BioC 3.3: CHECK report for msa on linux2.bioconductor.org

Package: msa

Version: 1.3.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings msa_1.3.0.tar.gz

StartedAt: 2015-10-27 06:07:07 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:12:56 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 348.7 seconds

RetCode: 0

Status:  OK

CheckDir: msa.Rcheck

Warnings: 0

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###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings msa_1.3.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘msa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘msa’ version ‘1.3.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘msa’ can be installed ... [276s/277s] OK
* checking installed package size ... NOTE
  installed size is 23.7Mb
  sub-directories of 1Mb or more:
    libs  22.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/9s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00check.log’
for details.

* installing *source* package ‘msa’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" `Rscript -e "Rcpp:::CxxFlags()"` -fpic  -g -O2  -c R_init_msa.cpp -o R_init_msa.o
make --file=msaMakefile --directory=gc-7.2
make[1]: Entering directory `/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/gc-7.2'
./configure --enable-cplusplus --enable-threads=pthreads --enable-shared --with-pic
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
checking GC version numbers... major=7 minor=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... /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 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 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 for inline... inline
checking for pthread_self in -lpthread... yes
configure: WARNING: "Explicit GC_INIT() calls may be required."
checking for xlc... no
checking whether gcc supports -fno-strict-aliasing... yes
checking for dlopen in -ldl... yes
checking whether to build shared libraries... yes
checking which machine-dependent code should be used... 
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /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... 3458764513820540925
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-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 mt... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking 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 how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether Solaris gcc optimization fix is necessary... no
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 pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for ATOMIC_OPS... no
checking which libatomic_ops to use... internal
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/private/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
config.status: executing default commands
=== configuring in libatomic_ops (/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/gc-7.2/libatomic_ops)
configure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr/local'  '--enable-cplusplus' '--enable-threads=pthreads' '--enable-shared' '--with-pic' 'PKG_CONFIG_PATH=:/usr/local/lib/pkgconfig/libsbml.pc' --cache-file=/dev/null --srcdir=.
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-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... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for ranlib... ranlib
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 whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /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 stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for ANSI C header files... (cached) yes
checking for PIC compiler flag... -fPIC
checking whether gcc -fPIC causes __PIC__ definition... yes
checking for pthread_self in -lpthread... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating pkgconfig/atomic_ops.pc
config.status: creating pkgconfig/atomic_ops-uninstalled.pc
config.status: creating doc/Makefile
config.status: creating src/Makefile
config.status: creating src/atomic_ops/Makefile
config.status: creating src/atomic_ops/sysdeps/Makefile
config.status: creating tests/Makefile
config.status: creating src/config.h
config.status: executing depfiles commands
config.status: executing default commands
make
make[2]: Entering directory `/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/gc-7.2'
make[3]: Entering directory `/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/gc-7.2'
depbase=`echo allchblk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT allchblk.lo -MD -MP -MF $depbase.Tpo -c -o allchblk.lo allchblk.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT allchblk.lo -MD -MP -MF .deps/allchblk.Tpo -c allchblk.c  -fPIC -DPIC -o .libs/allchblk.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT allchblk.lo -MD -MP -MF .deps/allchblk.Tpo -c allchblk.c  -fPIC -DPIC -o allchblk.o >/dev/null 2>&1
depbase=`echo alloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT alloc.lo -MD -MP -MF $depbase.Tpo -c -o alloc.lo alloc.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT alloc.lo -MD -MP -MF .deps/alloc.Tpo -c alloc.c  -fPIC -DPIC -o .libs/alloc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT alloc.lo -MD -MP -MF .deps/alloc.Tpo -c alloc.c  -fPIC -DPIC -o alloc.o >/dev/null 2>&1
depbase=`echo blacklst.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT blacklst.lo -MD -MP -MF $depbase.Tpo -c -o blacklst.lo blacklst.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT blacklst.lo -MD -MP -MF .deps/blacklst.Tpo -c blacklst.c  -fPIC -DPIC -o .libs/blacklst.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT blacklst.lo -MD -MP -MF .deps/blacklst.Tpo -c blacklst.c  -fPIC -DPIC -o blacklst.o >/dev/null 2>&1
depbase=`echo checksums.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT checksums.lo -MD -MP -MF $depbase.Tpo -c -o checksums.lo checksums.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT checksums.lo -MD -MP -MF .deps/checksums.Tpo -c checksums.c  -fPIC -DPIC -o .libs/checksums.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT checksums.lo -MD -MP -MF .deps/checksums.Tpo -c checksums.c  -fPIC -DPIC -o checksums.o >/dev/null 2>&1
depbase=`echo dbg_mlc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT dbg_mlc.lo -MD -MP -MF $depbase.Tpo -c -o dbg_mlc.lo dbg_mlc.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dbg_mlc.lo -MD -MP -MF .deps/dbg_mlc.Tpo -c dbg_mlc.c  -fPIC -DPIC -o .libs/dbg_mlc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dbg_mlc.lo -MD -MP -MF .deps/dbg_mlc.Tpo -c dbg_mlc.c  -fPIC -DPIC -o dbg_mlc.o >/dev/null 2>&1
depbase=`echo dyn_load.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT dyn_load.lo -MD -MP -MF $depbase.Tpo -c -o dyn_load.lo dyn_load.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dyn_load.lo -MD -MP -MF .deps/dyn_load.Tpo -c dyn_load.c  -fPIC -DPIC -o .libs/dyn_load.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dyn_load.lo -MD -MP -MF .deps/dyn_load.Tpo -c dyn_load.c  -fPIC -DPIC -o dyn_load.o >/dev/null 2>&1
depbase=`echo finalize.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT finalize.lo -MD -MP -MF $depbase.Tpo -c -o finalize.lo finalize.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT finalize.lo -MD -MP -MF .deps/finalize.Tpo -c finalize.c  -fPIC -DPIC -o .libs/finalize.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT finalize.lo -MD -MP -MF .deps/finalize.Tpo -c finalize.c  -fPIC -DPIC -o finalize.o >/dev/null 2>&1
depbase=`echo gc_dlopen.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT gc_dlopen.lo -MD -MP -MF $depbase.Tpo -c -o gc_dlopen.lo gc_dlopen.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT gc_dlopen.lo -MD -MP -MF .deps/gc_dlopen.Tpo -c gc_dlopen.c  -fPIC -DPIC -o .libs/gc_dlopen.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT gc_dlopen.lo -MD -MP -MF .deps/gc_dlopen.Tpo -c gc_dlopen.c  -fPIC -DPIC -o gc_dlopen.o >/dev/null 2>&1
depbase=`echo gcj_mlc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT gcj_mlc.lo -MD -MP -MF $depbase.Tpo -c -o gcj_mlc.lo gcj_mlc.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT gcj_mlc.lo -MD -MP -MF .deps/gcj_mlc.Tpo -c gcj_mlc.c  -fPIC -DPIC -o .libs/gcj_mlc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT gcj_mlc.lo -MD -MP -MF .deps/gcj_mlc.Tpo -c gcj_mlc.c  -fPIC -DPIC -o gcj_mlc.o >/dev/null 2>&1
depbase=`echo headers.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT headers.lo -MD -MP -MF $depbase.Tpo -c -o headers.lo headers.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT headers.lo -MD -MP -MF .deps/headers.Tpo -c headers.c  -fPIC -DPIC -o .libs/headers.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT headers.lo -MD -MP -MF .deps/headers.Tpo -c headers.c  -fPIC -DPIC -o headers.o >/dev/null 2>&1
depbase=`echo malloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT malloc.lo -MD -MP -MF $depbase.Tpo -c -o malloc.lo malloc.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT malloc.lo -MD -MP -MF .deps/malloc.Tpo -c malloc.c  -fPIC -DPIC -o .libs/malloc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT malloc.lo -MD -MP -MF .deps/malloc.Tpo -c malloc.c  -fPIC -DPIC -o malloc.o >/dev/null 2>&1
depbase=`echo mallocx.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT mallocx.lo -MD -MP -MF $depbase.Tpo -c -o mallocx.lo mallocx.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mallocx.lo -MD -MP -MF .deps/mallocx.Tpo -c mallocx.c  -fPIC -DPIC -o .libs/mallocx.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mallocx.lo -MD -MP -MF .deps/mallocx.Tpo -c mallocx.c  -fPIC -DPIC -o mallocx.o >/dev/null 2>&1
depbase=`echo mark.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT mark.lo -MD -MP -MF $depbase.Tpo -c -o mark.lo mark.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mark.lo -MD -MP -MF .deps/mark.Tpo -c mark.c  -fPIC -DPIC -o .libs/mark.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mark.lo -MD -MP -MF .deps/mark.Tpo -c mark.c  -fPIC -DPIC -o mark.o >/dev/null 2>&1
depbase=`echo mark_rts.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT mark_rts.lo -MD -MP -MF $depbase.Tpo -c -o mark_rts.lo mark_rts.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mark_rts.lo -MD -MP -MF .deps/mark_rts.Tpo -c mark_rts.c  -fPIC -DPIC -o .libs/mark_rts.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mark_rts.lo -MD -MP -MF .deps/mark_rts.Tpo -c mark_rts.c  -fPIC -DPIC -o mark_rts.o >/dev/null 2>&1
depbase=`echo misc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT misc.lo -MD -MP -MF $depbase.Tpo -c -o misc.lo misc.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT misc.lo -MD -MP -MF .deps/misc.Tpo -c misc.c  -fPIC -DPIC -o .libs/misc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT misc.lo -MD -MP -MF .deps/misc.Tpo -c misc.c  -fPIC -DPIC -o misc.o >/dev/null 2>&1
depbase=`echo new_hblk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT new_hblk.lo -MD -MP -MF $depbase.Tpo -c -o new_hblk.lo new_hblk.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT new_hblk.lo -MD -MP -MF .deps/new_hblk.Tpo -c new_hblk.c  -fPIC -DPIC -o .libs/new_hblk.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT new_hblk.lo -MD -MP -MF .deps/new_hblk.Tpo -c new_hblk.c  -fPIC -DPIC -o new_hblk.o >/dev/null 2>&1
depbase=`echo obj_map.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT obj_map.lo -MD -MP -MF $depbase.Tpo -c -o obj_map.lo obj_map.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT obj_map.lo -MD -MP -MF .deps/obj_map.Tpo -c obj_map.c  -fPIC -DPIC -o .libs/obj_map.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT obj_map.lo -MD -MP -MF .deps/obj_map.Tpo -c obj_map.c  -fPIC -DPIC -o obj_map.o >/dev/null 2>&1
depbase=`echo os_dep.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT os_dep.lo -MD -MP -MF $depbase.Tpo -c -o os_dep.lo os_dep.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT os_dep.lo -MD -MP -MF .deps/os_dep.Tpo -c os_dep.c  -fPIC -DPIC -o .libs/os_dep.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT os_dep.lo -MD -MP -MF .deps/os_dep.Tpo -c os_dep.c  -fPIC -DPIC -o os_dep.o >/dev/null 2>&1
depbase=`echo pcr_interface.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT pcr_interface.lo -MD -MP -MF $depbase.Tpo -c -o pcr_interface.lo pcr_interface.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pcr_interface.lo -MD -MP -MF .deps/pcr_interface.Tpo -c pcr_interface.c  -fPIC -DPIC -o .libs/pcr_interface.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pcr_interface.lo -MD -MP -MF .deps/pcr_interface.Tpo -c pcr_interface.c  -fPIC -DPIC -o pcr_interface.o >/dev/null 2>&1
depbase=`echo ptr_chck.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT ptr_chck.lo -MD -MP -MF $depbase.Tpo -c -o ptr_chck.lo ptr_chck.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT ptr_chck.lo -MD -MP -MF .deps/ptr_chck.Tpo -c ptr_chck.c  -fPIC -DPIC -o .libs/ptr_chck.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT ptr_chck.lo -MD -MP -MF .deps/ptr_chck.Tpo -c ptr_chck.c  -fPIC -DPIC -o ptr_chck.o >/dev/null 2>&1
depbase=`echo real_malloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT real_malloc.lo -MD -MP -MF $depbase.Tpo -c -o real_malloc.lo real_malloc.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT real_malloc.lo -MD -MP -MF .deps/real_malloc.Tpo -c real_malloc.c  -fPIC -DPIC -o .libs/real_malloc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT real_malloc.lo -MD -MP -MF .deps/real_malloc.Tpo -c real_malloc.c  -fPIC -DPIC -o real_malloc.o >/dev/null 2>&1
depbase=`echo reclaim.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT reclaim.lo -MD -MP -MF $depbase.Tpo -c -o reclaim.lo reclaim.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT reclaim.lo -MD -MP -MF .deps/reclaim.Tpo -c reclaim.c  -fPIC -DPIC -o .libs/reclaim.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT reclaim.lo -MD -MP -MF .deps/reclaim.Tpo -c reclaim.c  -fPIC -DPIC -o reclaim.o >/dev/null 2>&1
depbase=`echo specific.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT specific.lo -MD -MP -MF $depbase.Tpo -c -o specific.lo specific.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT specific.lo -MD -MP -MF .deps/specific.Tpo -c specific.c  -fPIC -DPIC -o .libs/specific.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT specific.lo -MD -MP -MF .deps/specific.Tpo -c specific.c  -fPIC -DPIC -o specific.o >/dev/null 2>&1
depbase=`echo stubborn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT stubborn.lo -MD -MP -MF $depbase.Tpo -c -o stubborn.lo stubborn.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT stubborn.lo -MD -MP -MF .deps/stubborn.Tpo -c stubborn.c  -fPIC -DPIC -o .libs/stubborn.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT stubborn.lo -MD -MP -MF .deps/stubborn.Tpo -c stubborn.c  -fPIC -DPIC -o stubborn.o >/dev/null 2>&1
depbase=`echo typd_mlc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT typd_mlc.lo -MD -MP -MF $depbase.Tpo -c -o typd_mlc.lo typd_mlc.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT typd_mlc.lo -MD -MP -MF .deps/typd_mlc.Tpo -c typd_mlc.c  -fPIC -DPIC -o .libs/typd_mlc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT typd_mlc.lo -MD -MP -MF .deps/typd_mlc.Tpo -c typd_mlc.c  -fPIC -DPIC -o typd_mlc.o >/dev/null 2>&1
depbase=`echo backgraph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT backgraph.lo -MD -MP -MF $depbase.Tpo -c -o backgraph.lo backgraph.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT backgraph.lo -MD -MP -MF .deps/backgraph.Tpo -c backgraph.c  -fPIC -DPIC -o .libs/backgraph.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT backgraph.lo -MD -MP -MF .deps/backgraph.Tpo -c backgraph.c  -fPIC -DPIC -o backgraph.o >/dev/null 2>&1
depbase=`echo thread_local_alloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT thread_local_alloc.lo -MD -MP -MF $depbase.Tpo -c -o thread_local_alloc.lo thread_local_alloc.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT thread_local_alloc.lo -MD -MP -MF .deps/thread_local_alloc.Tpo -c thread_local_alloc.c  -fPIC -DPIC -o .libs/thread_local_alloc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT thread_local_alloc.lo -MD -MP -MF .deps/thread_local_alloc.Tpo -c thread_local_alloc.c  -fPIC -DPIC -o thread_local_alloc.o >/dev/null 2>&1
depbase=`echo pthread_start.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_start.lo -MD -MP -MF $depbase.Tpo -c -o pthread_start.lo pthread_start.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_start.lo -MD -MP -MF .deps/pthread_start.Tpo -c pthread_start.c  -fPIC -DPIC -o .libs/pthread_start.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_start.lo -MD -MP -MF .deps/pthread_start.Tpo -c pthread_start.c  -fPIC -DPIC -o pthread_start.o >/dev/null 2>&1
depbase=`echo pthread_support.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_support.lo -MD -MP -MF $depbase.Tpo -c -o pthread_support.lo pthread_support.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_support.lo -MD -MP -MF .deps/pthread_support.Tpo -c pthread_support.c  -fPIC -DPIC -o .libs/pthread_support.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_support.lo -MD -MP -MF .deps/pthread_support.Tpo -c pthread_support.c  -fPIC -DPIC -o pthread_support.o >/dev/null 2>&1
depbase=`echo pthread_stop_world.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_stop_world.lo -MD -MP -MF $depbase.Tpo -c -o pthread_stop_world.lo pthread_stop_world.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_stop_world.lo -MD -MP -MF .deps/pthread_stop_world.Tpo -c pthread_stop_world.c  -fPIC -DPIC -o .libs/pthread_stop_world.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_stop_world.lo -MD -MP -MF .deps/pthread_stop_world.Tpo -c pthread_stop_world.c  -fPIC -DPIC -o pthread_stop_world.o >/dev/null 2>&1
depbase=`echo libatomic_ops/src/atomic_ops.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT libatomic_ops/src/atomic_ops.lo -MD -MP -MF $depbase.Tpo -c -o libatomic_ops/src/atomic_ops.lo libatomic_ops/src/atomic_ops.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT libatomic_ops/src/atomic_ops.lo -MD -MP -MF libatomic_ops/src/.deps/atomic_ops.Tpo -c libatomic_ops/src/atomic_ops.c  -fPIC -DPIC -o libatomic_ops/src/.libs/atomic_ops.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT libatomic_ops/src/atomic_ops.lo -MD -MP -MF libatomic_ops/src/.deps/atomic_ops.Tpo -c libatomic_ops/src/atomic_ops.c  -fPIC -DPIC -o libatomic_ops/src/atomic_ops.o >/dev/null 2>&1
depbase=`echo mach_dep.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT mach_dep.lo -MD -MP -MF $depbase.Tpo -c -o mach_dep.lo mach_dep.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mach_dep.lo -MD -MP -MF .deps/mach_dep.Tpo -c mach_dep.c  -fPIC -DPIC -o .libs/mach_dep.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mach_dep.lo -MD -MP -MF .deps/mach_dep.Tpo -c mach_dep.c  -fPIC -DPIC -o mach_dep.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=link gcc -fexceptions -g -O2 -fno-strict-aliasing  -version-info 1:3:0 -no-undefined  -o libgc.la -rpath /usr/local/lib allchblk.lo alloc.lo blacklst.lo checksums.lo dbg_mlc.lo dyn_load.lo finalize.lo gc_dlopen.lo gcj_mlc.lo headers.lo malloc.lo mallocx.lo mark.lo mark_rts.lo misc.lo new_hblk.lo obj_map.lo os_dep.lo pcr_interface.lo ptr_chck.lo real_malloc.lo reclaim.lo specific.lo stubborn.lo typd_mlc.lo backgraph.lo thread_local_alloc.lo pthread_start.lo pthread_support.lo pthread_stop_world.lo   libatomic_ops/src/atomic_ops.lo mach_dep.lo -lpthread -ldl   
libtool: link: gcc -shared  -fPIC -DPIC  .libs/allchblk.o .libs/alloc.o .libs/blacklst.o .libs/checksums.o .libs/dbg_mlc.o .libs/dyn_load.o .libs/finalize.o .libs/gc_dlopen.o .libs/gcj_mlc.o .libs/headers.o .libs/malloc.o .libs/mallocx.o .libs/mark.o .libs/mark_rts.o .libs/misc.o .libs/new_hblk.o .libs/obj_map.o .libs/os_dep.o .libs/pcr_interface.o .libs/ptr_chck.o .libs/real_malloc.o .libs/reclaim.o .libs/specific.o .libs/stubborn.o .libs/typd_mlc.o .libs/backgraph.o .libs/thread_local_alloc.o .libs/pthread_start.o .libs/pthread_support.o .libs/pthread_stop_world.o libatomic_ops/src/.libs/atomic_ops.o .libs/mach_dep.o   -lpthread -ldl  -g -O2   -Wl,-soname -Wl,libgc.so.1 -o .libs/libgc.so.1.0.3
libtool: link: (cd ".libs" && rm -f "libgc.so.1" && ln -s "libgc.so.1.0.3" "libgc.so.1")
libtool: link: (cd ".libs" && rm -f "libgc.so" && ln -s "libgc.so.1.0.3" "libgc.so")
libtool: link: ar cru .libs/libgc.a  allchblk.o alloc.o blacklst.o checksums.o dbg_mlc.o dyn_load.o finalize.o gc_dlopen.o gcj_mlc.o headers.o malloc.o mallocx.o mark.o mark_rts.o misc.o new_hblk.o obj_map.o os_dep.o pcr_interface.o ptr_chck.o real_malloc.o reclaim.o specific.o stubborn.o typd_mlc.o backgraph.o thread_local_alloc.o pthread_start.o pthread_support.o pthread_stop_world.o libatomic_ops/src/atomic_ops.o mach_dep.o
libtool: link: ranlib .libs/libgc.a
libtool: link: ( cd ".libs" && rm -f "libgc.la" && ln -s "../libgc.la" "libgc.la" )
depbase=`echo gc_cpp.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -MT gc_cpp.lo -MD -MP -MF $depbase.Tpo -c -o gc_cpp.lo gc_cpp.cc &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -MT gc_cpp.lo -MD -MP -MF .deps/gc_cpp.Tpo -c gc_cpp.cc  -fPIC -DPIC -o .libs/gc_cpp.o
libtool: compile:  g++ -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -MT gc_cpp.lo -MD -MP -MF .deps/gc_cpp.Tpo -c gc_cpp.cc  -fPIC -DPIC -o gc_cpp.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CXX   --mode=link g++ -fexceptions -g -O2 -version-info 1:3:0 -no-undefined  -o libgccpp.la -rpath /usr/local/lib gc_cpp.lo ./libgc.la 
libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/4.8/crtbeginS.o  .libs/gc_cpp.o   -Wl,-rpath -Wl,/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/gc-7.2/.libs ./.libs/libgc.so -lpthread -ldl -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/4.8/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/crtn.o  -g -O2   -Wl,-soname -Wl,libgccpp.so.1 -o .libs/libgccpp.so.1.0.3
libtool: link: (cd ".libs" && rm -f "libgccpp.so.1" && ln -s "libgccpp.so.1.0.3" "libgccpp.so.1")
libtool: link: (cd ".libs" && rm -f "libgccpp.so" && ln -s "libgccpp.so.1.0.3" "libgccpp.so")
libtool: link: ar cru .libs/libgccpp.a  gc_cpp.o
libtool: link: ranlib .libs/libgccpp.a
libtool: link: ( cd ".libs" && rm -f "libgccpp.la" && ln -s "../libgccpp.la" "libgccpp.la" )
depbase=`echo cord/cordbscs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordbscs.lo -MD -MP -MF $depbase.Tpo -c -o cord/cordbscs.lo cord/cordbscs.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordbscs.lo -MD -MP -MF cord/.deps/cordbscs.Tpo -c cord/cordbscs.c  -fPIC -DPIC -o cord/.libs/cordbscs.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordbscs.lo -MD -MP -MF cord/.deps/cordbscs.Tpo -c cord/cordbscs.c  -fPIC -DPIC -o cord/cordbscs.o >/dev/null 2>&1
depbase=`echo cord/cordprnt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordprnt.lo -MD -MP -MF $depbase.Tpo -c -o cord/cordprnt.lo cord/cordprnt.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordprnt.lo -MD -MP -MF cord/.deps/cordprnt.Tpo -c cord/cordprnt.c  -fPIC -DPIC -o cord/.libs/cordprnt.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordprnt.lo -MD -MP -MF cord/.deps/cordprnt.Tpo -c cord/cordprnt.c  -fPIC -DPIC -o cord/cordprnt.o >/dev/null 2>&1
depbase=`echo cord/cordtest.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordtest.lo -MD -MP -MF $depbase.Tpo -c -o cord/cordtest.lo cord/cordtest.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordtest.lo -MD -MP -MF cord/.deps/cordtest.Tpo -c cord/cordtest.c  -fPIC -DPIC -o cord/.libs/cordtest.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordtest.lo -MD -MP -MF cord/.deps/cordtest.Tpo -c cord/cordtest.c  -fPIC -DPIC -o cord/cordtest.o >/dev/null 2>&1
depbase=`echo cord/cordxtra.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordxtra.lo -MD -MP -MF $depbase.Tpo -c -o cord/cordxtra.lo cord/cordxtra.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordxtra.lo -MD -MP -MF cord/.deps/cordxtra.Tpo -c cord/cordxtra.c  -fPIC -DPIC -o cord/.libs/cordxtra.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordxtra.lo -MD -MP -MF cord/.deps/cordxtra.Tpo -c cord/cordxtra.c  -fPIC -DPIC -o cord/cordxtra.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=link gcc -fexceptions -g -O2 -fno-strict-aliasing -version-info 1:3:0 -no-undefined  -o libcord.la -rpath /usr/local/lib cord/cordbscs.lo cord/cordprnt.lo cord/cordtest.lo cord/cordxtra.lo ./libgc.la 
libtool: link: gcc -shared  -fPIC -DPIC  cord/.libs/cordbscs.o cord/.libs/cordprnt.o cord/.libs/cordtest.o cord/.libs/cordxtra.o   -Wl,-rpath -Wl,/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/gc-7.2/.libs ./.libs/libgc.so -lpthread -ldl  -g -O2   -Wl,-soname -Wl,libcord.so.1 -o .libs/libcord.so.1.0.3
libtool: link: (cd ".libs" && rm -f "libcord.so.1" && ln -s "libcord.so.1.0.3" "libcord.so.1")
libtool: link: (cd ".libs" && rm -f "libcord.so" && ln -s "libcord.so.1.0.3" "libcord.so")
libtool: link: ar cru .libs/libcord.a  cord/cordbscs.o cord/cordprnt.o cord/cordtest.o cord/cordxtra.o
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-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/gc-7.2'
make[2]: Leaving directory `/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/gc-7.2'
cp .libs/libgc.a ../
cp .libs/libgccpp.a ../ 
make[1]: Leaving directory `/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/gc-7.2'
----------------------------------------
------------------ GC  -----------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile --directory=Muscle
make[1]: Entering directory `/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/Muscle'
export PKG_CXXFLAGS=" -I"../gc-7.2/include" `Rscript -e "Rcpp:::CxxFlags()"`"
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
make[2]: Entering directory `/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/Muscle'
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c aligngivenpath.cpp -o aligngivenpath.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c aligngivenpathsw.cpp -o aligngivenpathsw.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c aligntwomsas.cpp -o aligntwomsas.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c aligntwoprofs.cpp -o aligntwoprofs.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c aln.cpp -o aln.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c alpha.cpp -o alpha.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c anchors.cpp -o anchors.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c bittraceback.cpp -o bittraceback.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c blosum62.cpp -o blosum62.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c blosumla.cpp -o blosumla.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c clust.cpp -o clust.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c cluster.cpp -o cluster.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c clwwt.cpp -o clwwt.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c color.cpp -o color.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c cons.cpp -o cons.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c diaglist.cpp -o diaglist.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c diffobjscore.cpp -o diffobjscore.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c diffpaths.cpp -o diffpaths.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c difftrees.cpp -o difftrees.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c difftreese.cpp -o difftreese.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c distcalc.cpp -o distcalc.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c distfunc.cpp -o distfunc.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c distpwkimura.cpp -o distpwkimura.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c domuscle.cpp -o domuscle.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c dosp.cpp -o dosp.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c dpreglist.cpp -o dpreglist.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c drawtree.cpp -o drawtree.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c edgelist.cpp -o edgelist.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c enumopts.cpp -o enumopts.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c enumtostr.cpp -o enumtostr.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c estring.cpp -o estring.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c fasta.cpp -o fasta.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c fasta2.cpp -o fasta2.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c fastclust.cpp -o fastclust.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c fastdist.cpp -o fastdist.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c fastdistjones.cpp -o fastdistjones.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c fastdistkbit.cpp -o fastdistkbit.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c fastdistkmer.cpp -o fastdistkmer.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c fastdistmafft.cpp -o fastdistmafft.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c fastdistnuc.cpp -o fastdistnuc.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c fastscorepath2.cpp -o fastscorepath2.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c finddiags.cpp -o finddiags.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c finddiagsn.cpp -o finddiagsn.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c glbalign.cpp -o glbalign.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c glbalign352.cpp -o glbalign352.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c glbaligndiag.cpp -o glbaligndiag.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c glbalignle.cpp -o glbalignle.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c glbalignsimple.cpp -o glbalignsimple.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c glbalignsp.cpp -o glbalignsp.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c glbalignspn.cpp -o glbalignspn.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c glbalignss.cpp -o glbalignss.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c glbalndimer.cpp -o glbalndimer.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c globals.cpp -o globals.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c globalslinux.cpp -o globalslinux.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c globalsosx.cpp -o globalsosx.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c globalsother.cpp -o globalsother.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c globalswin32.cpp -o globalswin32.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c gonnet.cpp -o gonnet.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c henikoffweight.cpp -o henikoffweight.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c henikoffweightpb.cpp -o henikoffweightpb.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c html.cpp -o html.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c hydro.cpp -o hydro.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c intmath.cpp -o intmath.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c local.cpp -o local.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c main.cpp -o main.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c makerootmsa.cpp -o makerootmsa.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c makerootmsab.cpp -o makerootmsab.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c maketree.cpp -o maketree.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c mhack.cpp -o mhack.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c mpam200.cpp -o mpam200.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c msa.cpp -o msa.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c msa2.cpp -o msa2.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c msadistkimura.cpp -o msadistkimura.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c msf.cpp -o msf.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c muscle.cpp -o muscle.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c muscleout.cpp -o muscleout.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c nucmx.cpp -o nucmx.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c nwdasimple.cpp -o nwdasimple.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c nwdasimple2.cpp -o nwdasimple2.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c nwdasmall.cpp -o nwdasmall.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c nwrec.cpp -o nwrec.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c nwsmall.cpp -o nwsmall.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c objscore.cpp -o objscore.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c objscore2.cpp -o objscore2.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c objscoreda.cpp -o objscoreda.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c onexception.cpp -o onexception.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c options.cpp -o options.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c outweights.cpp -o outweights.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c pam200mafft.cpp -o pam200mafft.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c params.cpp -o params.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c phy.cpp -o phy.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c phy2.cpp -o phy2.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c phy3.cpp -o phy3.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c phy4.cpp -o phy4.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c phyfromclust.cpp -o phyfromclust.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c phyfromfile.cpp -o phyfromfile.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c physeq.cpp -o physeq.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c phytofile.cpp -o phytofile.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c posgap.cpp -o posgap.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c ppscore.cpp -o ppscore.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c profdb.cpp -o profdb.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c profile.cpp -o profile.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c profilefrommsa.cpp -o profilefrommsa.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c progalign.cpp -o progalign.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c progress.cpp -o progress.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c progressivealign.cpp -o progressivealign.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c pwpath.cpp -o pwpath.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c readmx.cpp -o readmx.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c realigndiffs.cpp -o realigndiffs.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c realigndiffse.cpp -o realigndiffse.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c refine.cpp -o refine.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c refinehoriz.cpp -o refinehoriz.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c refinesubfams.cpp -o refinesubfams.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c refinetree.cpp -o refinetree.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c refinetreee.cpp -o refinetreee.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c refinevert.cpp -o refinevert.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c refinew.cpp -o refinew.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c savebest.cpp -o savebest.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c scoredist.cpp -o scoredist.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c scoregaps.cpp -o scoregaps.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c scorehistory.cpp -o scorehistory.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c scorepp.cpp -o scorepp.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c seq.cpp -o seq.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c seqvect.cpp -o seqvect.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c setblosumweights.cpp -o setblosumweights.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c setgscweights.cpp -o setgscweights.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c setnewhandler.cpp -o setnewhandler.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c spfast.cpp -o spfast.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c sptest.cpp -o sptest.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c stabilize.cpp -o stabilize.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c subfam.cpp -o subfam.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c subfams.cpp -o subfams.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c sw.cpp -o sw.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c termgaps.cpp -o termgaps.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c textfile.cpp -o textfile.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c threewaywt.cpp -o threewaywt.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c tomhydro.cpp -o tomhydro.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c traceback.cpp -o traceback.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c tracebackopt.cpp -o tracebackopt.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c tracebacksw.cpp -o tracebacksw.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c treefrommsa.cpp -o treefrommsa.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c typetostr.cpp -o typetostr.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c upgma2.cpp -o upgma2.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c usage.cpp -o usage.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c validateids.cpp -o validateids.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c vtml2.cpp -o vtml2.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c writescorefile.cpp -o writescorefile.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c RMuscle.cpp -o RMuscle.o
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/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/bbs-3.3-bioc/R/lib -lR
make[2]: Leaving directory `/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/Muscle'
make[2]: Entering directory `/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/Muscle'
make[2]: Leaving directory `/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00_pkg_src/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-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/Muscle'
----------------------------------------
---------------- MUSCLE ----------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile --directory=ClustalW
make[1]: Entering directory `/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/ClustalW'
./configure; \
	cd src; \
	export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I.  `Rscript -e "Rcpp:::CxxFlags()"`"; \
	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... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-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... /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... /bin/grep
checking for egrep... /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... yes
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
make[2]: Entering directory `/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/ClustalW/src'
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c pairwise/FullPairwiseAlign.cpp -o pairwise/FullPairwiseAlign.o
In file included from pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from pairwise/../alignment/Alignment.h:42,
                 from pairwise/PairwiseAlignBase.h:10,
                 from pairwise/FullPairwiseAlign.h:9,
                 from pairwise/FullPairwiseAlign.cpp:9:
pairwise/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
pairwise/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c pairwise/FastPairwiseAlign.cpp -o pairwise/FastPairwiseAlign.o
In file included from pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from pairwise/../alignment/Alignment.h:42,
                 from pairwise/PairwiseAlignBase.h:10,
                 from pairwise/FastPairwiseAlign.h:9,
                 from pairwise/FastPairwiseAlign.cpp:10:
pairwise/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
pairwise/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c fileInput/MSFFileParser.cpp -o fileInput/MSFFileParser.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c fileInput/FileReader.cpp -o fileInput/FileReader.o
In file included from fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from fileInput/../alignment/Alignment.h:42,
                 from fileInput/FileReader.h:12,
                 from fileInput/FileReader.cpp:29:
fileInput/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
fileInput/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c fileInput/PIRFileParser.cpp -o fileInput/PIRFileParser.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c fileInput/RSFFileParser.cpp -o fileInput/RSFFileParser.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c fileInput/GDEFileParser.cpp -o fileInput/GDEFileParser.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c fileInput/InFileStream.cpp -o fileInput/InFileStream.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c fileInput/ClustalFileParser.cpp -o fileInput/ClustalFileParser.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c fileInput/PearsonFileParser.cpp -o fileInput/PearsonFileParser.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c fileInput/FileParser.cpp -o fileInput/FileParser.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c fileInput/EMBLFileParser.cpp -o fileInput/EMBLFileParser.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c tree/UPGMA/RootedClusterTree.cpp -o tree/UPGMA/RootedClusterTree.o
In file included from tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from tree/UPGMA/../../alignment/Alignment.h:42,
                 from tree/UPGMA/../ClusterTree.h:20,
                 from tree/UPGMA/RootedClusterTree.h:8,
                 from tree/UPGMA/RootedClusterTree.cpp:9:
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c tree/UPGMA/UPGMAAlgorithm.cpp -o tree/UPGMA/UPGMAAlgorithm.o
In file included from tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from tree/UPGMA/../../alignment/Alignment.h:42,
                 from tree/UPGMA/RootedGuideTree.h:17,
                 from tree/UPGMA/UPGMAAlgorithm.h:8,
                 from tree/UPGMA/UPGMAAlgorithm.cpp:4:
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c tree/UPGMA/Node.cpp -o tree/UPGMA/Node.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c tree/UPGMA/RootedGuideTree.cpp -o tree/UPGMA/RootedGuideTree.o
In file included from tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from tree/UPGMA/../../alignment/Alignment.h:42,
                 from tree/UPGMA/RootedGuideTree.h:17,
                 from tree/UPGMA/RootedGuideTree.cpp:10:
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c tree/UPGMA/RootedTreeOutput.cpp -o tree/UPGMA/RootedTreeOutput.o
In file included from tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from tree/UPGMA/../../alignment/Alignment.h:42,
                 from tree/UPGMA/RootedGuideTree.h:17,
                 from tree/UPGMA/RootedTreeOutput.h:15,
                 from tree/UPGMA/RootedTreeOutput.cpp:9:
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c tree/Tree.cpp -o tree/Tree.o
In file included from tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from tree/../alignment/Alignment.h:42,
                 from tree/Tree.h:13,
                 from tree/Tree.cpp:10:
tree/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
tree/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c tree/ClusterTree.cpp -o tree/ClusterTree.o
In file included from tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from tree/../alignment/Alignment.h:42,
                 from tree/ClusterTree.h:20,
                 from tree/ClusterTree.cpp:9:
tree/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
tree/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c tree/TreeInterface.cpp -o tree/TreeInterface.o
In file included from tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from tree/../alignment/Alignment.h:42,
                 from tree/TreeInterface.h:19,
                 from tree/TreeInterface.cpp:15:
tree/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
tree/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c tree/UnRootedClusterTree.cpp -o tree/UnRootedClusterTree.o
In file included from tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from tree/../alignment/Alignment.h:42,
                 from tree/ClusterTree.h:20,
                 from tree/UnRootedClusterTree.h:8,
                 from tree/UnRootedClusterTree.cpp:9:
tree/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
tree/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c tree/ClusterTreeOutput.cpp -o tree/ClusterTreeOutput.o
In file included from tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from tree/../alignment/Alignment.h:42,
                 from tree/ClusterTreeOutput.h:11,
                 from tree/ClusterTreeOutput.cpp:9:
tree/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
tree/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c tree/RandomGenerator.cpp -o tree/RandomGenerator.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c tree/NJTree.cpp -o tree/NJTree.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c tree/AlignmentSteps.cpp -o tree/AlignmentSteps.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c interface/CommandLineParser.cpp -o interface/CommandLineParser.o
In file included from interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from interface/../fileInput/../alignment/Alignment.h:42,
                 from interface/../fileInput/FileReader.h:12,
                 from interface/../Clustal.h:18,
                 from interface/CommandLineParser.h:18,
                 from interface/CommandLineParser.cpp:13:
interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c substitutionMatrix/SubMatrix.cpp -o substitutionMatrix/SubMatrix.o
In file included from substitutionMatrix/SubMatrix.cpp:15:0:
substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c multipleAlign/Iteration.cpp -o multipleAlign/Iteration.o
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from multipleAlign/../alignment/Alignment.h:42,
                 from multipleAlign/Iteration.h:8,
                 from multipleAlign/Iteration.cpp:13:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
multipleAlign/Iteration.cpp: In member function ‘bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)’:
multipleAlign/Iteration.cpp:231:32: warning: ignoring return value of ‘char* tmpnam(char*)’, declared with attribute warn_unused_result [-Wunused-result]
                 tmpnam (buffer);
                                ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c multipleAlign/MSA.cpp -o multipleAlign/MSA.o
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from multipleAlign/../alignment/Alignment.h:42,
                 from multipleAlign/ProfileBase.h:14,
                 from multipleAlign/MSA.h:10,
                 from multipleAlign/MSA.cpp:16:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c multipleAlign/MyersMillerProfileAlign.cpp -o multipleAlign/MyersMillerProfileAlign.o
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from multipleAlign/../alignment/Alignment.h:42,
                 from multipleAlign/ProfileAlignAlgorithm.h:10,
                 from multipleAlign/MyersMillerProfileAlign.h:10,
                 from multipleAlign/MyersMillerProfileAlign.cpp:10:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c multipleAlign/ProfileStandard.cpp -o multipleAlign/ProfileStandard.o
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from multipleAlign/../alignment/Alignment.h:42,
                 from multipleAlign/ProfileStandard.h:9,
                 from multipleAlign/ProfileStandard.cpp:9:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c multipleAlign/ProfileWithSub.cpp -o multipleAlign/ProfileWithSub.o
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from multipleAlign/../alignment/Alignment.h:42,
                 from multipleAlign/ProfileWithSub.h:9,
                 from multipleAlign/ProfileWithSub.cpp:9:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c multipleAlign/ProfileBase.cpp -o multipleAlign/ProfileBase.o
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from multipleAlign/../alignment/Alignment.h:42,
                 from multipleAlign/ProfileBase.h:14,
                 from multipleAlign/ProfileBase.cpp:9:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c multipleAlign/LowScoreSegProfile.cpp -o multipleAlign/LowScoreSegProfile.o
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from multipleAlign/../alignment/Alignment.h:42,
                 from multipleAlign/LowScoreSegProfile.h:13,
                 from multipleAlign/LowScoreSegProfile.cpp:9:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c general/OutputFile.cpp -o general/OutputFile.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c general/UserParameters.cpp -o general/UserParameters.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c general/Utility.cpp -o general/Utility.o
general/Utility.cpp: In member function ‘double clustalw::Utility::getReal(const char*, double, double, double)’:
general/Utility.cpp:183:36: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
         fgets(line, MAXLINE, stdin);
                                    ^
general/Utility.cpp: In member function ‘int clustalw::Utility::getInt(const char*, int, int, int)’:
general/Utility.cpp:221:36: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
         fgets(line, MAXLINE, stdin);
                                    ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c general/InvalidCombination.cpp -o general/InvalidCombination.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c general/DebugLog.cpp -o general/DebugLog.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c general/ClustalWResources.cpp -o general/ClustalWResources.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c general/VectorOutOfRange.cpp -o general/VectorOutOfRange.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c general/SymMatrix.cpp -o general/SymMatrix.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c general/Stats.cpp -o general/Stats.o
In file included from general/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from general/../alignment/Alignment.h:42,
                 from general/Stats.cpp:15:
general/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
general/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c Help.cpp -o Help.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c alignment/Alignment.cpp -o alignment/Alignment.o
In file included from alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from alignment/Alignment.h:42,
                 from alignment/Alignment.cpp:25:
alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c alignment/AlignmentOutput.cpp -o alignment/AlignmentOutput.o
In file included from alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from alignment/Alignment.h:42,
                 from alignment/AlignmentOutput.h:24,
                 from alignment/AlignmentOutput.cpp:27:
alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c alignment/ObjectiveScore.cpp -o alignment/ObjectiveScore.o
In file included from alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from alignment/ObjectiveScore.h:15,
                 from alignment/ObjectiveScore.cpp:10:
alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c alignment/Sequence.cpp -o alignment/Sequence.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c Clustal.cpp -o Clustal.o
In file included from fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from fileInput/../alignment/Alignment.h:42,
                 from fileInput/FileReader.h:12,
                 from Clustal.h:18,
                 from Clustal.cpp:27:
fileInput/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
fileInput/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c RClustalWMain.cpp -o RClustalWMain.o
In file included from alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from alignment/Alignment.h:42,
                 from RClustalWMain.cpp:5:
alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c RClustalW.cpp -o RClustalW.o
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/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/bbs-3.3-bioc/R/lib -lR
multipleAlign/Iteration.o: In function `std::vector<clustalw::Sequence, std::allocator<clustalw::Sequence> >::operator=(std::vector<clustalw::Sequence, std::allocator<clustalw::Sequence> > const&)':
/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00_pkg_src/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-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/ClustalW/src'
make[2]: Entering directory `/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/ClustalW/src'
make[2]: Leaving directory `/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/ClustalW/src'
make[1]: Leaving directory `/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/ClustalW'
----------------------------------------
--------------- ClustalW ---------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile --directory=ClustalOmega
make[1]: Entering directory `/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/ClustalOmega'
./configure `Rscript -e "if (Sys.info()['sysname'] == 'Darwin') cat('--without-openmp')"`; \
	export PKG_LIBS=" "; \
	export PKG_CXXFLAGS="  -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I"../../gc-7.2/include" `Rscript -e "Rcpp:::CxxFlags()"`"; \
	export PKG_CFLAGS="  -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I"../../gc-7.2/include" `Rscript -e "Rcpp:::CxxFlags()"`"; \
	cd src; \
	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

              
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configure: creating ./config.status
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make[2]: Entering directory `/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/ClustalOmega/src'
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c exceptions4c/e4c_lite.c -o exceptions4c/e4c_lite.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c argtable2/argtable2.c -o argtable2/argtable2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c argtable2/arg_end.c -o argtable2/arg_end.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c argtable2/arg_rem.c -o argtable2/arg_rem.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c argtable2/arg_lit.c -o argtable2/arg_lit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c argtable2/arg_int.c -o argtable2/arg_int.o
argtable2/arg_int.c: In function ‘strtol0X’:
argtable2/arg_int.c:60:5: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration]
     while (isspace(*ptr))
     ^
argtable2/arg_int.c:89:4: warning: implicit declaration of function ‘toupper’ [-Wimplicit-function-declaration]
    if (toupper(*ptr++)!=toupper(X))
    ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c argtable2/arg_dbl.c -o argtable2/arg_dbl.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c argtable2/arg_str.c -o argtable2/arg_str.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c argtable2/arg_file.c -o argtable2/arg_file.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c kmpp/KMeans.cpp -o kmpp/KMeans.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c kmpp/KmTree.cpp -o kmpp/KmTree.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c kmpp/KmUtils.cpp -o kmpp/KmUtils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c clustal/hhalign_wrapper.c -o clustal/hhalign_wrapper.o
In file included from clustal/hhalign_wrapper.c:22:0:
./config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c clustal/ktuple_pair.c -o clustal/ktuple_pair.o
In file included from clustal/ktuple_pair.c:29:0:
./config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c clustal/list.c -o clustal/list.o
In file included from clustal/list.c:32:0:
./config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c clustal/log.c -o clustal/log.o
In file included from clustal/log.c:22:0:
./config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c clustal/muscle_upgma.c -o clustal/muscle_upgma.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c clustal/muscle_tree.c -o clustal/muscle_tree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c clustal/mbed.c -o clustal/mbed.o
In file included from clustal/mbed.c:28:0:
./config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c clustal/pair_dist.c -o clustal/pair_dist.o
In file included from clustal/pair_dist.c:22:0:
./config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c clustal/progress.c -o clustal/progress.o
In file included from clustal/progress.c:22:0:
./config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c clustal/seq.c -o clustal/seq.o
In file included from clustal/seq.c:30:0:
./config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c clustal/symmatrix.c -o clustal/symmatrix.o
In file included from clustal/symmatrix.c:30:0:
./config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c clustal/tree.c -o clustal/tree.o
In file included from clustal/tree.c:22:0:
./config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c clustal/util.c -o clustal/util.o
In file included from clustal/util.c:22:0:
./config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c clustal/weights.c -o clustal/weights.o
In file included from clustal/weights.c:72:0:
./config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/a2m.c -o squid/a2m.o
In file included from squid/squid.h:32:0,
                 from squid/a2m.c:20:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/aligneval.c -o squid/aligneval.o
In file included from squid/squid.h:32:0,
                 from squid/aligneval.c:59:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/alignio.c -o squid/alignio.o
In file included from squid/squid.h:32:0,
                 from squid/alignio.c:21:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/clustal.c -o squid/clustal.o
In file included from squid/squid.h:32:0,
                 from squid/clustal.c:24:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/cluster.c -o squid/cluster.o
In file included from squid/squid.h:32:0,
                 from squid/cluster.c:124:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/dayhoff.c -o squid/dayhoff.o
In file included from squid/squid.h:32:0,
                 from squid/dayhoff.c:28:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/eps.c -o squid/eps.o
In file included from squid/squid.h:32:0,
                 from squid/eps.c:23:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/file.c -o squid/file.o
In file included from squid/squid.h:32:0,
                 from squid/file.c:28:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/getopt.c -o squid/getopt.o
In file included from squid/squid.h:32:0,
                 from squid/getopt.c:17:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/gki.c -o squid/gki.o
In file included from squid/squid.h:32:0,
                 from squid/gki.c:82:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/gsi.c -o squid/gsi.o
In file included from squid/squid.h:32:0,
                 from squid/gsi.c:35:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/gsi64.c -o squid/gsi64.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/hsregex.c -o squid/hsregex.o
In file included from squid/squid.h:32:0,
                 from squid/hsregex.c:33:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/iupac.c -o squid/iupac.o
In file included from squid/squid.h:32:0,
                 from squid/iupac.c:17:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/msa.c -o squid/msa.o
In file included from squid/squid.h:32:0,
                 from squid/msa.c:22:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/msf.c -o squid/msf.o
In file included from squid/squid.h:32:0,
                 from squid/msf.c:25:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/phylip.c -o squid/phylip.o
In file included from squid/squid.h:32:0,
                 from squid/phylip.c:23:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/revcomp.c -o squid/revcomp.o
In file included from squid/squid.h:32:0,
                 from squid/revcomp.c:19:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/rk.c -o squid/rk.o
In file included from squid/squid.h:32:0,
                 from squid/rk.c:26:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/selex.c -o squid/selex.o
In file included from squid/squid.h:32:0,
                 from squid/selex.c:43:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/seqencode.c -o squid/seqencode.o
In file included from squid/squid.h:32:0,
                 from squid/seqencode.c:18:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/shuffle.c -o squid/shuffle.o
In file included from squid/squid.h:32:0,
                 from squid/shuffle.c:42:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/sqerror.c -o squid/sqerror.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/sqio.c -o squid/sqio.o
In file included from squid/squid.h:32:0,
                 from squid/sqio.c:57:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/squidcore.c -o squid/squidcore.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/sre_ctype.c -o squid/sre_ctype.o
In file included from squid/squid.h:32:0,
                 from squid/sre_ctype.c:19:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/sre_math.c -o squid/sre_math.o
In file included from squid/squid.h:32:0,
                 from squid/sre_math.c:19:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/sre_random.c -o squid/sre_random.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/sre_string.c -o squid/sre_string.o
In file included from squid/squid.h:32:0,
                 from squid/sre_string.c:23:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/ssi.c -o squid/ssi.o
In file included from squid/squid.h:32:0,
                 from squid/ssi.c:16:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
squid/ssi.c: In function ‘SSIAddPrimaryKeyToIndex’:
squid/ssi.c:754:8: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘long long unsigned int’ [-Wformat=]
        (unsigned long) L);
        ^
squid/ssi.c:754:8: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘long long unsigned int’ [-Wformat=]
squid/ssi.c: In function ‘activate_external_sort’:
squid/ssi.c:1411:8: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘long long unsigned int’ [-Wformat=]
        (unsigned long) g->pkeys[i].len);
        ^
squid/ssi.c:1411:8: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘long long unsigned int’ [-Wformat=]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/stack.c -o squid/stack.o
In file included from squid/squid.h:32:0,
                 from squid/stack.c:18:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/stockholm.c -o squid/stockholm.o
In file included from squid/squid.h:32:0,
                 from squid/stockholm.c:31:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/stopwatch.c -o squid/stopwatch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/translate.c -o squid/translate.o
In file included from squid/squid.h:32:0,
                 from squid/translate.c:19:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/types.c -o squid/types.o
In file included from squid/squid.h:32:0,
                 from squid/types.c:20:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/vectorops.c -o squid/vectorops.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c squid/weight.c -o squid/weight.o
In file included from squid/squid.h:32:0,
                 from squid/weight.c:19:
squid/../config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c hhalign/hhalign.cpp -o hhalign/hhalign.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c RClustalOmega.cpp -o RClustalOmega.o
In file included from RClustalOmega.cpp:27:0:
config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c mymain.c -o mymain.o
In file included from mymain.c:22:0:
config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include -fpic  -g -O2  -c clustal-omega.c -o clustal-omega.o
In file included from clustal-omega.c:22:0:
config.h:132:0: warning: "NDEBUG" redefined [enabled by default]
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/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/bbs-3.3-bioc/R/lib -lR
clustal-omega.o: In function `AlnToHHMFile':
/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00_pkg_src/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-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/ClustalOmega/src'
make[2]: Entering directory `/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/ClustalOmega/src'
make[2]: Leaving directory `/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/ClustalOmega/src'
make[1]: Leaving directory `/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/ClustalOmega'
----------------------------------------
------------- ClustalOmega -------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o msa.so R_init_msa.o -Wl,--whole-archive ./libgc.a ./libClustalW.a ./libClustalOmega.a ./libMuscle.a -Wl,--no-whole-archive -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
./libClustalW.a(Iteration.o): In function `std::vector<clustalw::Sequence, std::allocator<clustalw::Sequence> >::operator=(std::vector<clustalw::Sequence, std::allocator<clustalw::Sequence> > const&)':
/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/ClustalW/src/multipleAlign/Iteration.cpp:231: warning: the use of `tmpnam' is dangerous, better use `mkstemp'
./libClustalOmega.a(clustal-omega.o): In function `AlnToHHMFile':
/home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/00_pkg_src/msa/src/ClustalOmega/src/clustal-omega.c:389: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
installing to /home/biocbuild/bbs-3.3-bioc/meat/msa.Rcheck/msa/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘print’ from package ‘base’ in package ‘msa’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (msa)

name	user	system	elapsed
MsaMetaData-class	0.244	0.004	0.248
MsaMultipleAlignmentClasses	0.225	0.004	0.229
msa-package	0.163	0.004	0.167
msa	0.48	0.00	0.48
msaClustalOmega	0.414	0.000	0.414
msaClustalW	0.339	0.004	0.343
msaMuscle	0.473	0.004	0.479
msaPrettyPrint	4.254	0.064	4.326