.cpp textfile.cpp threewaywt.cpp tomhydro.cpp traceback.cpp tracebackopt.cpp tracebacksw.cpp treefrommsa.cpp typetostr.cpp upgma2.cpp usage.cpp validateids.cpp vtml2.cpp writescorefile.cpp RMuscle.cpp
using C++ compiler: ‘g++ (GCC) 10.3.1’
make[2]: Entering directory '/home/biocbuild/bbs-3.18-bioc/meat/msa/src/Muscle'
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c aligngivenpath.cpp -o aligngivenpath.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c aligngivenpathsw.cpp -o aligngivenpathsw.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c aligntwomsas.cpp -o aligntwomsas.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c aligntwoprofs.cpp -o aligntwoprofs.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c aln.cpp -o aln.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c alpha.cpp -o alpha.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c anchors.cpp -o anchors.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c bittraceback.cpp -o bittraceback.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c blosum62.cpp -o blosum62.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c blosumla.cpp -o blosumla.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c clust.cpp -o clust.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c cluster.cpp -o cluster.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c clwwt.cpp -o clwwt.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c color.cpp -o color.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c cons.cpp -o cons.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c diaglist.cpp -o diaglist.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c diffobjscore.cpp -o diffobjscore.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c diffpaths.cpp -o diffpaths.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c difftrees.cpp -o difftrees.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c difftreese.cpp -o difftreese.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c distcalc.cpp -o distcalc.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c distfunc.cpp -o distfunc.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c distpwkimura.cpp -o distpwkimura.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c domuscle.cpp -o domuscle.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c dosp.cpp -o dosp.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c dpreglist.cpp -o dpreglist.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c drawtree.cpp -o drawtree.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c edgelist.cpp -o edgelist.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c enumopts.cpp -o enumopts.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c enumtostr.cpp -o enumtostr.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c estring.cpp -o estring.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c fasta.cpp -o fasta.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c fasta2.cpp -o fasta2.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c fastclust.cpp -o fastclust.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c fastdist.cpp -o fastdist.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c fastdistjones.cpp -o fastdistjones.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c fastdistkbit.cpp -o fastdistkbit.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c fastdistkmer.cpp -o fastdistkmer.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c fastdistmafft.cpp -o fastdistmafft.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c fastdistnuc.cpp -o fastdistnuc.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c fastscorepath2.cpp -o fastscorepath2.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c finddiags.cpp -o finddiags.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c finddiagsn.cpp -o finddiagsn.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c glbalign.cpp -o glbalign.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c glbalign352.cpp -o glbalign352.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c glbaligndiag.cpp -o glbaligndiag.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c glbalignle.cpp -o glbalignle.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c glbalignsimple.cpp -o glbalignsimple.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c glbalignsp.cpp -o glbalignsp.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c glbalignspn.cpp -o glbalignspn.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c glbalignss.cpp -o glbalignss.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c glbalndimer.cpp -o glbalndimer.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c globals.cpp -o globals.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c globalslinux.cpp -o globalslinux.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c globalsosx.cpp -o globalsosx.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c globalsother.cpp -o globalsother.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c globalswin32.cpp -o globalswin32.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c gonnet.cpp -o gonnet.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c henikoffweight.cpp -o henikoffweight.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c henikoffweightpb.cpp -o henikoffweightpb.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c html.cpp -o html.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c hydro.cpp -o hydro.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c intmath.cpp -o intmath.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c local.cpp -o local.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c main.cpp -o main.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c makerootmsa.cpp -o makerootmsa.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c makerootmsab.cpp -o makerootmsab.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c maketree.cpp -o maketree.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c mhack.cpp -o mhack.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c mpam200.cpp -o mpam200.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c msa.cpp -o msa.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c msa2.cpp -o msa2.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c msadistkimura.cpp -o msadistkimura.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c msf.cpp -o msf.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c muscle.cpp -o muscle.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c muscleout.cpp -o muscleout.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c nucmx.cpp -o nucmx.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c nwdasimple.cpp -o nwdasimple.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c nwdasimple2.cpp -o nwdasimple2.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c nwdasmall.cpp -o nwdasmall.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c nwrec.cpp -o nwrec.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c nwsmall.cpp -o nwsmall.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c objscore.cpp -o objscore.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c objscore2.cpp -o objscore2.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c objscoreda.cpp -o objscoreda.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c onexception.cpp -o onexception.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c options.cpp -o options.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c outweights.cpp -o outweights.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c pam200mafft.cpp -o pam200mafft.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c params.cpp -o params.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c phy.cpp -o phy.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c phy2.cpp -o phy2.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c phy3.cpp -o phy3.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c phy4.cpp -o phy4.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c phyfromclust.cpp -o phyfromclust.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c phyfromfile.cpp -o phyfromfile.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c physeq.cpp -o physeq.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c phytofile.cpp -o phytofile.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c posgap.cpp -o posgap.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c ppscore.cpp -o ppscore.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c profdb.cpp -o profdb.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c profile.cpp -o profile.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c profilefrommsa.cpp -o profilefrommsa.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c progalign.cpp -o progalign.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c progress.cpp -o progress.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c progressivealign.cpp -o progressivealign.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c pwpath.cpp -o pwpath.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c readmx.cpp -o readmx.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c realigndiffs.cpp -o realigndiffs.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c realigndiffse.cpp -o realigndiffse.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c refine.cpp -o refine.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c refinehoriz.cpp -o refinehoriz.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c refinesubfams.cpp -o refinesubfams.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c refinetree.cpp -o refinetree.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c refinetreee.cpp -o refinetreee.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c refinevert.cpp -o refinevert.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c refinew.cpp -o refinew.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c savebest.cpp -o savebest.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c scoredist.cpp -o scoredist.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c scoregaps.cpp -o scoregaps.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c scorehistory.cpp -o scorehistory.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c scorepp.cpp -o scorepp.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c seq.cpp -o seq.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c seqvect.cpp -o seqvect.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c setblosumweights.cpp -o setblosumweights.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c setgscweights.cpp -o setgscweights.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c setnewhandler.cpp -o setnewhandler.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c spfast.cpp -o spfast.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c sptest.cpp -o sptest.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c stabilize.cpp -o stabilize.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c subfam.cpp -o subfam.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c subfams.cpp -o subfams.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c sw.cpp -o sw.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c termgaps.cpp -o termgaps.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c textfile.cpp -o textfile.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c threewaywt.cpp -o threewaywt.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c tomhydro.cpp -o tomhydro.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c traceback.cpp -o traceback.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c tracebackopt.cpp -o tracebackopt.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c tracebacksw.cpp -o tracebacksw.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c treefrommsa.cpp -o treefrommsa.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c typetostr.cpp -o typetostr.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c upgma2.cpp -o upgma2.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c usage.cpp -o usage.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c validateids.cpp -o validateids.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c vtml2.cpp -o vtml2.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c writescorefile.cpp -o writescorefile.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c RMuscle.cpp -o RMuscle.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o libMuscle.so aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o options.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o RMuscle.o -L/home/biocbuild/R/R-4.3.0/lib -lR
make[2]: Leaving directory '/home/biocbuild/bbs-3.18-bioc/meat/msa/src/Muscle'
ar rcs libMuscle.a aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o options.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o RMuscle.o
cp libMuscle.a ../
make[1]: Leaving directory '/home/biocbuild/bbs-3.18-bioc/meat/msa/src/Muscle'
----------------------------------------
---------------- MUSCLE ----------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile --directory=ClustalW
make[1]: Entering directory '/home/biocbuild/bbs-3.18-bioc/meat/msa/src/ClustalW'
./configure; \
cd src; \
export PKG_CXXFLAGS="-DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result"; \
/home/biocbuild/R/R-4.3.0/bin/R CMD SHLIB -o libClustalW.so pairwise/FullPairwiseAlign.cpp pairwise/FastPairwiseAlign.cpp fileInput/MSFFileParser.cpp fileInput/FileReader.cpp fileInput/PIRFileParser.cpp fileInput/RSFFileParser.cpp fileInput/GDEFileParser.cpp fileInput/InFileStream.cpp fileInput/ClustalFileParser.cpp fileInput/PearsonFileParser.cpp fileInput/FileParser.cpp fileInput/EMBLFileParser.cpp tree/UPGMA/RootedClusterTree.cpp tree/UPGMA/UPGMAAlgorithm.cpp tree/UPGMA/Node.cpp tree/UPGMA/RootedGuideTree.cpp tree/UPGMA/RootedTreeOutput.cpp tree/Tree.cpp tree/ClusterTree.cpp tree/TreeInterface.cpp tree/UnRootedClusterTree.cpp tree/ClusterTreeOutput.cpp tree/RandomGenerator.cpp tree/NJTree.cpp tree/AlignmentSteps.cpp interface/CommandLineParser.cpp substitutionMatrix/SubMatrix.cpp multipleAlign/Iteration.cpp multipleAlign/MSA.cpp multipleAlign/MyersMillerProfileAlign.cpp multipleAlign/ProfileStandard.cpp multipleAlign/ProfileWithSub.cpp multipleAlign/ProfileBase.cpp multipleAlign/LowScoreSegProfile.cpp general/OutputFile.cpp general/UserParameters.cpp general/Utility.cpp general/InvalidCombination.cpp general/DebugLog.cpp general/ClustalWResources.cpp general/VectorOutOfRange.cpp general/SymMatrix.cpp general/Stats.cpp Help.cpp alignment/Alignment.cpp alignment/AlignmentOutput.cpp alignment/ObjectiveScore.cpp alignment/Sequence.cpp Clustal.cpp RClustalWMain.cpp RClustalW.cpp && \
ar rcs libClustalW.a pairwise/FullPairwiseAlign.o pairwise/FastPairwiseAlign.o fileInput/MSFFileParser.o fileInput/FileReader.o fileInput/PIRFileParser.o fileInput/RSFFileParser.o fileInput/GDEFileParser.o fileInput/InFileStream.o fileInput/ClustalFileParser.o fileInput/PearsonFileParser.o fileInput/FileParser.o fileInput/EMBLFileParser.o tree/UPGMA/RootedClusterTree.o tree/UPGMA/UPGMAAlgorithm.o tree/UPGMA/Node.o tree/UPGMA/RootedGuideTree.o tree/UPGMA/RootedTreeOutput.o tree/Tree.o tree/ClusterTree.o tree/TreeInterface.o tree/UnRootedClusterTree.o tree/ClusterTreeOutput.o tree/RandomGenerator.o tree/NJTree.o tree/AlignmentSteps.o interface/CommandLineParser.o substitutionMatrix/SubMatrix.o multipleAlign/Iteration.o multipleAlign/MSA.o multipleAlign/MyersMillerProfileAlign.o multipleAlign/ProfileStandard.o multipleAlign/ProfileWithSub.o multipleAlign/ProfileBase.o multipleAlign/LowScoreSegProfile.o general/OutputFile.o general/UserParameters.o general/Utility.o general/InvalidCombination.o general/DebugLog.o general/ClustalWResources.o general/VectorOutOfRange.o general/SymMatrix.o general/Stats.o Help.o alignment/Alignment.o alignment/AlignmentOutput.o alignment/ObjectiveScore.o alignment/Sequence.o Clustal.o RClustalWMain.o RClustalW.o && \
cp libClustalW.a ../../
checking build system type... aarch64-unknown-linux-gnu
checking host system type... aarch64-unknown-linux-gnu
checking target system type... aarch64-unknown-linux-gnu
building for linux-gnu
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 sets $(MAKE)... (cached) yes
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 for style of include used by make... GNU
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 for ranlib... ranlib
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -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 stdbool.h that conforms to C99... no
checking for _Bool... no
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating m4/Makefile
config.status: creating src/Makefile
config.status: creating src/clustalw_version.h
config.status: creating src/config.h
config.status: executing depfiles commands
using C++ compiler: ‘g++ (GCC) 10.3.1’
make[2]: Entering directory '/home/biocbuild/bbs-3.18-bioc/meat/msa/src/ClustalW/src'
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c pairwise/FullPairwiseAlign.cpp -o pairwise/FullPairwiseAlign.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c pairwise/FastPairwiseAlign.cpp -o pairwise/FastPairwiseAlign.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c fileInput/MSFFileParser.cpp -o fileInput/MSFFileParser.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c fileInput/FileReader.cpp -o fileInput/FileReader.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c fileInput/PIRFileParser.cpp -o fileInput/PIRFileParser.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c fileInput/RSFFileParser.cpp -o fileInput/RSFFileParser.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c fileInput/GDEFileParser.cpp -o fileInput/GDEFileParser.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c fileInput/InFileStream.cpp -o fileInput/InFileStream.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c fileInput/ClustalFileParser.cpp -o fileInput/ClustalFileParser.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c fileInput/PearsonFileParser.cpp -o fileInput/PearsonFileParser.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c fileInput/FileParser.cpp -o fileInput/FileParser.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c fileInput/EMBLFileParser.cpp -o fileInput/EMBLFileParser.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c tree/UPGMA/RootedClusterTree.cpp -o tree/UPGMA/RootedClusterTree.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c tree/UPGMA/UPGMAAlgorithm.cpp -o tree/UPGMA/UPGMAAlgorithm.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c tree/UPGMA/Node.cpp -o tree/UPGMA/Node.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c tree/UPGMA/RootedGuideTree.cpp -o tree/UPGMA/RootedGuideTree.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c tree/UPGMA/RootedTreeOutput.cpp -o tree/UPGMA/RootedTreeOutput.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c tree/Tree.cpp -o tree/Tree.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c tree/ClusterTree.cpp -o tree/ClusterTree.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c tree/TreeInterface.cpp -o tree/TreeInterface.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c tree/UnRootedClusterTree.cpp -o tree/UnRootedClusterTree.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c tree/ClusterTreeOutput.cpp -o tree/ClusterTreeOutput.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c tree/RandomGenerator.cpp -o tree/RandomGenerator.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c tree/NJTree.cpp -o tree/NJTree.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c tree/AlignmentSteps.cpp -o tree/AlignmentSteps.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c interface/CommandLineParser.cpp -o interface/CommandLineParser.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c substitutionMatrix/SubMatrix.cpp -o substitutionMatrix/SubMatrix.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c multipleAlign/Iteration.cpp -o multipleAlign/Iteration.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c multipleAlign/MSA.cpp -o multipleAlign/MSA.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c multipleAlign/MyersMillerProfileAlign.cpp -o multipleAlign/MyersMillerProfileAlign.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c multipleAlign/ProfileStandard.cpp -o multipleAlign/ProfileStandard.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c multipleAlign/ProfileWithSub.cpp -o multipleAlign/ProfileWithSub.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c multipleAlign/ProfileBase.cpp -o multipleAlign/ProfileBase.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c multipleAlign/LowScoreSegProfile.cpp -o multipleAlign/LowScoreSegProfile.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c general/OutputFile.cpp -o general/OutputFile.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c general/UserParameters.cpp -o general/UserParameters.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c general/Utility.cpp -o general/Utility.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c general/InvalidCombination.cpp -o general/InvalidCombination.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c general/DebugLog.cpp -o general/DebugLog.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c general/ClustalWResources.cpp -o general/ClustalWResources.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c general/VectorOutOfRange.cpp -o general/VectorOutOfRange.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c general/SymMatrix.cpp -o general/SymMatrix.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c general/Stats.cpp -o general/Stats.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c Help.cpp -o Help.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c alignment/Alignment.cpp -o alignment/Alignment.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c alignment/AlignmentOutput.cpp -o alignment/AlignmentOutput.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c alignment/ObjectiveScore.cpp -o alignment/ObjectiveScore.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c alignment/Sequence.cpp -o alignment/Sequence.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c Clustal.cpp -o Clustal.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c RClustalWMain.cpp -o RClustalWMain.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -g -O2 -c RClustalW.cpp -o RClustalW.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o libClustalW.so pairwise/FullPairwiseAlign.o pairwise/FastPairwiseAlign.o fileInput/MSFFileParser.o fileInput/FileReader.o fileInput/PIRFileParser.o fileInput/RSFFileParser.o fileInput/GDEFileParser.o fileInput/InFileStream.o fileInput/ClustalFileParser.o fileInput/PearsonFileParser.o fileInput/FileParser.o fileInput/EMBLFileParser.o tree/UPGMA/RootedClusterTree.o tree/UPGMA/UPGMAAlgorithm.o tree/UPGMA/Node.o tree/UPGMA/RootedGuideTree.o tree/UPGMA/RootedTreeOutput.o tree/Tree.o tree/ClusterTree.o tree/TreeInterface.o tree/UnRootedClusterTree.o tree/ClusterTreeOutput.o tree/RandomGenerator.o tree/NJTree.o tree/AlignmentSteps.o interface/CommandLineParser.o substitutionMatrix/SubMatrix.o multipleAlign/Iteration.o multipleAlign/MSA.o multipleAlign/MyersMillerProfileAlign.o multipleAlign/ProfileStandard.o multipleAlign/ProfileWithSub.o multipleAlign/ProfileBase.o multipleAlign/LowScoreSegProfile.o general/OutputFile.o general/UserParameters.o general/Utility.o general/InvalidCombination.o general/DebugLog.o general/ClustalWResources.o general/VectorOutOfRange.o general/SymMatrix.o general/Stats.o Help.o alignment/Alignment.o alignment/AlignmentOutput.o alignment/ObjectiveScore.o alignment/Sequence.o Clustal.o RClustalWMain.o RClustalW.o -L/home/biocbuild/R/R-4.3.0/lib -lR
/usr/bin/ld: multipleAlign/Iteration.o: in function `clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)':
/home/biocbuild/bbs-3.18-bioc/meat/msa/src/ClustalW/src/multipleAlign/Iteration.cpp:231: warning: the use of `tmpnam' is dangerous, better use `mkstemp'
make[2]: Leaving directory '/home/biocbuild/bbs-3.18-bioc/meat/msa/src/ClustalW/src'
make[1]: Leaving directory '/home/biocbuild/bbs-3.18-bioc/meat/msa/src/ClustalW'
----------------------------------------
--------------- ClustalW ---------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile --directory=ClustalOmega
make[1]: Entering directory '/home/biocbuild/bbs-3.18-bioc/meat/msa/src/ClustalOmega'
./configure `/home/biocbuild/R/R-4.3.0/bin/Rscript -e "if (Sys.info()['sysname'] == 'Darwin') cat('--without-openmp')"`; \
export PKG_LIBS=" "; \
export PKG_CXXFLAGS=" `/home/biocbuild/R/R-4.3.0/bin/Rscript -e "if (Sys.info()['sysname'] == 'Darwin') cat('-DMATH_H_CLIB')"` -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include"; \
export PKG_CFLAGS=" -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include"; \
cd src; \
/home/biocbuild/R/R-4.3.0/bin/R CMD SHLIB -o libClustalOmega.so exceptions4c/e4c_lite.c argtable2/argtable2.c argtable2/arg_end.c argtable2/arg_rem.c argtable2/arg_lit.c argtable2/arg_int.c argtable2/arg_dbl.c argtable2/arg_str.c argtable2/arg_file.c kmpp/KMeans.cpp kmpp/KmTree.cpp kmpp/KmUtils.cpp clustal/hhalign_wrapper.c clustal/ktuple_pair.c clustal/list.c clustal/log.c clustal/muscle_upgma.c clustal/muscle_tree.c clustal/mbed.c clustal/pair_dist.c clustal/progress.c clustal/seq.c clustal/symmatrix.c clustal/tree.c clustal/util.c clustal/weights.c squid/a2m.c squid/aligneval.c squid/alignio.c squid/clustal.c squid/cluster.c squid/dayhoff.c squid/eps.c squid/file.c squid/getopt.c squid/gki.c squid/gsi.c squid/gsi64.c squid/hsregex.c squid/iupac.c squid/msa.c squid/msf.c squid/phylip.c squid/revcomp.c squid/rk.c squid/selex.c squid/seqencode.c squid/shuffle.c squid/sqerror.c squid/sqio.c squid/squidcore.c squid/sre_ctype.c squid/sre_math.c squid/sre_random.c squid/sre_string.c squid/ssi.c squid/stack.c squid/stockholm.c squid/stopwatch.c squid/translate.c squid/types.c squid/vectorops.c squid/weight.c hhalign/hhalign.cpp RClustalOmega.cpp mymain.c clustal-omega.c && \
ar rcs libClustalOmega.a exceptions4c/e4c_lite.o argtable2/argtable2.o argtable2/arg_end.o argtable2/arg_rem.o argtable2/arg_lit.o argtable2/arg_int.o argtable2/arg_dbl.o argtable2/arg_str.o argtable2/arg_file.o kmpp/KMeans.o kmpp/KmTree.o kmpp/KmUtils.o clustal/hhalign_wrapper.o clustal/ktuple_pair.o clustal/list.o clustal/log.o clustal/muscle_upgma.o clustal/muscle_tree.o clustal/mbed.o clustal/pair_dist.o clustal/progress.o clustal/seq.o clustal/symmatrix.o clustal/tree.o clustal/util.o clustal/weights.o squid/a2m.o squid/aligneval.o squid/alignio.o squid/clustal.o squid/cluster.o squid/dayhoff.o squid/eps.o squid/file.o squid/getopt.o squid/gki.o squid/gsi.o squid/gsi64.o squid/hsregex.o squid/iupac.o squid/msa.o squid/msf.o squid/phylip.o squid/revcomp.o squid/rk.o squid/selex.o squid/seqencode.o squid/shuffle.o squid/sqerror.o squid/sqio.o squid/squidcore.o squid/sre_ctype.o squid/sre_math.o squid/sre_random.o squid/sre_string.o squid/ssi.o squid/stack.o squid/stockholm.o squid/stopwatch.o squid/translate.o squid/types.o squid/vectorops.o squid/weight.o hhalign/hhalign.o RClustalOmega.o mymain.o clustal-omega.o && \
cp libClustalOmega.a ../../
configure:
Welcome to Clustal Omega - version 1.2.0 (AndreaGiacomo)
+NMMMMMMMMMS=
MMMMM? :MMMMM8
IMMMMS MMMMM,
~MMMMN ,MMMMM
=MMMMM MMMMM
?MMMMM +MMMMM
MMMMMS MMMMM
MMMMM MMMMM:
MMMMM MMMMM+
MMMMM MMMMM~
MMMMM MMMMM
MMMMMZ MMMMM
MMMMM ,MMMMZ
MMMM8 MMMM+
MMMMS MMMM,
MMMMO MMMM
,N SMMM MMM8 +8
,M7 M+ M+ :M8
,MMMMMMMMMMMMI MMMMMMMMMMMM8
,MMMMMMMMMMMM8 MMMMMMMMMMMM8
,MMMMMMMMMMMMN MMMMMMMMMMMM8
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 for style of include used by make... GNU
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 dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -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 minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking build system type... aarch64-unknown-linux-gnu
checking host system type... aarch64-unknown-linux-gnu
checking whether make sets $(MAKE)... (cached) yes
checking for a sed that does not truncate output... /usr/bin/sed
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 whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
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 ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
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) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
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... yes
checking whether to build static libraries... yes
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking dependency style of gcc... (cached) gcc3
checking how to run the C preprocessor... gcc -E
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 whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking dependency style of g++... (cached) gcc3
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) 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... no
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) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking how to run the C++ preprocessor... g++ -E
checking for ANSI C header files... (cached) yes
checking assert.h usability... yes
checking assert.h presence... yes
checking for assert.h... yes
checking ctype.h usability... yes
checking ctype.h presence... yes
checking for ctype.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking for memory.h... (cached) yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
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checking stdio.h usability... yes
checking stdio.h presence... yes
checking for stdio.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking time.h usability... yes
checking time.h presence... yes
checking for time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking for inline... inline
checking for log in -lm... yes
checking for log2 in -lm... yes
checking for OpenMP flag of C compiler... -fopenmp
checking whether byte ordering is bigendian... no
checking for ntohs... yes
checking for ntohl... yes
checking for ntons... no
checking for ntonl... no
checking size of unsigned short... 2
checking size of unsigned int... 4
checking size of unsigned long... 8
checking size of unsigned long long... 8
checking for stroul... no
checking for strtoull... yes
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checking for fseeko... yes
checking for ftello64... yes
checking for fseeko64... yes
checking for ftell64... no
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checking for off_t... yes
checking size of fpos_t... 16
checking if malloc debugging is wanted... no
checking whether to build with debug information... no
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating clustalo.pc
config.status: creating Doxyfile
config.status: creating src/exceptions4c/Makefile
config.status: creating src/clustal/Makefile
config.status: creating src/hhalign/Makefile
config.status: creating src/kmpp/Makefile
config.status: creating src/squid/Makefile
config.status: creating src/argtable2/Makefile
config.status: creating src/config.h
config.status: executing src/clustal-omega-config.h commands
config.status: creating src/clustal-omega-config.h - prefix CLUSTAL_OMEGA for src/config.h defines
config.status: src/clustal-omega-config.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
using C compiler: ‘gcc (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
make[2]: Entering directory '/home/biocbuild/bbs-3.18-bioc/meat/msa/src/ClustalOmega/src'
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c exceptions4c/e4c_lite.c -o exceptions4c/e4c_lite.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c argtable2/argtable2.c -o argtable2/argtable2.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c argtable2/arg_end.c -o argtable2/arg_end.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c argtable2/arg_rem.c -o argtable2/arg_rem.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c argtable2/arg_lit.c -o argtable2/arg_lit.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c argtable2/arg_int.c -o argtable2/arg_int.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c argtable2/arg_dbl.c -o argtable2/arg_dbl.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c argtable2/arg_str.c -o argtable2/arg_str.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c argtable2/arg_file.c -o argtable2/arg_file.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c kmpp/KMeans.cpp -o kmpp/KMeans.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c kmpp/KmTree.cpp -o kmpp/KmTree.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c kmpp/KmUtils.cpp -o kmpp/KmUtils.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c clustal/hhalign_wrapper.c -o clustal/hhalign_wrapper.o
In file included from clustal/hhalign_wrapper.c:22:
./config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c clustal/ktuple_pair.c -o clustal/ktuple_pair.o
In file included from clustal/ktuple_pair.c:29:
./config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c clustal/list.c -o clustal/list.o
In file included from clustal/list.c:32:
./config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c clustal/log.c -o clustal/log.o
In file included from clustal/log.c:22:
./config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c clustal/muscle_upgma.c -o clustal/muscle_upgma.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c clustal/muscle_tree.c -o clustal/muscle_tree.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c clustal/mbed.c -o clustal/mbed.o
In file included from clustal/mbed.c:28:
./config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c clustal/pair_dist.c -o clustal/pair_dist.o
In file included from clustal/pair_dist.c:22:
./config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c clustal/progress.c -o clustal/progress.o
In file included from clustal/progress.c:22:
./config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c clustal/seq.c -o clustal/seq.o
In file included from clustal/seq.c:30:
./config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c clustal/symmatrix.c -o clustal/symmatrix.o
In file included from clustal/symmatrix.c:30:
./config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c clustal/tree.c -o clustal/tree.o
In file included from clustal/tree.c:22:
./config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c clustal/util.c -o clustal/util.o
In file included from clustal/util.c:22:
./config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c clustal/weights.c -o clustal/weights.o
In file included from clustal/weights.c:72:
./config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/a2m.c -o squid/a2m.o
In file included from squid/squid.h:32,
from squid/a2m.c:20:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/aligneval.c -o squid/aligneval.o
In file included from squid/squid.h:32,
from squid/aligneval.c:59:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/alignio.c -o squid/alignio.o
In file included from squid/squid.h:32,
from squid/alignio.c:21:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/clustal.c -o squid/clustal.o
In file included from squid/squid.h:32,
from squid/clustal.c:24:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/cluster.c -o squid/cluster.o
In file included from squid/squid.h:32,
from squid/cluster.c:124:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/dayhoff.c -o squid/dayhoff.o
In file included from squid/squid.h:32,
from squid/dayhoff.c:28:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/eps.c -o squid/eps.o
In file included from squid/squid.h:32,
from squid/eps.c:23:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/file.c -o squid/file.o
In file included from squid/squid.h:32,
from squid/file.c:28:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/getopt.c -o squid/getopt.o
In file included from squid/squid.h:32,
from squid/getopt.c:17:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/gki.c -o squid/gki.o
In file included from squid/squid.h:32,
from squid/gki.c:82:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/gsi.c -o squid/gsi.o
In file included from squid/squid.h:32,
from squid/gsi.c:35:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/gsi64.c -o squid/gsi64.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/hsregex.c -o squid/hsregex.o
In file included from squid/squid.h:32,
from squid/hsregex.c:33:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/iupac.c -o squid/iupac.o
In file included from squid/squid.h:32,
from squid/iupac.c:17:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/msa.c -o squid/msa.o
In file included from squid/squid.h:32,
from squid/msa.c:22:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/msf.c -o squid/msf.o
In file included from squid/squid.h:32,
from squid/msf.c:25:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/phylip.c -o squid/phylip.o
In file included from squid/squid.h:32,
from squid/phylip.c:23:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/revcomp.c -o squid/revcomp.o
In file included from squid/squid.h:32,
from squid/revcomp.c:19:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/rk.c -o squid/rk.o
In file included from squid/squid.h:32,
from squid/rk.c:26:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/selex.c -o squid/selex.o
In file included from squid/squid.h:32,
from squid/selex.c:43:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/seqencode.c -o squid/seqencode.o
In file included from squid/squid.h:32,
from squid/seqencode.c:18:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/shuffle.c -o squid/shuffle.o
In file included from squid/squid.h:32,
from squid/shuffle.c:42:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/sqerror.c -o squid/sqerror.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/sqio.c -o squid/sqio.o
In file included from squid/squid.h:32,
from squid/sqio.c:57:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/squidcore.c -o squid/squidcore.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/sre_ctype.c -o squid/sre_ctype.o
In file included from squid/squid.h:32,
from squid/sre_ctype.c:19:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/sre_math.c -o squid/sre_math.o
In file included from squid/squid.h:32,
from squid/sre_math.c:19:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/sre_random.c -o squid/sre_random.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/sre_string.c -o squid/sre_string.o
In file included from squid/squid.h:32,
from squid/sre_string.c:23:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/ssi.c -o squid/ssi.o
In file included from squid/squid.h:32,
from squid/ssi.c:16:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/stack.c -o squid/stack.o
In file included from squid/squid.h:32,
from squid/stack.c:18:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/stockholm.c -o squid/stockholm.o
In file included from squid/squid.h:32,
from squid/stockholm.c:31:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/stopwatch.c -o squid/stopwatch.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/translate.c -o squid/translate.o
In file included from squid/squid.h:32,
from squid/translate.c:19:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/types.c -o squid/types.o
In file included from squid/squid.h:32,
from squid/types.c:20:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/vectorops.c -o squid/vectorops.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c squid/weight.c -o squid/weight.o
In file included from squid/squid.h:32,
from squid/weight.c:19:
squid/../config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c hhalign/hhalign.cpp -o hhalign/hhalign.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c RClustalOmega.cpp -o RClustalOmega.o
In file included from RClustalOmega.cpp:27:
config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c mymain.c -o mymain.o
In file included from mymain.c:22:
config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -g -O2 -c clustal-omega.c -o clustal-omega.o
In file included from clustal-omega.c:22:
config.h:132: warning: "NDEBUG" redefined
132 | #define NDEBUG /**/
|
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o libClustalOmega.so exceptions4c/e4c_lite.o argtable2/argtable2.o argtable2/arg_end.o argtable2/arg_rem.o argtable2/arg_lit.o argtable2/arg_int.o argtable2/arg_dbl.o argtable2/arg_str.o argtable2/arg_file.o kmpp/KMeans.o kmpp/KmTree.o kmpp/KmUtils.o clustal/hhalign_wrapper.o clustal/ktuple_pair.o clustal/list.o clustal/log.o clustal/muscle_upgma.o clustal/muscle_tree.o clustal/mbed.o clustal/pair_dist.o clustal/progress.o clustal/seq.o clustal/symmatrix.o clustal/tree.o clustal/util.o clustal/weights.o squid/a2m.o squid/aligneval.o squid/alignio.o squid/clustal.o squid/cluster.o squid/dayhoff.o squid/eps.o squid/file.o squid/getopt.o squid/gki.o squid/gsi.o squid/gsi64.o squid/hsregex.o squid/iupac.o squid/msa.o squid/msf.o squid/phylip.o squid/revcomp.o squid/rk.o squid/selex.o squid/seqencode.o squid/shuffle.o squid/sqerror.o squid/sqio.o squid/squidcore.o squid/sre_ctype.o squid/sre_math.o squid/sre_random.o squid/sre_string.o squid/ssi.o squid/stack.o squid/stockholm.o squid/stopwatch.o squid/translate.o squid/types.o squid/vectorops.o squid/weight.o hhalign/hhalign.o RClustalOmega.o mymain.o clustal-omega.o -L/home/biocbuild/R/R-4.3.0/lib -lR
/usr/bin/ld: clustal-omega.o: in function `AlnToHHMFile':
/home/biocbuild/bbs-3.18-bioc/meat/msa/src/ClustalOmega/src/clustal-omega.c:389: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
make[2]: Leaving directory '/home/biocbuild/bbs-3.18-bioc/meat/msa/src/ClustalOmega/src'
make[1]: Leaving directory '/home/biocbuild/bbs-3.18-bioc/meat/msa/src/ClustalOmega'
----------------------------------------
------------- ClustalOmega -------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o msa.so R_init_msa.o SplitCharVector2List.o SplitCharVector2Matrix.o -Wl,--whole-archive ./libgc.a ./libClustalW.a ./libClustalOmega.a ./libMuscle.a -Wl,--no-whole-archive -L/home/biocbuild/R/R-4.3.0/lib -lR
/usr/bin/ld: ./libClustalW.a(Iteration.o): in function `clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)':
/home/biocbuild/bbs-3.18-bioc/meat/msa/src/ClustalW/src/multipleAlign/Iteration.cpp:231: warning: the use of `tmpnam' is dangerous, better use `mkstemp'
/usr/bin/ld: ./libClustalOmega.a(clustal-omega.o): in function `AlnToHHMFile':
/home/biocbuild/bbs-3.18-bioc/meat/msa/src/ClustalOmega/src/clustal-omega.c:389: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-msa/00new/msa/libs
** R
** 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 (msa)