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  1. Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help
  2. BioC_mirror: https://bioconductor.org
  3. Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.1 (2017-06-30).
  4. Installing package(s) 'msa'
  5. trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/msa_1.8.0.tar.gz'
  6. Content type 'application/x-gzip' length 3772290 bytes (3.6 MB)
  7. ==================================================
  8. downloaded 3.6 MB
  9.  
  10. * installing *source* package 'msa' ...
  11. ** libs
  12. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src>
  13. > > >
  14. Save workspace image? [y/n/c]: > > > a.o
  15. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fpic -g -O2 -c SplitCharVector2List.cpp -o SplitCharVector2List.o
  16. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fpic -g -O2 -c SplitCharVector2Matrix.cpp -o SplitCharVector2Matrix.o
  17. make --file=msaMakefile --directory=gc-7.2
  18. make[1]: Entering directory '/tmp/RtmpGbVf2R/R.INSTALLa8314cd385fe/msa/src/gc-7.2'
  19. ./configure --enable-cplusplus --enable-threads=pthreads --enable-shared --with-pic
  20. checking build system type... x86_64-unknown-freebsd11.0
  21. checking host system type... x86_64-unknown-freebsd11.0
  22. checking target system type... x86_64-unknown-freebsd11.0
  23. checking GC version numbers... major=7 minor=2
  24. checking for a BSD-compatible install... /usr/bin/install -c
  25. checking whether build environment is sane... yes
  26. checking for a thread-safe mkdir -p... ./install-sh -c -d
  27. checking for gawk... no
  28. checking for mawk... no
  29. checking for nawk... nawk
  30. checking whether make sets $(MAKE)... yes
  31. checking whether make supports nested variables... yes
  32. checking whether to enable maintainer-specific portions of Makefiles... no
  33. checking for style of include used by make... GNU
  34. checking for gcc... gcc
  35. checking whether the C compiler works... yes
  36. checking for C compiler default output file name... a.out
  37. checking for suffix of executables...
  38. checking whether we are cross compiling... no
  39. checking for suffix of object files... o
  40. checking whether we are using the GNU C compiler... yes
  41. checking whether gcc accepts -g... yes
  42. checking for gcc option to accept ISO C89... none needed
  43. checking whether gcc understands -c and -o together... yes
  44. checking dependency style of gcc... gcc3
  45. checking for g++... g++
  46. checking whether we are using the GNU C++ compiler... yes
  47. checking whether g++ accepts -g... yes
  48. checking dependency style of g++... gcc3
  49. checking dependency style of gcc... gcc3
  50. checking for inline... inline
  51. checking for pthread_self in -lpthread... yes
  52. configure: WARNING: "FreeBSD does not yet fully support threads with Boehm GC."
  53. checking for xlc... no
  54. checking whether gcc supports -fno-strict-aliasing... yes
  55. checking for dlopen in -ldl... no
  56. checking whether to build shared libraries... yes
  57. checking which machine-dependent code should be used...
  58. checking how to print strings... printf
  59. checking for a sed that does not truncate output... /usr/bin/sed
  60. checking for grep that handles long lines and -e... /usr/bin/grep
  61. checking for egrep... /usr/bin/grep -E
  62. checking for fgrep... /usr/bin/grep -F
  63. checking for ld used by gcc... /usr/local/bin/ld
  64. checking if the linker (/usr/local/bin/ld) is GNU ld... yes
  65. checking for BSD- or MS-compatible name lister (nm)... /usr/local/bin/nm -B
  66. checking the name lister (/usr/local/bin/nm -B) interface... BSD nm
  67. checking whether ln -s works... yes
  68. checking the maximum length of command line arguments... 196608
  69. checking how to convert x86_64-unknown-freebsd11.0 file names to x86_64-unknown-freebsd11.0 format... func_convert_file_noop
  70. checking how to convert x86_64-unknown-freebsd11.0 file names to toolchain format... func_convert_file_noop
  71. checking for /usr/local/bin/ld option to reload object files... -r
  72. checking for objdump... objdump
  73. checking how to recognize dependent libraries... pass_all
  74. checking for dlltool... no
  75. checking how to associate runtime and link libraries... printf %s\n
  76. checking for ar... ar
  77. checking for archiver @FILE support... no
  78. checking for strip... strip
  79. checking for ranlib... ranlib
  80. checking command to parse /usr/local/bin/nm -B output from gcc object... ok
  81. checking for sysroot... no
  82. checking for mt... mt
  83. checking if mt is a manifest tool... no
  84. checking how to run the C preprocessor... gcc -E
  85. checking for ANSI C header files... yes
  86. checking for sys/types.h... yes
  87. checking for sys/stat.h... yes
  88. checking for stdlib.h... yes
  89. checking for string.h... yes
  90. checking for memory.h... yes
  91. checking for strings.h... yes
  92. checking for inttypes.h... yes
  93. checking for stdint.h... yes
  94. checking for unistd.h... yes
  95. checking for dlfcn.h... yes
  96. checking for objdir... .libs
  97. checking if gcc supports -fno-rtti -fno-exceptions... no
  98. checking for gcc option to produce PIC... -fPIC -DPIC
  99. checking if gcc PIC flag -fPIC -DPIC works... yes
  100. checking if gcc static flag -static works... yes
  101. checking if gcc supports -c -o file.o... yes
  102. checking if gcc supports -c -o file.o... (cached) yes
  103. checking whether the gcc linker (/usr/local/bin/ld) supports shared libraries... yes
  104. checking whether -lc should be explicitly linked in... no
  105. checking dynamic linker characteristics... freebsd11.0 ld.so
  106. checking how to hardcode library paths into programs... immediate
  107. checking whether stripping libraries is possible... no
  108. checking if libtool supports shared libraries... yes
  109. checking whether to build shared libraries... yes
  110. checking whether to build static libraries... yes
  111. checking how to run the C++ preprocessor... g++ -E
  112. checking for ld used by g++... /usr/local/bin/ld
  113. checking if the linker (/usr/local/bin/ld) is GNU ld... yes
  114. checking whether the g++ linker (/usr/local/bin/ld) supports shared libraries... yes
  115. checking for g++ option to produce PIC... -fPIC -DPIC
  116. checking if g++ PIC flag -fPIC -DPIC works... yes
  117. checking if g++ static flag -static works... yes
  118. checking if g++ supports -c -o file.o... yes
  119. checking if g++ supports -c -o file.o... (cached) yes
  120. checking whether the g++ linker (/usr/local/bin/ld) supports shared libraries... yes
  121. checking dynamic linker characteristics... freebsd11.0 ld.so
  122. checking how to hardcode library paths into programs... immediate
  123. checking whether Solaris gcc optimization fix is necessary... no
  124. checking sys/dg_sys_info.h usability... no
  125. checking sys/dg_sys_info.h presence... no
  126. checking for sys/dg_sys_info.h... no
  127. checking for pkg-config... no
  128. checking for ATOMIC_OPS... no
  129. checking which libatomic_ops to use... internal
  130. checking that generated files are newer than configure... done
  131. configure: creating ./config.status
  132. config.status: creating Makefile
  133. config.status: creating bdw-gc.pc
  134. config.status: creating include/private/config.h
  135. config.status: executing depfiles commands
  136. config.status: executing libtool commands
  137. config.status: executing default commands
  138. === configuring in libatomic_ops (/tmp/RtmpGbVf2R/R.INSTALLa8314cd385fe/msa/src/gc-7.2/libatomic_ops)
  139. configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/local' '--enable-cplusplus' '--enable-threads=pthreads' '--enable-shared' '--with-pic' --cache-file=/dev/null --srcdir=.
  140. checking build system type... x86_64-unknown-freebsd11.0
  141. checking host system type... x86_64-unknown-freebsd11.0
  142. checking target system type... x86_64-unknown-freebsd11.0
  143. checking for a BSD-compatible install... /usr/bin/install -c
  144. checking whether build environment is sane... yes
  145. checking for a thread-safe mkdir -p... ./install-sh -c -d
  146. checking for gawk... no
  147. checking for mawk... no
  148. checking for nawk... nawk
  149. checking whether make sets $(MAKE)... yes
  150. checking whether make supports nested variables... yes
  151. checking for ranlib... ranlib
  152. checking for style of include used by make... GNU
  153. checking for gcc... gcc
  154. checking whether the C compiler works... yes
  155. checking for C compiler default output file name... a.out
  156. checking for suffix of executables...
  157. checking whether we are cross compiling... no
  158. checking for suffix of object files... o
  159. checking whether we are using the GNU C compiler... yes
  160. checking whether gcc accepts -g... yes
  161. checking for gcc option to accept ISO C89... none needed
  162. checking whether gcc understands -c and -o together... yes
  163. checking dependency style of gcc... gcc3
  164. checking dependency style of gcc... gcc3
  165. checking how to run the C preprocessor... gcc -E
  166. checking for grep that handles long lines and -e... /usr/bin/grep
  167. checking for egrep... /usr/bin/grep -E
  168. checking for ANSI C header files... yes
  169. checking for sys/types.h... yes
  170. checking for sys/stat.h... yes
  171. checking for stdlib.h... yes
  172. checking for string.h... yes
  173. checking for memory.h... yes
  174. checking for strings.h... yes
  175. checking for inttypes.h... yes
  176. checking for stdint.h... yes
  177. checking for unistd.h... yes
  178. checking for stdlib.h... (cached) yes
  179. checking for unistd.h... (cached) yes
  180. checking for sys/param.h... yes
  181. checking for getpagesize... yes
  182. checking for working mmap... yes
  183. checking for ANSI C header files... (cached) yes
  184. checking for PIC compiler flag... -fPIC
  185. checking whether gcc -fPIC causes __PIC__ definition... yes
  186. checking for pthread_self in -lpthread... yes
  187. checking that generated files are newer than configure... done
  188. configure: creating ./config.status
  189. config.status: creating Makefile
  190. config.status: creating pkgconfig/atomic_ops.pc
  191. config.status: creating pkgconfig/atomic_ops-uninstalled.pc
  192. config.status: creating doc/Makefile
  193. config.status: creating src/Makefile
  194. config.status: creating src/atomic_ops/Makefile
  195. config.status: creating src/atomic_ops/sysdeps/Makefile
  196. config.status: creating tests/Makefile
  197. config.status: creating src/config.h
  198. config.status: executing depfiles commands
  199. config.status: executing default commands
  200. make
  201. make[2]: Entering directory '/tmp/RtmpGbVf2R/R.INSTALLa8314cd385fe/msa/src/gc-7.2'
  202. make[3]: Entering directory '/tmp/RtmpGbVf2R/R.INSTALLa8314cd385fe/msa/src/gc-7.2'
  203. depbase=`echo allchblk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  204. /bin/sh ./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 &&\
  205. mv -f $depbase.Tpo $depbase.Plo
  206. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT allchblk.lo -MD -MP -MF .deps/allchblk.Tpo -c allchblk.c -fPIC -DPIC -o .libs/allchblk.o
  207. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT allchblk.lo -MD -MP -MF .deps/allchblk.Tpo -c allchblk.c -fPIC -DPIC -o allchblk.o >/dev/null 2>&1
  208. depbase=`echo alloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  209. /bin/sh ./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 &&\
  210. mv -f $depbase.Tpo $depbase.Plo
  211. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT alloc.lo -MD -MP -MF .deps/alloc.Tpo -c alloc.c -fPIC -DPIC -o .libs/alloc.o
  212. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT alloc.lo -MD -MP -MF .deps/alloc.Tpo -c alloc.c -fPIC -DPIC -o alloc.o >/dev/null 2>&1
  213. depbase=`echo blacklst.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  214. /bin/sh ./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 &&\
  215. mv -f $depbase.Tpo $depbase.Plo
  216. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT blacklst.lo -MD -MP -MF .deps/blacklst.Tpo -c blacklst.c -fPIC -DPIC -o .libs/blacklst.o
  217. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT blacklst.lo -MD -MP -MF .deps/blacklst.Tpo -c blacklst.c -fPIC -DPIC -o blacklst.o >/dev/null 2>&1
  218. depbase=`echo checksums.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  219. /bin/sh ./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 &&\
  220. mv -f $depbase.Tpo $depbase.Plo
  221. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT checksums.lo -MD -MP -MF .deps/checksums.Tpo -c checksums.c -fPIC -DPIC -o .libs/checksums.o
  222. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT checksums.lo -MD -MP -MF .deps/checksums.Tpo -c checksums.c -fPIC -DPIC -o checksums.o >/dev/null 2>&1
  223. depbase=`echo dbg_mlc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  224. /bin/sh ./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 &&\
  225. mv -f $depbase.Tpo $depbase.Plo
  226. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dbg_mlc.lo -MD -MP -MF .deps/dbg_mlc.Tpo -c dbg_mlc.c -fPIC -DPIC -o .libs/dbg_mlc.o
  227. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dbg_mlc.lo -MD -MP -MF .deps/dbg_mlc.Tpo -c dbg_mlc.c -fPIC -DPIC -o dbg_mlc.o >/dev/null 2>&1
  228. depbase=`echo dyn_load.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  229. /bin/sh ./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 &&\
  230. mv -f $depbase.Tpo $depbase.Plo
  231. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dyn_load.lo -MD -MP -MF .deps/dyn_load.Tpo -c dyn_load.c -fPIC -DPIC -o .libs/dyn_load.o
  232. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dyn_load.lo -MD -MP -MF .deps/dyn_load.Tpo -c dyn_load.c -fPIC -DPIC -o dyn_load.o >/dev/null 2>&1
  233. depbase=`echo finalize.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  234. /bin/sh ./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 &&\
  235. mv -f $depbase.Tpo $depbase.Plo
  236. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT finalize.lo -MD -MP -MF .deps/finalize.Tpo -c finalize.c -fPIC -DPIC -o .libs/finalize.o
  237. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT finalize.lo -MD -MP -MF .deps/finalize.Tpo -c finalize.c -fPIC -DPIC -o finalize.o >/dev/null 2>&1
  238. depbase=`echo gc_dlopen.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  239. /bin/sh ./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 &&\
  240. mv -f $depbase.Tpo $depbase.Plo
  241. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT gc_dlopen.lo -MD -MP -MF .deps/gc_dlopen.Tpo -c gc_dlopen.c -fPIC -DPIC -o .libs/gc_dlopen.o
  242. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT gc_dlopen.lo -MD -MP -MF .deps/gc_dlopen.Tpo -c gc_dlopen.c -fPIC -DPIC -o gc_dlopen.o >/dev/null 2>&1
  243. depbase=`echo gcj_mlc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  244. /bin/sh ./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 &&\
  245. mv -f $depbase.Tpo $depbase.Plo
  246. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT gcj_mlc.lo -MD -MP -MF .deps/gcj_mlc.Tpo -c gcj_mlc.c -fPIC -DPIC -o .libs/gcj_mlc.o
  247. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT gcj_mlc.lo -MD -MP -MF .deps/gcj_mlc.Tpo -c gcj_mlc.c -fPIC -DPIC -o gcj_mlc.o >/dev/null 2>&1
  248. depbase=`echo headers.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  249. /bin/sh ./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 &&\
  250. mv -f $depbase.Tpo $depbase.Plo
  251. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT headers.lo -MD -MP -MF .deps/headers.Tpo -c headers.c -fPIC -DPIC -o .libs/headers.o
  252. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT headers.lo -MD -MP -MF .deps/headers.Tpo -c headers.c -fPIC -DPIC -o headers.o >/dev/null 2>&1
  253. depbase=`echo malloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  254. /bin/sh ./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 &&\
  255. mv -f $depbase.Tpo $depbase.Plo
  256. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT malloc.lo -MD -MP -MF .deps/malloc.Tpo -c malloc.c -fPIC -DPIC -o .libs/malloc.o
  257. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT malloc.lo -MD -MP -MF .deps/malloc.Tpo -c malloc.c -fPIC -DPIC -o malloc.o >/dev/null 2>&1
  258. depbase=`echo mallocx.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  259. /bin/sh ./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 &&\
  260. mv -f $depbase.Tpo $depbase.Plo
  261. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mallocx.lo -MD -MP -MF .deps/mallocx.Tpo -c mallocx.c -fPIC -DPIC -o .libs/mallocx.o
  262. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mallocx.lo -MD -MP -MF .deps/mallocx.Tpo -c mallocx.c -fPIC -DPIC -o mallocx.o >/dev/null 2>&1
  263. depbase=`echo mark.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  264. /bin/sh ./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 &&\
  265. mv -f $depbase.Tpo $depbase.Plo
  266. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mark.lo -MD -MP -MF .deps/mark.Tpo -c mark.c -fPIC -DPIC -o .libs/mark.o
  267. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mark.lo -MD -MP -MF .deps/mark.Tpo -c mark.c -fPIC -DPIC -o mark.o >/dev/null 2>&1
  268. depbase=`echo mark_rts.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  269. /bin/sh ./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 &&\
  270. mv -f $depbase.Tpo $depbase.Plo
  271. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mark_rts.lo -MD -MP -MF .deps/mark_rts.Tpo -c mark_rts.c -fPIC -DPIC -o .libs/mark_rts.o
  272. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mark_rts.lo -MD -MP -MF .deps/mark_rts.Tpo -c mark_rts.c -fPIC -DPIC -o mark_rts.o >/dev/null 2>&1
  273. depbase=`echo misc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  274. /bin/sh ./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 &&\
  275. mv -f $depbase.Tpo $depbase.Plo
  276. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT misc.lo -MD -MP -MF .deps/misc.Tpo -c misc.c -fPIC -DPIC -o .libs/misc.o
  277. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT misc.lo -MD -MP -MF .deps/misc.Tpo -c misc.c -fPIC -DPIC -o misc.o >/dev/null 2>&1
  278. depbase=`echo new_hblk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  279. /bin/sh ./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 &&\
  280. mv -f $depbase.Tpo $depbase.Plo
  281. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT new_hblk.lo -MD -MP -MF .deps/new_hblk.Tpo -c new_hblk.c -fPIC -DPIC -o .libs/new_hblk.o
  282. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT new_hblk.lo -MD -MP -MF .deps/new_hblk.Tpo -c new_hblk.c -fPIC -DPIC -o new_hblk.o >/dev/null 2>&1
  283. depbase=`echo obj_map.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  284. /bin/sh ./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 &&\
  285. mv -f $depbase.Tpo $depbase.Plo
  286. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT obj_map.lo -MD -MP -MF .deps/obj_map.Tpo -c obj_map.c -fPIC -DPIC -o .libs/obj_map.o
  287. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT obj_map.lo -MD -MP -MF .deps/obj_map.Tpo -c obj_map.c -fPIC -DPIC -o obj_map.o >/dev/null 2>&1
  288. depbase=`echo os_dep.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  289. /bin/sh ./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 &&\
  290. mv -f $depbase.Tpo $depbase.Plo
  291. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT os_dep.lo -MD -MP -MF .deps/os_dep.Tpo -c os_dep.c -fPIC -DPIC -o .libs/os_dep.o
  292. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT os_dep.lo -MD -MP -MF .deps/os_dep.Tpo -c os_dep.c -fPIC -DPIC -o os_dep.o >/dev/null 2>&1
  293. depbase=`echo pcr_interface.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  294. /bin/sh ./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 &&\
  295. mv -f $depbase.Tpo $depbase.Plo
  296. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pcr_interface.lo -MD -MP -MF .deps/pcr_interface.Tpo -c pcr_interface.c -fPIC -DPIC -o .libs/pcr_interface.o
  297. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pcr_interface.lo -MD -MP -MF .deps/pcr_interface.Tpo -c pcr_interface.c -fPIC -DPIC -o pcr_interface.o >/dev/null 2>&1
  298. depbase=`echo ptr_chck.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  299. /bin/sh ./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 &&\
  300. mv -f $depbase.Tpo $depbase.Plo
  301. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT ptr_chck.lo -MD -MP -MF .deps/ptr_chck.Tpo -c ptr_chck.c -fPIC -DPIC -o .libs/ptr_chck.o
  302. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT ptr_chck.lo -MD -MP -MF .deps/ptr_chck.Tpo -c ptr_chck.c -fPIC -DPIC -o ptr_chck.o >/dev/null 2>&1
  303. depbase=`echo real_malloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  304. /bin/sh ./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 &&\
  305. mv -f $depbase.Tpo $depbase.Plo
  306. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT real_malloc.lo -MD -MP -MF .deps/real_malloc.Tpo -c real_malloc.c -fPIC -DPIC -o .libs/real_malloc.o
  307. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT real_malloc.lo -MD -MP -MF .deps/real_malloc.Tpo -c real_malloc.c -fPIC -DPIC -o real_malloc.o >/dev/null 2>&1
  308. depbase=`echo reclaim.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  309. /bin/sh ./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 &&\
  310. mv -f $depbase.Tpo $depbase.Plo
  311. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT reclaim.lo -MD -MP -MF .deps/reclaim.Tpo -c reclaim.c -fPIC -DPIC -o .libs/reclaim.o
  312. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT reclaim.lo -MD -MP -MF .deps/reclaim.Tpo -c reclaim.c -fPIC -DPIC -o reclaim.o >/dev/null 2>&1
  313. depbase=`echo specific.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  314. /bin/sh ./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 &&\
  315. mv -f $depbase.Tpo $depbase.Plo
  316. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT specific.lo -MD -MP -MF .deps/specific.Tpo -c specific.c -fPIC -DPIC -o .libs/specific.o
  317. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT specific.lo -MD -MP -MF .deps/specific.Tpo -c specific.c -fPIC -DPIC -o specific.o >/dev/null 2>&1
  318. depbase=`echo stubborn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  319. /bin/sh ./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 &&\
  320. mv -f $depbase.Tpo $depbase.Plo
  321. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT stubborn.lo -MD -MP -MF .deps/stubborn.Tpo -c stubborn.c -fPIC -DPIC -o .libs/stubborn.o
  322. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT stubborn.lo -MD -MP -MF .deps/stubborn.Tpo -c stubborn.c -fPIC -DPIC -o stubborn.o >/dev/null 2>&1
  323. depbase=`echo typd_mlc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  324. /bin/sh ./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 &&\
  325. mv -f $depbase.Tpo $depbase.Plo
  326. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT typd_mlc.lo -MD -MP -MF .deps/typd_mlc.Tpo -c typd_mlc.c -fPIC -DPIC -o .libs/typd_mlc.o
  327. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT typd_mlc.lo -MD -MP -MF .deps/typd_mlc.Tpo -c typd_mlc.c -fPIC -DPIC -o typd_mlc.o >/dev/null 2>&1
  328. depbase=`echo backgraph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  329. /bin/sh ./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 &&\
  330. mv -f $depbase.Tpo $depbase.Plo
  331. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT backgraph.lo -MD -MP -MF .deps/backgraph.Tpo -c backgraph.c -fPIC -DPIC -o .libs/backgraph.o
  332. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT backgraph.lo -MD -MP -MF .deps/backgraph.Tpo -c backgraph.c -fPIC -DPIC -o backgraph.o >/dev/null 2>&1
  333. depbase=`echo thread_local_alloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  334. /bin/sh ./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 &&\
  335. mv -f $depbase.Tpo $depbase.Plo
  336. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT thread_local_alloc.lo -MD -MP -MF .deps/thread_local_alloc.Tpo -c thread_local_alloc.c -fPIC -DPIC -o .libs/thread_local_alloc.o
  337. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT thread_local_alloc.lo -MD -MP -MF .deps/thread_local_alloc.Tpo -c thread_local_alloc.c -fPIC -DPIC -o thread_local_alloc.o >/dev/null 2>&1
  338. depbase=`echo pthread_start.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  339. /bin/sh ./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 &&\
  340. mv -f $depbase.Tpo $depbase.Plo
  341. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_start.lo -MD -MP -MF .deps/pthread_start.Tpo -c pthread_start.c -fPIC -DPIC -o .libs/pthread_start.o
  342. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_start.lo -MD -MP -MF .deps/pthread_start.Tpo -c pthread_start.c -fPIC -DPIC -o pthread_start.o >/dev/null 2>&1
  343. depbase=`echo pthread_support.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  344. /bin/sh ./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 &&\
  345. mv -f $depbase.Tpo $depbase.Plo
  346. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_support.lo -MD -MP -MF .deps/pthread_support.Tpo -c pthread_support.c -fPIC -DPIC -o .libs/pthread_support.o
  347. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_support.lo -MD -MP -MF .deps/pthread_support.Tpo -c pthread_support.c -fPIC -DPIC -o pthread_support.o >/dev/null 2>&1
  348. depbase=`echo pthread_stop_world.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  349. /bin/sh ./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 &&\
  350. mv -f $depbase.Tpo $depbase.Plo
  351. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_stop_world.lo -MD -MP -MF .deps/pthread_stop_world.Tpo -c pthread_stop_world.c -fPIC -DPIC -o .libs/pthread_stop_world.o
  352. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_stop_world.lo -MD -MP -MF .deps/pthread_stop_world.Tpo -c pthread_stop_world.c -fPIC -DPIC -o pthread_stop_world.o >/dev/null 2>&1
  353. depbase=`echo libatomic_ops/src/atomic_ops.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  354. /bin/sh ./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 &&\
  355. mv -f $depbase.Tpo $depbase.Plo
  356. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT libatomic_ops/src/atomic_ops.lo -MD -MP -MF libatomic_ops/src/.deps/atomic_ops.Tpo -c libatomic_ops/src/atomic_ops.c -fPIC -DPIC -o libatomic_ops/src/.libs/atomic_ops.o
  357. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT libatomic_ops/src/atomic_ops.lo -MD -MP -MF libatomic_ops/src/.deps/atomic_ops.Tpo -c libatomic_ops/src/atomic_ops.c -fPIC -DPIC -o libatomic_ops/src/atomic_ops.o >/dev/null 2>&1
  358. depbase=`echo mach_dep.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  359. /bin/sh ./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 &&\
  360. mv -f $depbase.Tpo $depbase.Plo
  361. 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
  362. 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
  363. /bin/sh ./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
  364. 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 -g -O2 -Wl,-soname -Wl,libgc.so.1 -o .libs/libgc.so.1
  365. libtool: link: (cd ".libs" && rm -f "libgc.so" && ln -s "libgc.so.1" "libgc.so")
  366. libtool: link: (cd ".libs" && rm -f "libgc.so" && ln -s "libgc.so.1" "libgc.so")
  367. 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
  368. libtool: link: ranlib .libs/libgc.a
  369. libtool: link: ( cd ".libs" && rm -f "libgc.la" && ln -s "../libgc.la" "libgc.la" )
  370. depbase=`echo gc_cpp.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  371. /bin/sh ./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 &&\
  372. mv -f $depbase.Tpo $depbase.Plo
  373. libtool: compile: g++ -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -MT gc_cpp.lo -MD -MP -MF .deps/gc_cpp.Tpo -c gc_cpp.cc -fPIC -DPIC -o .libs/gc_cpp.o
  374. libtool: compile: g++ -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -MT gc_cpp.lo -MD -MP -MF .deps/gc_cpp.Tpo -c gc_cpp.cc -fPIC -DPIC -o gc_cpp.o >/dev/null 2>&1
  375. /bin/sh ./libtool --tag=CXX --mode=link g++ -fexceptions -g -O2 -version-info 1:3:0 -no-undefined -o libgccpp.la -rpath /usr/local/lib gc_cpp.lo ./libgc.la
  376. libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/local/lib/gcc5/gcc/x86_64-portbld-freebsd11.0/5.4.0/crtbeginS.o .libs/gc_cpp.o -Wl,-rpath -Wl,/tmp/RtmpGbVf2R/R.INSTALLa8314cd385fe/msa/src/gc-7.2/.libs -Wl,-rpath -Wl,/usr/local/lib ./.libs/libgc.so -lpthread -L/usr/local/lib/gcc5/gcc/x86_64-portbld-freebsd11.0/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-freebsd11.0/5.4.0/../../../../../x86_64-portbld-freebsd11.0/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-freebsd11.0/5.4.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/local/lib/gcc5/gcc/x86_64-portbld-freebsd11.0/5.4.0/crtendS.o /usr/lib/crtn.o -g -O2 -Wl,-soname -Wl,libgccpp.so.1 -o .libs/libgccpp.so.1
  377. libtool: link: (cd ".libs" && rm -f "libgccpp.so" && ln -s "libgccpp.so.1" "libgccpp.so")
  378. libtool: link: (cd ".libs" && rm -f "libgccpp.so" && ln -s "libgccpp.so.1" "libgccpp.so")
  379. libtool: link: ar cru .libs/libgccpp.a gc_cpp.o
  380. libtool: link: ranlib .libs/libgccpp.a
  381. libtool: link: ( cd ".libs" && rm -f "libgccpp.la" && ln -s "../libgccpp.la" "libgccpp.la" )
  382. depbase=`echo cord/cordbscs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  383. /bin/sh ./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 &&\
  384. mv -f $depbase.Tpo $depbase.Plo
  385. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordbscs.lo -MD -MP -MF cord/.deps/cordbscs.Tpo -c cord/cordbscs.c -fPIC -DPIC -o cord/.libs/cordbscs.o
  386. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordbscs.lo -MD -MP -MF cord/.deps/cordbscs.Tpo -c cord/cordbscs.c -fPIC -DPIC -o cord/cordbscs.o >/dev/null 2>&1
  387. depbase=`echo cord/cordprnt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  388. /bin/sh ./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 &&\
  389. mv -f $depbase.Tpo $depbase.Plo
  390. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordprnt.lo -MD -MP -MF cord/.deps/cordprnt.Tpo -c cord/cordprnt.c -fPIC -DPIC -o cord/.libs/cordprnt.o
  391. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordprnt.lo -MD -MP -MF cord/.deps/cordprnt.Tpo -c cord/cordprnt.c -fPIC -DPIC -o cord/cordprnt.o >/dev/null 2>&1
  392. depbase=`echo cord/cordtest.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  393. /bin/sh ./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 &&\
  394. mv -f $depbase.Tpo $depbase.Plo
  395. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordtest.lo -MD -MP -MF cord/.deps/cordtest.Tpo -c cord/cordtest.c -fPIC -DPIC -o cord/.libs/cordtest.o
  396. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordtest.lo -MD -MP -MF cord/.deps/cordtest.Tpo -c cord/cordtest.c -fPIC -DPIC -o cord/cordtest.o >/dev/null 2>&1
  397. depbase=`echo cord/cordxtra.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  398. /bin/sh ./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 &&\
  399. mv -f $depbase.Tpo $depbase.Plo
  400. 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
  401. 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
  402. /bin/sh ./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
  403. 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,/tmp/RtmpGbVf2R/R.INSTALLa8314cd385fe/msa/src/gc-7.2/.libs -Wl,-rpath -Wl,/usr/local/lib ./.libs/libgc.so -lpthread -g -O2 -Wl,-soname -Wl,libcord.so.1 -o .libs/libcord.so.1
  404. libtool: link: (cd ".libs" && rm -f "libcord.so" && ln -s "libcord.so.1" "libcord.so")
  405. libtool: link: (cd ".libs" && rm -f "libcord.so" && ln -s "libcord.so.1" "libcord.so")
  406. libtool: link: ar cru .libs/libcord.a cord/cordbscs.o cord/cordprnt.o cord/cordtest.o cord/cordxtra.o
  407. libtool: link: ranlib .libs/libcord.a
  408. libtool: link: ( cd ".libs" && rm -f "libcord.la" && ln -s "../libcord.la" "libcord.la" )
  409. make[3]: Leaving directory '/tmp/RtmpGbVf2R/R.INSTALLa8314cd385fe/msa/src/gc-7.2'
  410. make[2]: Leaving directory '/tmp/RtmpGbVf2R/R.INSTALLa8314cd385fe/msa/src/gc-7.2'
  411. cp .libs/libgc.a ../
  412. cp .libs/libgccpp.a ../
  413. make[1]: Leaving directory '/tmp/RtmpGbVf2R/R.INSTALLa8314cd385fe/msa/src/gc-7.2'
  414. ----------------------------------------
  415. ------------------ GC -----------------
  416. ----------------------------------------
  417. --------- Compilation finished ---------
  418. ----------------------------------------
  419. make --file=msaMakefile --directory=Muscle
  420. make[1]: Entering directory '/tmp/RtmpGbVf2R/R.INSTALLa8314cd385fe/msa/src/Muscle'
  421. export PKG_CXXFLAGS=" -I../gc-7.2/include"
  422. /home/my_user_name/R-3.4.1/bin/R CMD SHLIB -o libMuscle.so aligngivenpath.cpp aligngivenpathsw.cpp aligntwomsas.cpp aligntwoprofs.cpp aln.cpp alpha.cpp anchors.cpp bittraceback.cpp blosum62.cpp blosumla.cpp clust.cpp cluster.cpp clwwt.cpp color.cpp cons.cpp diaglist.cpp diffobjscore.cpp diffpaths.cpp difftrees.cpp difftreese.cpp distcalc.cpp distfunc.cpp distpwkimura.cpp domuscle.cpp dosp.cpp dpreglist.cpp drawtree.cpp edgelist.cpp enumopts.cpp enumtostr.cpp estring.cpp fasta.cpp fasta2.cpp fastclust.cpp fastdist.cpp fastdistjones.cpp fastdistkbit.cpp fastdistkmer.cpp fastdistmafft.cpp fastdistnuc.cpp fastscorepath2.cpp finddiags.cpp finddiagsn.cpp glbalign.cpp glbalign352.cpp glbaligndiag.cpp glbalignle.cpp glbalignsimple.cpp glbalignsp.cpp glbalignspn.cpp glbalignss.cpp glbalndimer.cpp globals.cpp globalslinux.cpp globalsosx.cpp globalsother.cpp globalswin32.cpp gonnet.cpp henikoffweight.cpp henikoffweightpb.cpp html.cpp hydro.cpp intmath.cpp local.cpp main.cpp makerootmsa.cpp makerootmsab.cpp maketree.cpp mhack.cpp mpam200.cpp msa.cpp msa2.cpp msadistkimura.cpp msf.cpp muscle.cpp muscleout.cpp nucmx.cpp nwdasimple.cpp nwdasimple2.cpp nwdasmall.cpp nwrec.cpp nwsmall.cpp objscore.cpp objscore2.cpp objscoreda.cpp onexception.cpp options.cpp outweights.cpp pam200mafft.cpp params.cpp phy.cpp phy2.cpp phy3.cpp phy4.cpp phyfromclust.cpp phyfromfile.cpp physeq.cpp phytofile.cpp posgap.cpp ppscore.cpp profdb.cpp profile.cpp profilefrommsa.cpp progalign.cpp progress.cpp progressivealign.cpp pwpath.cpp readmx.cpp realigndiffs.cpp realigndiffse.cpp refine.cpp refinehoriz.cpp refinesubfams.cpp refinetree.cpp refinetreee.cpp refinevert.cpp refinew.cpp savebest.cpp scoredist.cpp scoregaps.cpp scorehistory.cpp scorepp.cpp seq.cpp seqvect.cpp setblosumweights.cpp setgscweights.cpp setnewhandler.cpp spfast.cpp sptest.cpp stabilize.cpp subfam.cpp subfams.cpp sw.cpp termgaps.cpp textfile.cpp threewaywt.cpp tomhydro.cpp traceback.cpp tracebackopt.cpp tracebacksw.cpp treefrommsa.cpp typetostr.cpp upgma2.cpp usage.cpp validateids.cpp vtml2.cpp writescorefile.cpp RMuscle.cpp
  423. make[2]: Entering directory '/tmp/RtmpGbVf2R/R.INSTALLa8314cd385fe/msa/src/Muscle'
  424. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c aligngivenpath.cpp -o aligngivenpath.o
  425. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c aligngivenpathsw.cpp -o aligngivenpathsw.o
  426. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c aligntwomsas.cpp -o aligntwomsas.o
  427. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c aligntwoprofs.cpp -o aligntwoprofs.o
  428. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c aln.cpp -o aln.o
  429. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c alpha.cpp -o alpha.o
  430. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c anchors.cpp -o anchors.o
  431. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c bittraceback.cpp -o bittraceback.o
  432. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c blosum62.cpp -o blosum62.o
  433. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c blosumla.cpp -o blosumla.o
  434. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c clust.cpp -o clust.o
  435. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c cluster.cpp -o cluster.o
  436. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c clwwt.cpp -o clwwt.o
  437. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c color.cpp -o color.o
  438. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c cons.cpp -o cons.o
  439. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c diaglist.cpp -o diaglist.o
  440. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c diffobjscore.cpp -o diffobjscore.o
  441. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c diffpaths.cpp -o diffpaths.o
  442. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c difftrees.cpp -o difftrees.o
  443. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c difftreese.cpp -o difftreese.o
  444. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c distcalc.cpp -o distcalc.o
  445. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c distfunc.cpp -o distfunc.o
  446. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c distpwkimura.cpp -o distpwkimura.o
  447. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c domuscle.cpp -o domuscle.o
  448. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c dosp.cpp -o dosp.o
  449. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c dpreglist.cpp -o dpreglist.o
  450. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c drawtree.cpp -o drawtree.o
  451. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c edgelist.cpp -o edgelist.o
  452. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c enumopts.cpp -o enumopts.o
  453. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c enumtostr.cpp -o enumtostr.o
  454. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c estring.cpp -o estring.o
  455. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c fasta.cpp -o fasta.o
  456. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c fasta2.cpp -o fasta2.o
  457. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c fastclust.cpp -o fastclust.o
  458. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c fastdist.cpp -o fastdist.o
  459. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c fastdistjones.cpp -o fastdistjones.o
  460. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c fastdistkbit.cpp -o fastdistkbit.o
  461. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c fastdistkmer.cpp -o fastdistkmer.o
  462. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c fastdistmafft.cpp -o fastdistmafft.o
  463. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c fastdistnuc.cpp -o fastdistnuc.o
  464. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c fastscorepath2.cpp -o fastscorepath2.o
  465. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c finddiags.cpp -o finddiags.o
  466. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c finddiagsn.cpp -o finddiagsn.o
  467. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c glbalign.cpp -o glbalign.o
  468. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c glbalign352.cpp -o glbalign352.o
  469. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c glbaligndiag.cpp -o glbaligndiag.o
  470. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c glbalignle.cpp -o glbalignle.o
  471. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c glbalignsimple.cpp -o glbalignsimple.o
  472. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c glbalignsp.cpp -o glbalignsp.o
  473. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c glbalignspn.cpp -o glbalignspn.o
  474. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c glbalignss.cpp -o glbalignss.o
  475. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c glbalndimer.cpp -o glbalndimer.o
  476. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c globals.cpp -o globals.o
  477. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c globalslinux.cpp -o globalslinux.o
  478. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c globalsosx.cpp -o globalsosx.o
  479. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c globalsother.cpp -o globalsother.o
  480. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c globalswin32.cpp -o globalswin32.o
  481. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c gonnet.cpp -o gonnet.o
  482. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c henikoffweight.cpp -o henikoffweight.o
  483. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c henikoffweightpb.cpp -o henikoffweightpb.o
  484. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c html.cpp -o html.o
  485. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c hydro.cpp -o hydro.o
  486. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c intmath.cpp -o intmath.o
  487. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c local.cpp -o local.o
  488. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c main.cpp -o main.o
  489. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c makerootmsa.cpp -o makerootmsa.o
  490. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c makerootmsab.cpp -o makerootmsab.o
  491. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c maketree.cpp -o maketree.o
  492. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c mhack.cpp -o mhack.o
  493. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c mpam200.cpp -o mpam200.o
  494. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c msa.cpp -o msa.o
  495. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c msa2.cpp -o msa2.o
  496. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c msadistkimura.cpp -o msadistkimura.o
  497. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c msf.cpp -o msf.o
  498. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c muscle.cpp -o muscle.o
  499. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c muscleout.cpp -o muscleout.o
  500. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c nucmx.cpp -o nucmx.o
  501. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c nwdasimple.cpp -o nwdasimple.o
  502. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c nwdasimple2.cpp -o nwdasimple2.o
  503. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c nwdasmall.cpp -o nwdasmall.o
  504. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c nwrec.cpp -o nwrec.o
  505. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c nwsmall.cpp -o nwsmall.o
  506. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c objscore.cpp -o objscore.o
  507. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c objscore2.cpp -o objscore2.o
  508. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c objscoreda.cpp -o objscoreda.o
  509. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c onexception.cpp -o onexception.o
  510. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c options.cpp -o options.o
  511. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c outweights.cpp -o outweights.o
  512. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c pam200mafft.cpp -o pam200mafft.o
  513. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c params.cpp -o params.o
  514. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c phy.cpp -o phy.o
  515. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c phy2.cpp -o phy2.o
  516. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c phy3.cpp -o phy3.o
  517. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c phy4.cpp -o phy4.o
  518. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c phyfromclust.cpp -o phyfromclust.o
  519. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c phyfromfile.cpp -o phyfromfile.o
  520. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c physeq.cpp -o physeq.o
  521. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c phytofile.cpp -o phytofile.o
  522. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c posgap.cpp -o posgap.o
  523. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c ppscore.cpp -o ppscore.o
  524. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c profdb.cpp -o profdb.o
  525. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c profile.cpp -o profile.o
  526. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c profilefrommsa.cpp -o profilefrommsa.o
  527. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c progalign.cpp -o progalign.o
  528. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c progress.cpp -o progress.o
  529. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c progressivealign.cpp -o progressivealign.o
  530. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c pwpath.cpp -o pwpath.o
  531. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c readmx.cpp -o readmx.o
  532. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c realigndiffs.cpp -o realigndiffs.o
  533. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c realigndiffse.cpp -o realigndiffse.o
  534. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c refine.cpp -o refine.o
  535. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c refinehoriz.cpp -o refinehoriz.o
  536. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c refinesubfams.cpp -o refinesubfams.o
  537. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c refinetree.cpp -o refinetree.o
  538. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c refinetreee.cpp -o refinetreee.o
  539. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c refinevert.cpp -o refinevert.o
  540. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c refinew.cpp -o refinew.o
  541. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c savebest.cpp -o savebest.o
  542. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c scoredist.cpp -o scoredist.o
  543. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c scoregaps.cpp -o scoregaps.o
  544. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c scorehistory.cpp -o scorehistory.o
  545. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c scorepp.cpp -o scorepp.o
  546. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c seq.cpp -o seq.o
  547. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c seqvect.cpp -o seqvect.o
  548. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c setblosumweights.cpp -o setblosumweights.o
  549. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c setgscweights.cpp -o setgscweights.o
  550. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c setnewhandler.cpp -o setnewhandler.o
  551. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c spfast.cpp -o spfast.o
  552. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c sptest.cpp -o sptest.o
  553. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c stabilize.cpp -o stabilize.o
  554. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c subfam.cpp -o subfam.o
  555. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c subfams.cpp -o subfams.o
  556. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c sw.cpp -o sw.o
  557. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c termgaps.cpp -o termgaps.o
  558. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c textfile.cpp -o textfile.o
  559. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c threewaywt.cpp -o threewaywt.o
  560. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c tomhydro.cpp -o tomhydro.o
  561. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c traceback.cpp -o traceback.o
  562. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c tracebackopt.cpp -o tracebackopt.o
  563. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c tracebacksw.cpp -o tracebacksw.o
  564. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c treefrommsa.cpp -o treefrommsa.o
  565. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c typetostr.cpp -o typetostr.o
  566. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c upgma2.cpp -o upgma2.o
  567. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c usage.cpp -o usage.o
  568. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c validateids.cpp -o validateids.o
  569. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c vtml2.cpp -o vtml2.o
  570. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c writescorefile.cpp -o writescorefile.o
  571. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c RMuscle.cpp -o RMuscle.o
  572. g++ -shared -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
  573. make[2]: Leaving directory '/tmp/RtmpGbVf2R/R.INSTALLa8314cd385fe/msa/src/Muscle'
  574. 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
  575. cp libMuscle.a ../
  576. make[1]: Leaving directory '/tmp/RtmpGbVf2R/R.INSTALLa8314cd385fe/msa/src/Muscle'
  577. ----------------------------------------
  578. ---------------- MUSCLE ----------------
  579. ----------------------------------------
  580. --------- Compilation finished ---------
  581. ----------------------------------------
  582. make --file=msaMakefile --directory=ClustalW
  583. make[1]: Entering directory '/tmp/RtmpGbVf2R/R.INSTALLa8314cd385fe/msa/src/ClustalW'
  584. ./configure; \
  585. cd src; \
  586. export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. "; \
  587. /home/my_user_name/R-3.4.1/bin/R CMD SHLIB -o libClustalW.so pairwise/FullPairwiseAlign.cpp pairwise/FastPairwiseAlign.cpp fileInput/MSFFileParser.cpp fileInput/FileReader.cpp fileInput/PIRFileParser.cpp fileInput/RSFFileParser.cpp fileInput/GDEFileParser.cpp fileInput/InFileStream.cpp fileInput/ClustalFileParser.cpp fileInput/PearsonFileParser.cpp fileInput/FileParser.cpp fileInput/EMBLFileParser.cpp tree/UPGMA/RootedClusterTree.cpp tree/UPGMA/UPGMAAlgorithm.cpp tree/UPGMA/Node.cpp tree/UPGMA/RootedGuideTree.cpp tree/UPGMA/RootedTreeOutput.cpp tree/Tree.cpp tree/ClusterTree.cpp tree/TreeInterface.cpp tree/UnRootedClusterTree.cpp tree/ClusterTreeOutput.cpp tree/RandomGenerator.cpp tree/NJTree.cpp tree/AlignmentSteps.cpp interface/CommandLineParser.cpp substitutionMatrix/SubMatrix.cpp multipleAlign/Iteration.cpp multipleAlign/MSA.cpp multipleAlign/MyersMillerProfileAlign.cpp multipleAlign/ProfileStandard.cpp multipleAlign/ProfileWithSub.cpp multipleAlign/ProfileBase.cpp multipleAlign/LowScoreSegProfile.cpp general/OutputFile.cpp general/UserParameters.cpp general/Utility.cpp general/InvalidCombination.cpp general/DebugLog.cpp general/ClustalWResources.cpp general/VectorOutOfRange.cpp general/SymMatrix.cpp general/Stats.cpp Help.cpp alignment/Alignment.cpp alignment/AlignmentOutput.cpp alignment/ObjectiveScore.cpp alignment/Sequence.cpp Clustal.cpp RClustalWMain.cpp RClustalW.cpp && \
  588. 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 && \
  589. cp libClustalW.a ../../
  590. checking build system type... x86_64-unknown-freebsd11.0
  591. checking host system type... x86_64-unknown-freebsd11.0
  592. checking target system type... x86_64-unknown-freebsd11.0
  593. building for freebsd11.0
  594. checking for a BSD-compatible install... /usr/bin/install -c
  595. checking whether build environment is sane... yes
  596. checking for a thread-safe mkdir -p... ./install-sh -c -d
  597. checking for gawk... no
  598. checking for mawk... no
  599. checking for nawk... nawk
  600. checking whether make sets $(MAKE)... yes
  601. checking whether make sets $(MAKE)... (cached) yes
  602. checking for gcc... gcc
  603. checking whether the C compiler works... yes
  604. checking for C compiler default output file name... a.out
  605. checking for suffix of executables...
  606. checking whether we are cross compiling... no
  607. checking for suffix of object files... o
  608. checking whether we are using the GNU C compiler... yes
  609. checking whether gcc accepts -g... yes
  610. checking for gcc option to accept ISO C89... none needed
  611. checking for style of include used by make... GNU
  612. checking dependency style of gcc... gcc3
  613. checking for g++... g++
  614. checking whether we are using the GNU C++ compiler... yes
  615. checking whether g++ accepts -g... yes
  616. checking dependency style of g++... gcc3
  617. checking for ranlib... ranlib
  618. checking how to run the C++ preprocessor... g++ -E
  619. checking for grep that handles long lines and -e... /usr/bin/grep
  620. checking for egrep... /usr/bin/grep -E
  621. checking for ANSI C header files... yes
  622. checking for sys/types.h... yes
  623. checking for sys/stat.h... yes
  624. checking for stdlib.h... yes
  625. checking for string.h... yes
  626. checking for memory.h... yes
  627. checking for strings.h... yes
  628. checking for inttypes.h... yes
  629. checking for stdint.h... yes
  630. checking for unistd.h... yes
  631. checking for stdbool.h that conforms to C99... yes
  632. checking for _Bool... no
  633. checking for an ANSI C-conforming const... yes
  634. checking for size_t... yes
  635. checking for stdlib.h... (cached) yes
  636. checking for GNU libc compatible malloc... yes
  637. configure: creating ./config.status
  638. config.status: creating Makefile
  639. config.status: creating m4/Makefile
  640. config.status: creating src/Makefile
  641. config.status: creating src/clustalw_version.h
  642. config.status: creating src/config.h
  643. config.status: executing depfiles commands
  644. make[2]: Entering directory '/tmp/RtmpGbVf2R/R.INSTALLa8314cd385fe/msa/src/ClustalW/src'
  645. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c pairwise/FullPairwiseAlign.cpp -o pairwise/FullPairwiseAlign.o
  646. In file included from pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
  647. from pairwise/../alignment/Alignment.h:42,
  648. from pairwise/PairwiseAlignBase.h:10,
  649. from pairwise/FullPairwiseAlign.h:9,
  650. from pairwise/FullPairwiseAlign.cpp:9:
  651. pairwise/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  652. void printInFormat(vector<short>& temp, char* name = "tempfile.out");
  653. ^
  654. pairwise/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  655. void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
  656. ^
  657. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c pairwise/FastPairwiseAlign.cpp -o pairwise/FastPairwiseAlign.o
  658. In file included from pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
  659. from pairwise/../alignment/Alignment.h:42,
  660. from pairwise/PairwiseAlignBase.h:10,
  661. from pairwise/FastPairwiseAlign.h:9,
  662. from pairwise/FastPairwiseAlign.cpp:10:
  663. pairwise/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  664. void printInFormat(vector<short>& temp, char* name = "tempfile.out");
  665. ^
  666. pairwise/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  667. void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
  668. ^
  669. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c fileInput/MSFFileParser.cpp -o fileInput/MSFFileParser.o
  670. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c fileInput/FileReader.cpp -o fileInput/FileReader.o
  671. In file included from fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
  672. from fileInput/../alignment/Alignment.h:42,
  673. from fileInput/FileReader.h:12,
  674. from fileInput/FileReader.cpp:29:
  675. fileInput/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  676. void printInFormat(vector<short>& temp, char* name = "tempfile.out");
  677. ^
  678. fileInput/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  679. void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
  680. ^
  681. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c fileInput/PIRFileParser.cpp -o fileInput/PIRFileParser.o
  682. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c fileInput/RSFFileParser.cpp -o fileInput/RSFFileParser.o
  683. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c fileInput/GDEFileParser.cpp -o fileInput/GDEFileParser.o
  684. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c fileInput/InFileStream.cpp -o fileInput/InFileStream.o
  685. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c fileInput/ClustalFileParser.cpp -o fileInput/ClustalFileParser.o
  686. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c fileInput/PearsonFileParser.cpp -o fileInput/PearsonFileParser.o
  687. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c fileInput/FileParser.cpp -o fileInput/FileParser.o
  688. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c fileInput/EMBLFileParser.cpp -o fileInput/EMBLFileParser.o
  689. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c tree/UPGMA/RootedClusterTree.cpp -o tree/UPGMA/RootedClusterTree.o
  690. In file included from tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0,
  691. from tree/UPGMA/../../alignment/Alignment.h:42,
  692. from tree/UPGMA/../ClusterTree.h:20,
  693. from tree/UPGMA/RootedClusterTree.h:8,
  694. from tree/UPGMA/RootedClusterTree.cpp:9:
  695. tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  696. void printInFormat(vector<short>& temp, char* name = "tempfile.out");
  697. ^
  698. tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  699. void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
  700. ^
  701. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c tree/UPGMA/UPGMAAlgorithm.cpp -o tree/UPGMA/UPGMAAlgorithm.o
  702. In file included from tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0,
  703. from tree/UPGMA/../../alignment/Alignment.h:42,
  704. from tree/UPGMA/RootedGuideTree.h:17,
  705. from tree/UPGMA/UPGMAAlgorithm.h:8,
  706. from tree/UPGMA/UPGMAAlgorithm.cpp:4:
  707. tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  708. void printInFormat(vector<short>& temp, char* name = "tempfile.out");
  709. ^
  710. tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  711. void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
  712. ^
  713. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c tree/UPGMA/Node.cpp -o tree/UPGMA/Node.o
  714. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c tree/UPGMA/RootedGuideTree.cpp -o tree/UPGMA/RootedGuideTree.o
  715. In file included from tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0,
  716. from tree/UPGMA/../../alignment/Alignment.h:42,
  717. from tree/UPGMA/RootedGuideTree.h:17,
  718. from tree/UPGMA/RootedGuideTree.cpp:10:
  719. tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  720. void printInFormat(vector<short>& temp, char* name = "tempfile.out");
  721. ^
  722. tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  723. void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
  724. ^
  725. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c tree/UPGMA/RootedTreeOutput.cpp -o tree/UPGMA/RootedTreeOutput.o
  726. In file included from tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0,
  727. from tree/UPGMA/../../alignment/Alignment.h:42,
  728. from tree/UPGMA/RootedGuideTree.h:17,
  729. from tree/UPGMA/RootedTreeOutput.h:15,
  730. from tree/UPGMA/RootedTreeOutput.cpp:9:
  731. tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  732. void printInFormat(vector<short>& temp, char* name = "tempfile.out");
  733. ^
  734. tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  735. void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
  736. ^
  737. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c tree/Tree.cpp -o tree/Tree.o
  738. In file included from tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
  739. from tree/../alignment/Alignment.h:42,
  740. from tree/Tree.h:13,
  741. from tree/Tree.cpp:10:
  742. tree/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  743. void printInFormat(vector<short>& temp, char* name = "tempfile.out");
  744. ^
  745. tree/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  746. void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
  747. ^
  748. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c tree/ClusterTree.cpp -o tree/ClusterTree.o
  749. In file included from tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
  750. from tree/../alignment/Alignment.h:42,
  751. from tree/ClusterTree.h:20,
  752. from tree/ClusterTree.cpp:9:
  753. tree/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  754. void printInFormat(vector<short>& temp, char* name = "tempfile.out");
  755. ^
  756. tree/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  757. void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
  758. ^
  759. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c tree/TreeInterface.cpp -o tree/TreeInterface.o
  760. In file included from tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
  761. from tree/../alignment/Alignment.h:42,
  762. from tree/TreeInterface.h:19,
  763. from tree/TreeInterface.cpp:15:
  764. tree/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  765. void printInFormat(vector<short>& temp, char* name = "tempfile.out");
  766. ^
  767. tree/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  768. void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
  769. ^
  770. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c tree/UnRootedClusterTree.cpp -o tree/UnRootedClusterTree.o
  771. In file included from tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
  772. from tree/../alignment/Alignment.h:42,
  773. from tree/ClusterTree.h:20,
  774. from tree/UnRootedClusterTree.h:8,
  775. from tree/UnRootedClusterTree.cpp:9:
  776. tree/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  777. void printInFormat(vector<short>& temp, char* name = "tempfile.out");
  778. ^
  779. tree/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  780. void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
  781. ^
  782. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c tree/ClusterTreeOutput.cpp -o tree/ClusterTreeOutput.o
  783. In file included from tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
  784. from tree/../alignment/Alignment.h:42,
  785. from tree/ClusterTreeOutput.h:11,
  786. from tree/ClusterTreeOutput.cpp:9:
  787. tree/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  788. void printInFormat(vector<short>& temp, char* name = "tempfile.out");
  789. ^
  790. tree/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  791. void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
  792. ^
  793. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c tree/RandomGenerator.cpp -o tree/RandomGenerator.o
  794. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c tree/NJTree.cpp -o tree/NJTree.o
  795. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c tree/AlignmentSteps.cpp -o tree/AlignmentSteps.o
  796. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c interface/CommandLineParser.cpp -o interface/CommandLineParser.o
  797. In file included from interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
  798. from interface/../fileInput/../alignment/Alignment.h:42,
  799. from interface/../fileInput/FileReader.h:12,
  800. from interface/../Clustal.h:18,
  801. from interface/CommandLineParser.h:18,
  802. from interface/CommandLineParser.cpp:13:
  803. interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  804. void printInFormat(vector<short>& temp, char* name = "tempfile.out");
  805. ^
  806. interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  807. void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
  808. ^
  809. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c substitutionMatrix/SubMatrix.cpp -o substitutionMatrix/SubMatrix.o
  810. In file included from substitutionMatrix/SubMatrix.cpp:15:0:
  811. substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  812. void printInFormat(vector<short>& temp, char* name = "tempfile.out");
  813. ^
  814. substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  815. void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
  816. ^
  817. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c multipleAlign/Iteration.cpp -o multipleAlign/Iteration.o
  818. In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
  819. from multipleAlign/../alignment/Alignment.h:42,
  820. from multipleAlign/Iteration.h:8,
  821. from multipleAlign/Iteration.cpp:13:
  822. multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  823. void printInFormat(vector<short>& temp, char* name = "tempfile.out");
  824. ^
  825. multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  826. void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
  827. ^
  828. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c multipleAlign/MSA.cpp -o multipleAlign/MSA.o
  829. In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
  830. from multipleAlign/../alignment/Alignment.h:42,
  831. from multipleAlign/ProfileBase.h:14,
  832. from multipleAlign/MSA.h:10,
  833. from multipleAlign/MSA.cpp:16:
  834. multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  835. void printInFormat(vector<short>& temp, char* name = "tempfile.out");
  836. ^
  837. multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  838. void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
  839. ^
  840. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c multipleAlign/MyersMillerProfileAlign.cpp -o multipleAlign/MyersMillerProfileAlign.o
  841. In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
  842. from multipleAlign/../alignment/Alignment.h:42,
  843. from multipleAlign/ProfileAlignAlgorithm.h:10,
  844. from multipleAlign/MyersMillerProfileAlign.h:10,
  845. from multipleAlign/MyersMillerProfileAlign.cpp:10:
  846. multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  847. void printInFormat(vector<short>& temp, char* name = "tempfile.out");
  848. ^
  849. multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  850. void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
  851. ^
  852. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c multipleAlign/ProfileStandard.cpp -o multipleAlign/ProfileStandard.o
  853. In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
  854. from multipleAlign/../alignment/Alignment.h:42,
  855. from multipleAlign/ProfileStandard.h:9,
  856. from multipleAlign/ProfileStandard.cpp:9:
  857. multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  858. void printInFormat(vector<short>& temp, char* name = "tempfile.out");
  859. ^
  860. multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  861. void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
  862. ^
  863. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c multipleAlign/ProfileWithSub.cpp -o multipleAlign/ProfileWithSub.o
  864. In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
  865. from multipleAlign/../alignment/Alignment.h:42,
  866. from multipleAlign/ProfileWithSub.h:9,
  867. from multipleAlign/ProfileWithSub.cpp:9:
  868. multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  869. void printInFormat(vector<short>& temp, char* name = "tempfile.out");
  870. ^
  871. multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  872. void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
  873. ^
  874. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c multipleAlign/ProfileBase.cpp -o multipleAlign/ProfileBase.o
  875. In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
  876. from multipleAlign/../alignment/Alignment.h:42,
  877. from multipleAlign/ProfileBase.h:14,
  878. from multipleAlign/ProfileBase.cpp:9:
  879. multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  880. void printInFormat(vector<short>& temp, char* name = "tempfile.out");
  881. ^
  882. multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  883. void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
  884. ^
  885. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c multipleAlign/LowScoreSegProfile.cpp -o multipleAlign/LowScoreSegProfile.o
  886. In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
  887. from multipleAlign/../alignment/Alignment.h:42,
  888. from multipleAlign/LowScoreSegProfile.h:13,
  889. from multipleAlign/LowScoreSegProfile.cpp:9:
  890. multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  891. void printInFormat(vector<short>& temp, char* name = "tempfile.out");
  892. ^
  893. multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  894. void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
  895. ^
  896. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c general/OutputFile.cpp -o general/OutputFile.o
  897. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c general/UserParameters.cpp -o general/UserParameters.o
  898. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c general/Utility.cpp -o general/Utility.o
  899. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c general/InvalidCombination.cpp -o general/InvalidCombination.o
  900. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c general/DebugLog.cpp -o general/DebugLog.o
  901. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c general/ClustalWResources.cpp -o general/ClustalWResources.o
  902. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c general/VectorOutOfRange.cpp -o general/VectorOutOfRange.o
  903. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c general/SymMatrix.cpp -o general/SymMatrix.o
  904. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c general/Stats.cpp -o general/Stats.o
  905. In file included from general/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
  906. from general/../alignment/Alignment.h:42,
  907. from general/Stats.cpp:15:
  908. general/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  909. void printInFormat(vector<short>& temp, char* name = "tempfile.out");
  910. ^
  911. general/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  912. void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
  913. ^
  914. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c Help.cpp -o Help.o
  915. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c alignment/Alignment.cpp -o alignment/Alignment.o
  916. In file included from alignment/../substitutionMatrix/globalmatrix.h:8:0,
  917. from alignment/Alignment.h:42,
  918. from alignment/Alignment.cpp:25:
  919. alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  920. void printInFormat(vector<short>& temp, char* name = "tempfile.out");
  921. ^
  922. alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  923. void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
  924. ^
  925. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c alignment/AlignmentOutput.cpp -o alignment/AlignmentOutput.o
  926. In file included from alignment/../substitutionMatrix/globalmatrix.h:8:0,
  927. from alignment/Alignment.h:42,
  928. from alignment/AlignmentOutput.h:24,
  929. from alignment/AlignmentOutput.cpp:27:
  930. alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  931. void printInFormat(vector<short>& temp, char* name = "tempfile.out");
  932. ^
  933. alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  934. void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
  935. ^
  936. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c alignment/ObjectiveScore.cpp -o alignment/ObjectiveScore.o
  937. In file included from alignment/../substitutionMatrix/globalmatrix.h:8:0,
  938. from alignment/ObjectiveScore.h:15,
  939. from alignment/ObjectiveScore.cpp:10:
  940. alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  941. void printInFormat(vector<short>& temp, char* name = "tempfile.out");
  942. ^
  943. alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  944. void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
  945. ^
  946. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c alignment/Sequence.cpp -o alignment/Sequence.o
  947. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c Clustal.cpp -o Clustal.o
  948. In file included from fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
  949. from fileInput/../alignment/Alignment.h:42,
  950. from fileInput/FileReader.h:12,
  951. from Clustal.h:18,
  952. from Clustal.cpp:27:
  953. fileInput/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  954. void printInFormat(vector<short>& temp, char* name = "tempfile.out");
  955. ^
  956. fileInput/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  957. void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
  958. ^
  959. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c RClustalWMain.cpp -o RClustalWMain.o
  960. In file included from alignment/../substitutionMatrix/globalmatrix.h:8:0,
  961. from alignment/Alignment.h:42,
  962. from RClustalWMain.cpp:5:
  963. alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  964. void printInFormat(vector<short>& temp, char* name = "tempfile.out");
  965. ^
  966. alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  967. void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
  968. ^
  969. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -DHAVE_CONFIG_H -I. -fpic -g -O2 -c RClustalW.cpp -o RClustalW.o
  970. g++ -shared -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
  971. multipleAlign/Iteration.o: In function `clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)':
  972. /tmp/RtmpGbVf2R/R.INSTALLa8314cd385fe/msa/src/ClustalW/src/multipleAlign/Iteration.cpp:231: warning: warning: tmpnam() possibly used unsafely; consider using mkstemp()
  973. make[2]: Leaving directory '/tmp/RtmpGbVf2R/R.INSTALLa8314cd385fe/msa/src/ClustalW/src'
  974. make[1]: Leaving directory '/tmp/RtmpGbVf2R/R.INSTALLa8314cd385fe/msa/src/ClustalW'
  975. ----------------------------------------
  976. --------------- ClustalW ---------------
  977. ----------------------------------------
  978. --------- Compilation finished ---------
  979. ----------------------------------------
  980. make --file=msaMakefile --directory=ClustalOmega
  981. make[1]: Entering directory '/tmp/RtmpGbVf2R/R.INSTALLa8314cd385fe/msa/src/ClustalOmega'
  982. ./configure `/home/my_user_name/R-3.4.1/bin/Rscript -e "if (Sys.info()['sysname'] == 'Darwin') cat('--without-openmp')"`; \
  983. export PKG_LIBS=" "; \
  984. export PKG_CXXFLAGS=" `/home/my_user_name/R-3.4.1/bin/Rscript -e "if (Sys.info()['sysname'] == 'Darwin') cat('-DMATH_H_CLIB')"` -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
  985. export PKG_CFLAGS=" -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
  986. cd src; \
  987. /home/my_user_name/R-3.4.1/bin/R CMD SHLIB -o libClustalOmega.so exceptions4c/e4c_lite.c argtable2/argtable2.c argtable2/arg_end.c argtable2/arg_rem.c argtable2/arg_lit.c argtable2/arg_int.c argtable2/arg_dbl.c argtable2/arg_str.c argtable2/arg_file.c kmpp/KMeans.cpp kmpp/KmTree.cpp kmpp/KmUtils.cpp clustal/hhalign_wrapper.c clustal/ktuple_pair.c clustal/list.c clustal/log.c clustal/muscle_upgma.c clustal/muscle_tree.c clustal/mbed.c clustal/pair_dist.c clustal/progress.c clustal/seq.c clustal/symmatrix.c clustal/tree.c clustal/util.c clustal/weights.c squid/a2m.c squid/aligneval.c squid/alignio.c squid/clustal.c squid/cluster.c squid/dayhoff.c squid/eps.c squid/file.c squid/getopt.c squid/gki.c squid/gsi.c squid/gsi64.c squid/hsregex.c squid/iupac.c squid/msa.c squid/msf.c squid/phylip.c squid/revcomp.c squid/rk.c squid/selex.c squid/seqencode.c squid/shuffle.c squid/sqerror.c squid/sqio.c squid/squidcore.c squid/sre_ctype.c squid/sre_math.c squid/sre_random.c squid/sre_string.c squid/ssi.c squid/stack.c squid/stockholm.c squid/stopwatch.c squid/translate.c squid/types.c squid/vectorops.c squid/weight.c hhalign/hhalign.cpp RClustalOmega.cpp mymain.c clustal-omega.c && \
  988. 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 && \
  989. cp libClustalOmega.a ../../
  990. configure:
  991.  
  992. Welcome to Clustal Omega - version 1.2.0 (AndreaGiacomo)
  993.  
  994. +NMMMMMMMMMS=
  995. MMMMM? :MMMMM8
  996. IMMMMS MMMMM,
  997. ~MMMMN ,MMMMM
  998. =MMMMM MMMMM
  999. ?MMMMM +MMMMM
  1000. MMMMMS MMMMM
  1001. MMMMM MMMMM:
  1002. MMMMM MMMMM+
  1003. MMMMM MMMMM~
  1004. MMMMM MMMMM
  1005. MMMMMZ MMMMM
  1006. MMMMM ,MMMMZ
  1007. MMMM8 MMMM+
  1008. MMMMS MMMM,
  1009. MMMMO MMMM
  1010. ,N SMMM MMM8 +8
  1011. ,M7 M+ M+ :M8
  1012. ,MMMMMMMMMMMMI MMMMMMMMMMMM8
  1013. ,MMMMMMMMMMMM8 MMMMMMMMMMMM8
  1014. ,MMMMMMMMMMMMN MMMMMMMMMMMM8
  1015.  
  1016.  
  1017. checking for a BSD-compatible install... /usr/bin/install -c
  1018. checking whether build environment is sane... yes
  1019. checking for a thread-safe mkdir -p... ./install-sh -c -d
  1020. checking for gawk... no
  1021. checking for mawk... no
  1022. checking for nawk... nawk
  1023. checking whether make sets $(MAKE)... yes
  1024. checking for style of include used by make... GNU
  1025. checking for gcc... gcc
  1026. checking whether the C compiler works... yes
  1027. checking for C compiler default output file name... a.out
  1028. checking for suffix of executables...
  1029. checking whether we are cross compiling... no
  1030. checking for suffix of object files... o
  1031. checking whether we are using the GNU C compiler... yes
  1032. checking whether gcc accepts -g... yes
  1033. checking for gcc option to accept ISO C89... none needed
  1034. checking dependency style of gcc... gcc3
  1035. checking how to run the C preprocessor... gcc -E
  1036. checking for grep that handles long lines and -e... /usr/bin/grep
  1037. checking for egrep... /usr/bin/grep -E
  1038. checking for ANSI C header files... yes
  1039. checking for sys/types.h... yes
  1040. checking for sys/stat.h... yes
  1041. checking for stdlib.h... yes
  1042. checking for string.h... yes
  1043. checking for memory.h... yes
  1044. checking for strings.h... yes
  1045. checking for inttypes.h... yes
  1046. checking for stdint.h... yes
  1047. checking for unistd.h... yes
  1048. checking minix/config.h usability... no
  1049. checking minix/config.h presence... no
  1050. checking for minix/config.h... no
  1051. checking whether it is safe to define __EXTENSIONS__... yes
  1052. checking build system type... x86_64-unknown-freebsd11.0
  1053. checking host system type... x86_64-unknown-freebsd11.0
  1054. checking whether make sets $(MAKE)... (cached) yes
  1055. checking for a sed that does not truncate output... /usr/bin/sed
  1056. checking for fgrep... /usr/bin/grep -F
  1057. checking for ld used by gcc... /usr/local/bin/ld
  1058. checking if the linker (/usr/local/bin/ld) is GNU ld... yes
  1059. checking for BSD- or MS-compatible name lister (nm)... /usr/local/bin/nm -B
  1060. checking the name lister (/usr/local/bin/nm -B) interface... BSD nm
  1061. checking whether ln -s works... yes
  1062. checking the maximum length of command line arguments... 196608
  1063. checking whether the shell understands some XSI constructs... yes
  1064. checking whether the shell understands "+="... no
  1065. checking for /usr/local/bin/ld option to reload object files... -r
  1066. checking for objdump... objdump
  1067. checking how to recognize dependent libraries... pass_all
  1068. checking for ar... ar
  1069. checking for strip... strip
  1070. checking for ranlib... ranlib
  1071. checking command to parse /usr/local/bin/nm -B output from gcc object... ok
  1072. checking for dlfcn.h... yes
  1073. checking for objdir... .libs
  1074. checking if gcc supports -fno-rtti -fno-exceptions... no
  1075. checking for gcc option to produce PIC... -fPIC -DPIC
  1076. checking if gcc PIC flag -fPIC -DPIC works... yes
  1077. checking if gcc static flag -static works... yes
  1078. checking if gcc supports -c -o file.o... yes
  1079. checking if gcc supports -c -o file.o... (cached) yes
  1080. checking whether the gcc linker (/usr/local/bin/ld) supports shared libraries... yes
  1081. checking whether -lc should be explicitly linked in... no
  1082. checking dynamic linker characteristics... no
  1083. checking how to hardcode library paths into programs... immediate
  1084. checking whether stripping libraries is possible... no
  1085. checking if libtool supports shared libraries... no
  1086. checking whether to build shared libraries... no
  1087. checking whether to build static libraries... yes
  1088. checking for gcc... (cached) gcc
  1089. checking whether we are using the GNU C compiler... (cached) yes
  1090. checking whether gcc accepts -g... (cached) yes
  1091. checking for gcc option to accept ISO C89... (cached) none needed
  1092. checking dependency style of gcc... (cached) gcc3
  1093. checking how to run the C preprocessor... gcc -E
  1094. checking for g++... g++
  1095. checking whether we are using the GNU C++ compiler... yes
  1096. checking whether g++ accepts -g... yes
  1097. checking dependency style of g++... gcc3
  1098. checking whether we are using the GNU C++ compiler... (cached) yes
  1099. checking whether g++ accepts -g... (cached) yes
  1100. checking dependency style of g++... (cached) gcc3
  1101. checking how to run the C++ preprocessor... g++ -E
  1102. checking for ld used by g++... /usr/local/bin/ld
  1103. checking if the linker (/usr/local/bin/ld) is GNU ld... yes
  1104. checking whether the g++ linker (/usr/local/bin/ld) supports shared libraries... no
  1105. checking for g++ option to produce PIC... -fPIC -DPIC
  1106. checking if g++ PIC flag -fPIC -DPIC works... yes
  1107. checking if g++ static flag -static works... yes
  1108. checking if g++ supports -c -o file.o... yes
  1109. checking if g++ supports -c -o file.o... (cached) yes
  1110. checking whether the g++ linker (/usr/local/bin/ld) supports shared libraries... no
  1111. checking dynamic linker characteristics... no
  1112. checking how to hardcode library paths into programs... immediate
  1113. checking how to run the C++ preprocessor... g++ -E
  1114. checking for ANSI C header files... (cached) yes
  1115. checking assert.h usability... yes
  1116. checking assert.h presence... yes
  1117. checking for assert.h... yes
  1118. checking ctype.h usability... yes
  1119. checking ctype.h presence... yes
  1120. checking for ctype.h... yes
  1121. checking float.h usability... yes
  1122. checking float.h presence... yes
  1123. checking for float.h... yes
  1124. checking limits.h usability... yes
  1125. checking limits.h presence... yes
  1126. checking for limits.h... yes
  1127. checking math.h usability... yes
  1128. checking math.h presence... yes
  1129. checking for math.h... yes
  1130. checking for memory.h... (cached) yes
  1131. checking stdarg.h usability... yes
  1132. checking stdarg.h presence... yes
  1133. checking for stdarg.h... yes
  1134. checking stdio.h usability... yes
  1135. checking stdio.h presence... yes
  1136. checking for stdio.h... yes
  1137. checking for stdlib.h... (cached) yes
  1138. checking for string.h... (cached) yes
  1139. checking time.h usability... yes
  1140. checking time.h presence... yes
  1141. checking for time.h... yes
  1142. checking for unistd.h... (cached) yes
  1143. checking for an ANSI C-conforming const... yes
  1144. checking for size_t... yes
  1145. checking for inline... inline
  1146. checking for log in -lm... yes
  1147. checking for log2 in -lm... yes
  1148. checking for OpenMP flag of C compiler... -fopenmp
  1149. checking whether byte ordering is bigendian... no
  1150. checking for ntohs... yes
  1151. checking for ntohl... yes
  1152. checking for ntons... no
  1153. checking for ntonl... no
  1154. checking size of unsigned short... 2
  1155. checking size of unsigned int... 4
  1156. checking size of unsigned long... 8
  1157. checking size of unsigned long long... 8
  1158. checking for stroul... no
  1159. checking for strtoull... yes
  1160. checking for ftello... yes
  1161. checking for fseeko... yes
  1162. checking for ftello64... no
  1163. checking for fseeko64... no
  1164. checking for ftell64... no
  1165. checking for fseek64... no
  1166. checking for off_t... yes
  1167. checking size of fpos_t... 8
  1168. checking if malloc debugging is wanted... no
  1169. checking whether to build with debug information... no
  1170. configure: creating ./config.status
  1171. config.status: creating Makefile
  1172. config.status: creating src/Makefile
  1173. config.status: creating clustalo.pc
  1174. config.status: creating Doxyfile
  1175. config.status: creating src/exceptions4c/Makefile
  1176. config.status: creating src/clustal/Makefile
  1177. config.status: creating src/hhalign/Makefile
  1178. config.status: creating src/kmpp/Makefile
  1179. config.status: creating src/squid/Makefile
  1180. config.status: creating src/argtable2/Makefile
  1181. config.status: creating src/config.h
  1182. config.status: executing src/clustal-omega-config.h commands
  1183. config.status: creating src/clustal-omega-config.h - prefix CLUSTAL_OMEGA for src/config.h defines
  1184. config.status: executing depfiles commands
  1185. config.status: executing libtool commands
  1186. make[2]: Entering directory '/tmp/RtmpGbVf2R/R.INSTALLa8314cd385fe/msa/src/ClustalOmega/src'
  1187. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c exceptions4c/e4c_lite.c -o exceptions4c/e4c_lite.o
  1188. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c argtable2/argtable2.c -o argtable2/argtable2.o
  1189. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c argtable2/arg_end.c -o argtable2/arg_end.o
  1190. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c argtable2/arg_rem.c -o argtable2/arg_rem.o
  1191. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c argtable2/arg_lit.c -o argtable2/arg_lit.o
  1192. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c argtable2/arg_int.c -o argtable2/arg_int.o
  1193. argtable2/arg_int.c: In function 'strtol0X':
  1194. argtable2/arg_int.c:60:12: warning: implicit declaration of function 'isspace' [-Wimplicit-function-declaration]
  1195. while (isspace(*ptr))
  1196. ^
  1197. argtable2/arg_int.c:89:8: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration]
  1198. if (toupper(*ptr++)!=toupper(X))
  1199. ^
  1200. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c argtable2/arg_dbl.c -o argtable2/arg_dbl.o
  1201. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c argtable2/arg_str.c -o argtable2/arg_str.o
  1202. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c argtable2/arg_file.c -o argtable2/arg_file.o
  1203. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c kmpp/KMeans.cpp -o kmpp/KMeans.o
  1204. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c kmpp/KmTree.cpp -o kmpp/KmTree.o
  1205. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c kmpp/KmUtils.cpp -o kmpp/KmUtils.o
  1206. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c clustal/hhalign_wrapper.c -o clustal/hhalign_wrapper.o
  1207. In file included from clustal/hhalign_wrapper.c:22:0:
  1208. ./config.h:132:0: warning: "NDEBUG" redefined
  1209. #define NDEBUG /**/
  1210. ^
  1211. <command-line>:0:0: note: this is the location of the previous definition
  1212. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c clustal/ktuple_pair.c -o clustal/ktuple_pair.o
  1213. In file included from clustal/ktuple_pair.c:29:0:
  1214. ./config.h:132:0: warning: "NDEBUG" redefined
  1215. #define NDEBUG /**/
  1216. ^
  1217. <command-line>:0:0: note: this is the location of the previous definition
  1218. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c clustal/list.c -o clustal/list.o
  1219. In file included from clustal/list.c:32:0:
  1220. ./config.h:132:0: warning: "NDEBUG" redefined
  1221. #define NDEBUG /**/
  1222. ^
  1223. <command-line>:0:0: note: this is the location of the previous definition
  1224. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c clustal/log.c -o clustal/log.o
  1225. In file included from clustal/log.c:22:0:
  1226. ./config.h:132:0: warning: "NDEBUG" redefined
  1227. #define NDEBUG /**/
  1228. ^
  1229. <command-line>:0:0: note: this is the location of the previous definition
  1230. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c clustal/muscle_upgma.c -o clustal/muscle_upgma.o
  1231. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c clustal/muscle_tree.c -o clustal/muscle_tree.o
  1232. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c clustal/mbed.c -o clustal/mbed.o
  1233. In file included from clustal/mbed.c:28:0:
  1234. ./config.h:132:0: warning: "NDEBUG" redefined
  1235. #define NDEBUG /**/
  1236. ^
  1237. <command-line>:0:0: note: this is the location of the previous definition
  1238. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c clustal/pair_dist.c -o clustal/pair_dist.o
  1239. In file included from clustal/pair_dist.c:22:0:
  1240. ./config.h:132:0: warning: "NDEBUG" redefined
  1241. #define NDEBUG /**/
  1242. ^
  1243. <command-line>:0:0: note: this is the location of the previous definition
  1244. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c clustal/progress.c -o clustal/progress.o
  1245. In file included from clustal/progress.c:22:0:
  1246. ./config.h:132:0: warning: "NDEBUG" redefined
  1247. #define NDEBUG /**/
  1248. ^
  1249. <command-line>:0:0: note: this is the location of the previous definition
  1250. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c clustal/seq.c -o clustal/seq.o
  1251. In file included from clustal/seq.c:30:0:
  1252. ./config.h:132:0: warning: "NDEBUG" redefined
  1253. #define NDEBUG /**/
  1254. ^
  1255. <command-line>:0:0: note: this is the location of the previous definition
  1256. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c clustal/symmatrix.c -o clustal/symmatrix.o
  1257. In file included from clustal/symmatrix.c:30:0:
  1258. ./config.h:132:0: warning: "NDEBUG" redefined
  1259. #define NDEBUG /**/
  1260. ^
  1261. <command-line>:0:0: note: this is the location of the previous definition
  1262. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c clustal/tree.c -o clustal/tree.o
  1263. In file included from clustal/tree.c:22:0:
  1264. ./config.h:132:0: warning: "NDEBUG" redefined
  1265. #define NDEBUG /**/
  1266. ^
  1267. <command-line>:0:0: note: this is the location of the previous definition
  1268. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c clustal/util.c -o clustal/util.o
  1269. In file included from clustal/util.c:22:0:
  1270. ./config.h:132:0: warning: "NDEBUG" redefined
  1271. #define NDEBUG /**/
  1272. ^
  1273. <command-line>:0:0: note: this is the location of the previous definition
  1274. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c clustal/weights.c -o clustal/weights.o
  1275. In file included from clustal/weights.c:72:0:
  1276. ./config.h:132:0: warning: "NDEBUG" redefined
  1277. #define NDEBUG /**/
  1278. ^
  1279. <command-line>:0:0: note: this is the location of the previous definition
  1280. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/a2m.c -o squid/a2m.o
  1281. In file included from squid/squid.h:32:0,
  1282. from squid/a2m.c:20:
  1283. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1284. #define NDEBUG /**/
  1285. ^
  1286. <command-line>:0:0: note: this is the location of the previous definition
  1287. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/aligneval.c -o squid/aligneval.o
  1288. In file included from squid/squid.h:32:0,
  1289. from squid/aligneval.c:59:
  1290. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1291. #define NDEBUG /**/
  1292. ^
  1293. <command-line>:0:0: note: this is the location of the previous definition
  1294. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/alignio.c -o squid/alignio.o
  1295. In file included from squid/squid.h:32:0,
  1296. from squid/alignio.c:21:
  1297. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1298. #define NDEBUG /**/
  1299. ^
  1300. <command-line>:0:0: note: this is the location of the previous definition
  1301. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/clustal.c -o squid/clustal.o
  1302. In file included from squid/squid.h:32:0,
  1303. from squid/clustal.c:24:
  1304. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1305. #define NDEBUG /**/
  1306. ^
  1307. <command-line>:0:0: note: this is the location of the previous definition
  1308. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/cluster.c -o squid/cluster.o
  1309. In file included from squid/squid.h:32:0,
  1310. from squid/cluster.c:124:
  1311. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1312. #define NDEBUG /**/
  1313. ^
  1314. <command-line>:0:0: note: this is the location of the previous definition
  1315. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/dayhoff.c -o squid/dayhoff.o
  1316. In file included from squid/squid.h:32:0,
  1317. from squid/dayhoff.c:28:
  1318. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1319. #define NDEBUG /**/
  1320. ^
  1321. <command-line>:0:0: note: this is the location of the previous definition
  1322. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/eps.c -o squid/eps.o
  1323. In file included from squid/squid.h:32:0,
  1324. from squid/eps.c:23:
  1325. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1326. #define NDEBUG /**/
  1327. ^
  1328. <command-line>:0:0: note: this is the location of the previous definition
  1329. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/file.c -o squid/file.o
  1330. In file included from squid/squid.h:32:0,
  1331. from squid/file.c:28:
  1332. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1333. #define NDEBUG /**/
  1334. ^
  1335. <command-line>:0:0: note: this is the location of the previous definition
  1336. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/getopt.c -o squid/getopt.o
  1337. In file included from squid/squid.h:32:0,
  1338. from squid/getopt.c:17:
  1339. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1340. #define NDEBUG /**/
  1341. ^
  1342. <command-line>:0:0: note: this is the location of the previous definition
  1343. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/gki.c -o squid/gki.o
  1344. In file included from squid/squid.h:32:0,
  1345. from squid/gki.c:82:
  1346. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1347. #define NDEBUG /**/
  1348. ^
  1349. <command-line>:0:0: note: this is the location of the previous definition
  1350. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/gsi.c -o squid/gsi.o
  1351. In file included from squid/squid.h:32:0,
  1352. from squid/gsi.c:35:
  1353. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1354. #define NDEBUG /**/
  1355. ^
  1356. <command-line>:0:0: note: this is the location of the previous definition
  1357. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/gsi64.c -o squid/gsi64.o
  1358. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/hsregex.c -o squid/hsregex.o
  1359. In file included from squid/squid.h:32:0,
  1360. from squid/hsregex.c:33:
  1361. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1362. #define NDEBUG /**/
  1363. ^
  1364. <command-line>:0:0: note: this is the location of the previous definition
  1365. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/iupac.c -o squid/iupac.o
  1366. In file included from squid/squid.h:32:0,
  1367. from squid/iupac.c:17:
  1368. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1369. #define NDEBUG /**/
  1370. ^
  1371. <command-line>:0:0: note: this is the location of the previous definition
  1372. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/msa.c -o squid/msa.o
  1373. In file included from squid/squid.h:32:0,
  1374. from squid/msa.c:22:
  1375. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1376. #define NDEBUG /**/
  1377. ^
  1378. <command-line>:0:0: note: this is the location of the previous definition
  1379. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/msf.c -o squid/msf.o
  1380. In file included from squid/squid.h:32:0,
  1381. from squid/msf.c:25:
  1382. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1383. #define NDEBUG /**/
  1384. ^
  1385. <command-line>:0:0: note: this is the location of the previous definition
  1386. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/phylip.c -o squid/phylip.o
  1387. In file included from squid/squid.h:32:0,
  1388. from squid/phylip.c:23:
  1389. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1390. #define NDEBUG /**/
  1391. ^
  1392. <command-line>:0:0: note: this is the location of the previous definition
  1393. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/revcomp.c -o squid/revcomp.o
  1394. In file included from squid/squid.h:32:0,
  1395. from squid/revcomp.c:19:
  1396. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1397. #define NDEBUG /**/
  1398. ^
  1399. <command-line>:0:0: note: this is the location of the previous definition
  1400. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/rk.c -o squid/rk.o
  1401. In file included from squid/squid.h:32:0,
  1402. from squid/rk.c:26:
  1403. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1404. #define NDEBUG /**/
  1405. ^
  1406. <command-line>:0:0: note: this is the location of the previous definition
  1407. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/selex.c -o squid/selex.o
  1408. In file included from squid/squid.h:32:0,
  1409. from squid/selex.c:43:
  1410. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1411. #define NDEBUG /**/
  1412. ^
  1413. <command-line>:0:0: note: this is the location of the previous definition
  1414. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/seqencode.c -o squid/seqencode.o
  1415. In file included from squid/squid.h:32:0,
  1416. from squid/seqencode.c:18:
  1417. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1418. #define NDEBUG /**/
  1419. ^
  1420. <command-line>:0:0: note: this is the location of the previous definition
  1421. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/shuffle.c -o squid/shuffle.o
  1422. In file included from squid/squid.h:32:0,
  1423. from squid/shuffle.c:42:
  1424. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1425. #define NDEBUG /**/
  1426. ^
  1427. <command-line>:0:0: note: this is the location of the previous definition
  1428. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/sqerror.c -o squid/sqerror.o
  1429. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/sqio.c -o squid/sqio.o
  1430. In file included from squid/squid.h:32:0,
  1431. from squid/sqio.c:57:
  1432. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1433. #define NDEBUG /**/
  1434. ^
  1435. <command-line>:0:0: note: this is the location of the previous definition
  1436. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/squidcore.c -o squid/squidcore.o
  1437. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/sre_ctype.c -o squid/sre_ctype.o
  1438. In file included from squid/squid.h:32:0,
  1439. from squid/sre_ctype.c:19:
  1440. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1441. #define NDEBUG /**/
  1442. ^
  1443. <command-line>:0:0: note: this is the location of the previous definition
  1444. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/sre_math.c -o squid/sre_math.o
  1445. In file included from squid/squid.h:32:0,
  1446. from squid/sre_math.c:19:
  1447. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1448. #define NDEBUG /**/
  1449. ^
  1450. <command-line>:0:0: note: this is the location of the previous definition
  1451. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/sre_random.c -o squid/sre_random.o
  1452. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/sre_string.c -o squid/sre_string.o
  1453. In file included from squid/squid.h:32:0,
  1454. from squid/sre_string.c:23:
  1455. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1456. #define NDEBUG /**/
  1457. ^
  1458. <command-line>:0:0: note: this is the location of the previous definition
  1459. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/ssi.c -o squid/ssi.o
  1460. In file included from squid/squid.h:32:0,
  1461. from squid/ssi.c:16:
  1462. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1463. #define NDEBUG /**/
  1464. ^
  1465. <command-line>:0:0: note: this is the location of the previous definition
  1466. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/stack.c -o squid/stack.o
  1467. In file included from squid/squid.h:32:0,
  1468. from squid/stack.c:18:
  1469. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1470. #define NDEBUG /**/
  1471. ^
  1472. <command-line>:0:0: note: this is the location of the previous definition
  1473. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/stockholm.c -o squid/stockholm.o
  1474. In file included from squid/squid.h:32:0,
  1475. from squid/stockholm.c:31:
  1476. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1477. #define NDEBUG /**/
  1478. ^
  1479. <command-line>:0:0: note: this is the location of the previous definition
  1480. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/stopwatch.c -o squid/stopwatch.o
  1481. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/translate.c -o squid/translate.o
  1482. In file included from squid/squid.h:32:0,
  1483. from squid/translate.c:19:
  1484. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1485. #define NDEBUG /**/
  1486. ^
  1487. <command-line>:0:0: note: this is the location of the previous definition
  1488. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/types.c -o squid/types.o
  1489. In file included from squid/squid.h:32:0,
  1490. from squid/types.c:20:
  1491. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1492. #define NDEBUG /**/
  1493. ^
  1494. <command-line>:0:0: note: this is the location of the previous definition
  1495. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/vectorops.c -o squid/vectorops.o
  1496. gcc -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c squid/weight.c -o squid/weight.o
  1497. In file included from squid/squid.h:32:0,
  1498. from squid/weight.c:19:
  1499. squid/../config.h:132:0: warning: "NDEBUG" redefined
  1500. #define NDEBUG /**/
  1501. ^
  1502. <command-line>:0:0: note: this is the location of the previous definition
  1503. g++ -I/home/my_user_name/R-3.4.1/include -DNDEBUG -I"/usr/home/my_user_name/R-3.4.1/library/Rcpp/include" -I/usr/local/include -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic -g -O2 -c hhalign/hhalign.cpp -o hhalign/hhalign.o
  1504. In file included from hhalign/hhalign.cpp:78:0:
  1505. hhalign/hhhit-C.h: In member function 'int Hit::Forward(HMM&, HMM&, float**)':
  1506. hhalign/hhhit-C.h:736:20: error: 'isnan' was not declared in this scope
  1507. if (isnan(score) || isinf(score) || isnan(Pforward) || isinf(Pforward) ){
  1508. ^
  1509. hhalign/hhhit-C.h:736:20: note: suggested alternative:
  1510. In file included from hhalign/hhalign.cpp:43:0:
  1511. /usr/local/lib/gcc5/include/c++/cmath:862:5: note: 'std::isnan'
  1512. isnan(_Tp __f)
  1513. ^
  1514. In file included from hhalign/hhalign.cpp:78:0:
  1515. hhalign/hhhit-C.h:736:36: error: 'isinf' was not declared in this scope
  1516. if (isnan(score) || isinf(score) || isnan(Pforward) || isinf(Pforward) ){
  1517. ^
  1518. hhalign/hhhit-C.h:736:36: note: suggested alternative:
  1519. In file included from hhalign/hhalign.cpp:43:0:
  1520. /usr/local/lib/gcc5/include/c++/cmath:853:5: note: 'std::isinf'
  1521. isinf(_Tp __f)
  1522. ^
  1523. In file included from hhalign/hhalign.cpp:78:0:
  1524. hhalign/hhhit-C.h:748:69: error: 'isinf' was not declared in this scope
  1525. if (isinf(F_MM[i][j]+F_MI[i][j]+F_IM[i][j]+F_DG[i][j]+F_GD[i][j])){
  1526. ^
  1527. hhalign/hhhit-C.h:748:69: note: suggested alternative:
  1528. In file included from hhalign/hhalign.cpp:43:0:
  1529. /usr/local/lib/gcc5/include/c++/cmath:853:5: note: 'std::isinf'
  1530. isinf(_Tp __f)
  1531. ^
  1532. In file included from hhalign/hhalign.cpp:78:0:
  1533. hhalign/hhhit-C.h: In member function 'int Hit::Backward(HMM&, HMM&)':
  1534. hhalign/hhhit-C.h:917:20: error: 'isnan' was not declared in this scope
  1535. if (isnan(score) || isinf(score)){
  1536. ^
  1537. hhalign/hhhit-C.h:917:20: note: suggested alternative:
  1538. In file included from hhalign/hhalign.cpp:43:0:
  1539. /usr/local/lib/gcc5/include/c++/cmath:862:5: note: 'std::isnan'
  1540. isnan(_Tp __f)
  1541. ^
  1542. In file included from hhalign/hhalign.cpp:78:0:
  1543. hhalign/hhhit-C.h:917:36: error: 'isinf' was not declared in this scope
  1544. if (isnan(score) || isinf(score)){
  1545. ^
  1546. hhalign/hhhit-C.h:917:36: note: suggested alternative:
  1547. In file included from hhalign/hhalign.cpp:43:0:
  1548. /usr/local/lib/gcc5/include/c++/cmath:853:5: note: 'std::isinf'
  1549. isinf(_Tp __f)
  1550. ^
  1551. In file included from hhalign/hhalign.cpp:78:0:
  1552. hhalign/hhhit-C.h:923:69: error: 'isinf' was not declared in this scope
  1553. if (isinf(B_MM[i][j]+B_MI[i][j]+B_IM[i][j]+B_DG[i][j]+B_GD[i][j])){
  1554. ^
  1555. hhalign/hhhit-C.h:923:69: note: suggested alternative:
  1556. In file included from hhalign/hhalign.cpp:43:0:
  1557. /usr/local/lib/gcc5/include/c++/cmath:853:5: note: 'std::isinf'
  1558. isinf(_Tp __f)
  1559. ^
  1560. hhalign/hhalign.cpp: In function 'int hhalign(char**, int, double*, char**, int, double*, double*, hmm_light*, char*, char*, char*, char*, hhalign_para, hhalign_scores*, int, int, char*, char*)':
  1561. hhalign/hhalign.cpp:1101:39: error: 'isnan' was not declared in this scope
  1562. if ((isnan(hit.score)) || (isnan(hit.Pforward))){
  1563. ^
  1564. hhalign/hhalign.cpp:1101:39: note: suggested alternative:
  1565. In file included from hhalign/hhalign.cpp:43:0:
  1566. /usr/local/lib/gcc5/include/c++/cmath:862:5: note: 'std::isnan'
  1567. isnan(_Tp __f)
  1568. ^
  1569. hhalign/hhalign.cpp:1105:39: error: 'isnan' was not declared in this scope
  1570. if ((isnan(hit.score)) || (isnan(hit.Pforward))){
  1571. ^
  1572. hhalign/hhalign.cpp:1105:39: note: suggested alternative:
  1573. In file included from hhalign/hhalign.cpp:43:0:
  1574. /usr/local/lib/gcc5/include/c++/cmath:862:5: note: 'std::isnan'
  1575. isnan(_Tp __f)
  1576. ^
  1577. make[2]: *** [/home/my_user_name/R-3.4.1/etc/Makeconf:166: hhalign/hhalign.o] Error 1
  1578. make[2]: Leaving directory '/tmp/RtmpGbVf2R/R.INSTALLa8314cd385fe/msa/src/ClustalOmega/src'
  1579. make[1]: *** [msaMakefile:48: clustalomega] Error 1
  1580. make[1]: Leaving directory '/tmp/RtmpGbVf2R/R.INSTALLa8314cd385fe/msa/src/ClustalOmega'
  1581. make: *** [Makevars:36: build_clustalomega] Error 2
  1582. ERROR: compilation failed for package 'msa'
  1583. * removing '/usr/home/my_user_name/R-3.4.1/library/msa'
  1584.  
  1585. The downloaded source packages are in
  1586. '/tmp/RtmpkMKv88/downloaded_packages'
  1587. Old packages: 'tibble'
  1588. Warning message:
  1589. In install.packages(pkgs = doing, lib = lib, ...) :
  1590. installation of package 'msa' had non-zero exit status
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