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  1. R version 4.0.1 (2020-06-06) -- "See Things Now"
  2. Copyright (C) 2020 The R Foundation for Statistical Computing
  3. Platform: x86_64-pc-linux-gnu (64-bit)
  4.  
  5. R is free software and comes with ABSOLUTELY NO WARRANTY.
  6. You are welcome to redistribute it under certain conditions.
  7. Type 'license()' or 'licence()' for distribution details.
  8.  
  9.   Natural language support but running in an English locale
  10.  
  11. R is a collaborative project with many contributors.
  12. Type 'contributors()' for more information and
  13. 'citation()' on how to cite R or R packages in publications.
  14.  
  15. Type 'demo()' for some demos, 'help()' for on-line help, or
  16. 'help.start()' for an HTML browser interface to help.
  17. Type 'q()' to quit R.
  18.  
  19. > library(BiocManager)
  20. Bioconductor version 3.11 (BiocManager 1.30.10), ?BiocManager::install for help
  21. > BiocManager::install('msa')
  22. Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06)
  23. Installing package(s) 'msa'
  24. trying URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/msa_1.20.0.tar.gz'
  25. Content type 'application/x-gzip' length 3767459 bytes (3.6 MB)
  26. ==================================================
  27. downloaded 3.6 MB
  28.  
  29. * installing *source* package ‘msa’ ...
  30. ** using staged installation
  31. ** libs
  32. g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG  -I'/home/freddie/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -D_FORTIFY_SOURCE=2  -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c R_init_msa.cpp -o R_init_msa.o
  33. In file included from ./Muscle/RMuscle.h:4,
  34.                  from R_init_msa.cpp:3:
  35. ./Muscle/muscle.h:54: warning: "assert" redefined
  36.    54 | #define assert(exp)     ((void)0)
  37.       |
  38. In file included from /usr/include/c++/10.1.0/cassert:44,
  39.                  from /home/freddie/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp/utils/tinyformat/tinyformat.h:137,
  40.                  from /home/freddie/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp/utils/tinyformat.h:40,
  41.                  from /home/freddie/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/RcppCommon.h:70,
  42.                  from /home/freddie/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp.h:27,
  43.                  from ./ClustalOmega/src/RClustalOmega.h:4,
  44.                  from R_init_msa.cpp:1:
  45. /usr/include/assert.h:50: note: this is the location of the previous definition
  46.    50 | # define assert(expr)  (__ASSERT_VOID_CAST (0))
  47.       |
  48. g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG  -I'/home/freddie/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -D_FORTIFY_SOURCE=2  -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c SplitCharVector2List.cpp -o SplitCharVector2List.o
  49. g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG  -I'/home/freddie/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -D_FORTIFY_SOURCE=2  -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c SplitCharVector2Matrix.cpp -o SplitCharVector2Matrix.o
  50. make --file=msaMakefile --directory=gc-7.2
  51. make[1]: Entering directory '/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2'
  52. ./configure --enable-cplusplus --enable-threads=pthreads --enable-shared --with-pic
  53. checking build system type... x86_64-unknown-linux-gnu
  54. checking host system type... x86_64-unknown-linux-gnu
  55. checking target system type... x86_64-unknown-linux-gnu
  56. checking GC version numbers... major=7 minor=2
  57. checking for a BSD-compatible install... /usr/bin/install -c
  58. checking whether build environment is sane... yes
  59. checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
  60. checking for gawk... gawk
  61. checking whether make sets $(MAKE)... yes
  62. checking whether make supports nested variables... yes
  63. checking whether to enable maintainer-specific portions of Makefiles... no
  64. checking for style of include used by make... GNU
  65. checking for gcc... gcc
  66. checking whether the C compiler works... yes
  67. checking for C compiler default output file name... a.out
  68. checking for suffix of executables...
  69. checking whether we are cross compiling... no
  70. checking for suffix of object files... o
  71. checking whether we are using the GNU C compiler... yes
  72. checking whether gcc accepts -g... yes
  73. checking for gcc option to accept ISO C89... none needed
  74. checking whether gcc understands -c and -o together... yes
  75. checking dependency style of gcc... gcc3
  76. checking for g++... g++
  77. checking whether we are using the GNU C++ compiler... yes
  78. checking whether g++ accepts -g... yes
  79. checking dependency style of g++... gcc3
  80. checking dependency style of gcc... gcc3
  81. checking for inline... inline
  82. checking for pthread_self in -lpthread... yes
  83. configure: WARNING: "Explicit GC_INIT() calls may be required."
  84. checking for xlc... no
  85. checking whether gcc supports -fno-strict-aliasing... yes
  86. checking for dlopen in -ldl... yes
  87. checking whether to build shared libraries... yes
  88. checking which machine-dependent code should be used...
  89. checking how to print strings... printf
  90. checking for a sed that does not truncate output... /usr/bin/sed
  91. checking for grep that handles long lines and -e... /usr/bin/grep
  92. checking for egrep... /usr/bin/grep -E
  93. checking for fgrep... /usr/bin/grep -F
  94. checking for ld used by gcc... /usr/bin/ld
  95. checking if the linker (/usr/bin/ld) is GNU ld... yes
  96. checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
  97. checking the name lister (/usr/bin/nm -B) interface... BSD nm
  98. checking whether ln -s works... yes
  99. checking the maximum length of command line arguments... 1572864
  100. checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
  101. checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
  102. checking for /usr/bin/ld option to reload object files... -r
  103. checking for objdump... objdump
  104. checking how to recognize dependent libraries... pass_all
  105. checking for dlltool... no
  106. checking how to associate runtime and link libraries... printf %s\n
  107. checking for ar... ar
  108. checking for archiver @FILE support... @
  109. checking for strip... strip
  110. checking for ranlib... ranlib
  111. checking command to parse /usr/bin/nm -B output from gcc object... ok
  112. checking for sysroot... no
  113. checking for mt... no
  114. checking if : is a manifest tool... no
  115. checking how to run the C preprocessor... gcc -E
  116. checking for ANSI C header files... yes
  117. checking for sys/types.h... yes
  118. checking for sys/stat.h... yes
  119. checking for stdlib.h... yes
  120. checking for string.h... yes
  121. checking for memory.h... yes
  122. checking for strings.h... yes
  123. checking for inttypes.h... yes
  124. checking for stdint.h... yes
  125. checking for unistd.h... yes
  126. checking for dlfcn.h... yes
  127. checking for objdir... .libs
  128. checking if gcc supports -fno-rtti -fno-exceptions... no
  129. checking for gcc option to produce PIC... -fPIC -DPIC
  130. checking if gcc PIC flag -fPIC -DPIC works... yes
  131. checking if gcc static flag -static works... yes
  132. checking if gcc supports -c -o file.o... yes
  133. checking if gcc supports -c -o file.o... (cached) yes
  134. checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
  135. checking whether -lc should be explicitly linked in... no
  136. checking dynamic linker characteristics... GNU/Linux ld.so
  137. checking how to hardcode library paths into programs... immediate
  138. checking whether stripping libraries is possible... yes
  139. checking if libtool supports shared libraries... yes
  140. checking whether to build shared libraries... yes
  141. checking whether to build static libraries... yes
  142. checking how to run the C++ preprocessor... g++ -E
  143. checking for ld used by g++... /usr/bin/ld -m elf_x86_64
  144. checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
  145. checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
  146. checking for g++ option to produce PIC... -fPIC -DPIC
  147. checking if g++ PIC flag -fPIC -DPIC works... yes
  148. checking if g++ static flag -static works... yes
  149. checking if g++ supports -c -o file.o... yes
  150. checking if g++ supports -c -o file.o... (cached) yes
  151. checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
  152. checking dynamic linker characteristics... (cached) GNU/Linux ld.so
  153. checking how to hardcode library paths into programs... immediate
  154. checking whether Solaris gcc optimization fix is necessary... no
  155. checking sys/dg_sys_info.h usability... no
  156. checking sys/dg_sys_info.h presence... no
  157. checking for sys/dg_sys_info.h... no
  158. checking for pkg-config... /usr/bin/pkg-config
  159. checking pkg-config is at least version 0.9.0... yes
  160. checking for ATOMIC_OPS... yes
  161. checking which libatomic_ops to use... external
  162. checking that generated files are newer than configure... done
  163. configure: creating ./config.status
  164. config.status: creating Makefile
  165. config.status: creating bdw-gc.pc
  166. config.status: creating include/private/config.h
  167. config.status: executing depfiles commands
  168. config.status: executing libtool commands
  169. config.status: executing default commands
  170. make
  171. make[2]: Entering directory '/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2'
  172. make[3]: Entering directory '/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2'
  173. depbase=`echo allchblk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  174. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT allchblk.lo -MD -MP -MF $depbase.Tpo -c -o allchblk.lo allchblk.c &&\
  175. mv -f $depbase.Tpo $depbase.Plo
  176. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT allchblk.lo -MD -MP -MF .deps/allchblk.Tpo -c allchblk.c  -fPIC -DPIC -o .libs/allchblk.o
  177. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT allchblk.lo -MD -MP -MF .deps/allchblk.Tpo -c allchblk.c  -fPIC -DPIC -o allchblk.o >/dev/null 2>&1
  178. depbase=`echo alloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  179. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT alloc.lo -MD -MP -MF $depbase.Tpo -c -o alloc.lo alloc.c &&\
  180. mv -f $depbase.Tpo $depbase.Plo
  181. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT alloc.lo -MD -MP -MF .deps/alloc.Tpo -c alloc.c  -fPIC -DPIC -o .libs/alloc.o
  182. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT alloc.lo -MD -MP -MF .deps/alloc.Tpo -c alloc.c  -fPIC -DPIC -o alloc.o >/dev/null 2>&1
  183. depbase=`echo blacklst.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  184. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT blacklst.lo -MD -MP -MF $depbase.Tpo -c -o blacklst.lo blacklst.c &&\
  185. mv -f $depbase.Tpo $depbase.Plo
  186. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT blacklst.lo -MD -MP -MF .deps/blacklst.Tpo -c blacklst.c  -fPIC -DPIC -o .libs/blacklst.o
  187. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT blacklst.lo -MD -MP -MF .deps/blacklst.Tpo -c blacklst.c  -fPIC -DPIC -o blacklst.o >/dev/null 2>&1
  188. depbase=`echo checksums.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  189. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT checksums.lo -MD -MP -MF $depbase.Tpo -c -o checksums.lo checksums.c &&\
  190. mv -f $depbase.Tpo $depbase.Plo
  191. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT checksums.lo -MD -MP -MF .deps/checksums.Tpo -c checksums.c  -fPIC -DPIC -o .libs/checksums.o
  192. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT checksums.lo -MD -MP -MF .deps/checksums.Tpo -c checksums.c  -fPIC -DPIC -o checksums.o >/dev/null 2>&1
  193. depbase=`echo dbg_mlc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  194. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT dbg_mlc.lo -MD -MP -MF $depbase.Tpo -c -o dbg_mlc.lo dbg_mlc.c &&\
  195. mv -f $depbase.Tpo $depbase.Plo
  196. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT dbg_mlc.lo -MD -MP -MF .deps/dbg_mlc.Tpo -c dbg_mlc.c  -fPIC -DPIC -o .libs/dbg_mlc.o
  197. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT dbg_mlc.lo -MD -MP -MF .deps/dbg_mlc.Tpo -c dbg_mlc.c  -fPIC -DPIC -o dbg_mlc.o >/dev/null 2>&1
  198. depbase=`echo dyn_load.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  199. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT dyn_load.lo -MD -MP -MF $depbase.Tpo -c -o dyn_load.lo dyn_load.c &&\
  200. mv -f $depbase.Tpo $depbase.Plo
  201. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT dyn_load.lo -MD -MP -MF .deps/dyn_load.Tpo -c dyn_load.c  -fPIC -DPIC -o .libs/dyn_load.o
  202. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT dyn_load.lo -MD -MP -MF .deps/dyn_load.Tpo -c dyn_load.c  -fPIC -DPIC -o dyn_load.o >/dev/null 2>&1
  203. depbase=`echo finalize.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  204. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT finalize.lo -MD -MP -MF $depbase.Tpo -c -o finalize.lo finalize.c &&\
  205. mv -f $depbase.Tpo $depbase.Plo
  206. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT finalize.lo -MD -MP -MF .deps/finalize.Tpo -c finalize.c  -fPIC -DPIC -o .libs/finalize.o
  207. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT finalize.lo -MD -MP -MF .deps/finalize.Tpo -c finalize.c  -fPIC -DPIC -o finalize.o >/dev/null 2>&1
  208. depbase=`echo gc_dlopen.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  209. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT gc_dlopen.lo -MD -MP -MF $depbase.Tpo -c -o gc_dlopen.lo gc_dlopen.c &&\
  210. mv -f $depbase.Tpo $depbase.Plo
  211. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT gc_dlopen.lo -MD -MP -MF .deps/gc_dlopen.Tpo -c gc_dlopen.c  -fPIC -DPIC -o .libs/gc_dlopen.o
  212. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT gc_dlopen.lo -MD -MP -MF .deps/gc_dlopen.Tpo -c gc_dlopen.c  -fPIC -DPIC -o gc_dlopen.o >/dev/null 2>&1
  213. depbase=`echo gcj_mlc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  214. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT gcj_mlc.lo -MD -MP -MF $depbase.Tpo -c -o gcj_mlc.lo gcj_mlc.c &&\
  215. mv -f $depbase.Tpo $depbase.Plo
  216. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT gcj_mlc.lo -MD -MP -MF .deps/gcj_mlc.Tpo -c gcj_mlc.c  -fPIC -DPIC -o .libs/gcj_mlc.o
  217. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT gcj_mlc.lo -MD -MP -MF .deps/gcj_mlc.Tpo -c gcj_mlc.c  -fPIC -DPIC -o gcj_mlc.o >/dev/null 2>&1
  218. depbase=`echo headers.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  219. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT headers.lo -MD -MP -MF $depbase.Tpo -c -o headers.lo headers.c &&\
  220. mv -f $depbase.Tpo $depbase.Plo
  221. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT headers.lo -MD -MP -MF .deps/headers.Tpo -c headers.c  -fPIC -DPIC -o .libs/headers.o
  222. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT headers.lo -MD -MP -MF .deps/headers.Tpo -c headers.c  -fPIC -DPIC -o headers.o >/dev/null 2>&1
  223. depbase=`echo malloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  224. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT malloc.lo -MD -MP -MF $depbase.Tpo -c -o malloc.lo malloc.c &&\
  225. mv -f $depbase.Tpo $depbase.Plo
  226. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT malloc.lo -MD -MP -MF .deps/malloc.Tpo -c malloc.c  -fPIC -DPIC -o .libs/malloc.o
  227. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT malloc.lo -MD -MP -MF .deps/malloc.Tpo -c malloc.c  -fPIC -DPIC -o malloc.o >/dev/null 2>&1
  228. depbase=`echo mallocx.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  229. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT mallocx.lo -MD -MP -MF $depbase.Tpo -c -o mallocx.lo mallocx.c &&\
  230. mv -f $depbase.Tpo $depbase.Plo
  231. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT mallocx.lo -MD -MP -MF .deps/mallocx.Tpo -c mallocx.c  -fPIC -DPIC -o .libs/mallocx.o
  232. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT mallocx.lo -MD -MP -MF .deps/mallocx.Tpo -c mallocx.c  -fPIC -DPIC -o mallocx.o >/dev/null 2>&1
  233. depbase=`echo mark.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  234. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT mark.lo -MD -MP -MF $depbase.Tpo -c -o mark.lo mark.c &&\
  235. mv -f $depbase.Tpo $depbase.Plo
  236. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT mark.lo -MD -MP -MF .deps/mark.Tpo -c mark.c  -fPIC -DPIC -o .libs/mark.o
  237. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT mark.lo -MD -MP -MF .deps/mark.Tpo -c mark.c  -fPIC -DPIC -o mark.o >/dev/null 2>&1
  238. depbase=`echo mark_rts.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  239. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT mark_rts.lo -MD -MP -MF $depbase.Tpo -c -o mark_rts.lo mark_rts.c &&\
  240. mv -f $depbase.Tpo $depbase.Plo
  241. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT mark_rts.lo -MD -MP -MF .deps/mark_rts.Tpo -c mark_rts.c  -fPIC -DPIC -o .libs/mark_rts.o
  242. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT mark_rts.lo -MD -MP -MF .deps/mark_rts.Tpo -c mark_rts.c  -fPIC -DPIC -o mark_rts.o >/dev/null 2>&1
  243. depbase=`echo misc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  244. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT misc.lo -MD -MP -MF $depbase.Tpo -c -o misc.lo misc.c &&\
  245. mv -f $depbase.Tpo $depbase.Plo
  246. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT misc.lo -MD -MP -MF .deps/misc.Tpo -c misc.c  -fPIC -DPIC -o .libs/misc.o
  247. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT misc.lo -MD -MP -MF .deps/misc.Tpo -c misc.c  -fPIC -DPIC -o misc.o >/dev/null 2>&1
  248. depbase=`echo new_hblk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  249. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT new_hblk.lo -MD -MP -MF $depbase.Tpo -c -o new_hblk.lo new_hblk.c &&\
  250. mv -f $depbase.Tpo $depbase.Plo
  251. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT new_hblk.lo -MD -MP -MF .deps/new_hblk.Tpo -c new_hblk.c  -fPIC -DPIC -o .libs/new_hblk.o
  252. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT new_hblk.lo -MD -MP -MF .deps/new_hblk.Tpo -c new_hblk.c  -fPIC -DPIC -o new_hblk.o >/dev/null 2>&1
  253. depbase=`echo obj_map.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  254. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT obj_map.lo -MD -MP -MF $depbase.Tpo -c -o obj_map.lo obj_map.c &&\
  255. mv -f $depbase.Tpo $depbase.Plo
  256. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT obj_map.lo -MD -MP -MF .deps/obj_map.Tpo -c obj_map.c  -fPIC -DPIC -o .libs/obj_map.o
  257. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT obj_map.lo -MD -MP -MF .deps/obj_map.Tpo -c obj_map.c  -fPIC -DPIC -o obj_map.o >/dev/null 2>&1
  258. depbase=`echo os_dep.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  259. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT os_dep.lo -MD -MP -MF $depbase.Tpo -c -o os_dep.lo os_dep.c &&\
  260. mv -f $depbase.Tpo $depbase.Plo
  261. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT os_dep.lo -MD -MP -MF .deps/os_dep.Tpo -c os_dep.c  -fPIC -DPIC -o .libs/os_dep.o
  262. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT os_dep.lo -MD -MP -MF .deps/os_dep.Tpo -c os_dep.c  -fPIC -DPIC -o os_dep.o >/dev/null 2>&1
  263. depbase=`echo pcr_interface.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  264. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT pcr_interface.lo -MD -MP -MF $depbase.Tpo -c -o pcr_interface.lo pcr_interface.c &&\
  265. mv -f $depbase.Tpo $depbase.Plo
  266. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT pcr_interface.lo -MD -MP -MF .deps/pcr_interface.Tpo -c pcr_interface.c  -fPIC -DPIC -o .libs/pcr_interface.o
  267. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT pcr_interface.lo -MD -MP -MF .deps/pcr_interface.Tpo -c pcr_interface.c  -fPIC -DPIC -o pcr_interface.o >/dev/null 2>&1
  268. depbase=`echo ptr_chck.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  269. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT ptr_chck.lo -MD -MP -MF $depbase.Tpo -c -o ptr_chck.lo ptr_chck.c &&\
  270. mv -f $depbase.Tpo $depbase.Plo
  271. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT ptr_chck.lo -MD -MP -MF .deps/ptr_chck.Tpo -c ptr_chck.c  -fPIC -DPIC -o .libs/ptr_chck.o
  272. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT ptr_chck.lo -MD -MP -MF .deps/ptr_chck.Tpo -c ptr_chck.c  -fPIC -DPIC -o ptr_chck.o >/dev/null 2>&1
  273. depbase=`echo real_malloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  274. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT real_malloc.lo -MD -MP -MF $depbase.Tpo -c -o real_malloc.lo real_malloc.c &&\
  275. mv -f $depbase.Tpo $depbase.Plo
  276. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT real_malloc.lo -MD -MP -MF .deps/real_malloc.Tpo -c real_malloc.c  -fPIC -DPIC -o .libs/real_malloc.o
  277. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT real_malloc.lo -MD -MP -MF .deps/real_malloc.Tpo -c real_malloc.c  -fPIC -DPIC -o real_malloc.o >/dev/null 2>&1
  278. depbase=`echo reclaim.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  279. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT reclaim.lo -MD -MP -MF $depbase.Tpo -c -o reclaim.lo reclaim.c &&\
  280. mv -f $depbase.Tpo $depbase.Plo
  281. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT reclaim.lo -MD -MP -MF .deps/reclaim.Tpo -c reclaim.c  -fPIC -DPIC -o .libs/reclaim.o
  282. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT reclaim.lo -MD -MP -MF .deps/reclaim.Tpo -c reclaim.c  -fPIC -DPIC -o reclaim.o >/dev/null 2>&1
  283. depbase=`echo specific.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  284. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT specific.lo -MD -MP -MF $depbase.Tpo -c -o specific.lo specific.c &&\
  285. mv -f $depbase.Tpo $depbase.Plo
  286. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT specific.lo -MD -MP -MF .deps/specific.Tpo -c specific.c  -fPIC -DPIC -o .libs/specific.o
  287. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT specific.lo -MD -MP -MF .deps/specific.Tpo -c specific.c  -fPIC -DPIC -o specific.o >/dev/null 2>&1
  288. depbase=`echo stubborn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  289. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT stubborn.lo -MD -MP -MF $depbase.Tpo -c -o stubborn.lo stubborn.c &&\
  290. mv -f $depbase.Tpo $depbase.Plo
  291. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT stubborn.lo -MD -MP -MF .deps/stubborn.Tpo -c stubborn.c  -fPIC -DPIC -o .libs/stubborn.o
  292. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT stubborn.lo -MD -MP -MF .deps/stubborn.Tpo -c stubborn.c  -fPIC -DPIC -o stubborn.o >/dev/null 2>&1
  293. depbase=`echo typd_mlc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  294. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT typd_mlc.lo -MD -MP -MF $depbase.Tpo -c -o typd_mlc.lo typd_mlc.c &&\
  295. mv -f $depbase.Tpo $depbase.Plo
  296. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT typd_mlc.lo -MD -MP -MF .deps/typd_mlc.Tpo -c typd_mlc.c  -fPIC -DPIC -o .libs/typd_mlc.o
  297. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT typd_mlc.lo -MD -MP -MF .deps/typd_mlc.Tpo -c typd_mlc.c  -fPIC -DPIC -o typd_mlc.o >/dev/null 2>&1
  298. depbase=`echo backgraph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  299. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT backgraph.lo -MD -MP -MF $depbase.Tpo -c -o backgraph.lo backgraph.c &&\
  300. mv -f $depbase.Tpo $depbase.Plo
  301. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT backgraph.lo -MD -MP -MF .deps/backgraph.Tpo -c backgraph.c  -fPIC -DPIC -o .libs/backgraph.o
  302. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT backgraph.lo -MD -MP -MF .deps/backgraph.Tpo -c backgraph.c  -fPIC -DPIC -o backgraph.o >/dev/null 2>&1
  303. depbase=`echo thread_local_alloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  304. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -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 &&\
  305. mv -f $depbase.Tpo $depbase.Plo
  306. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT thread_local_alloc.lo -MD -MP -MF .deps/thread_local_alloc.Tpo -c thread_local_alloc.c  -fPIC -DPIC -o .libs/thread_local_alloc.o
  307. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT thread_local_alloc.lo -MD -MP -MF .deps/thread_local_alloc.Tpo -c thread_local_alloc.c  -fPIC -DPIC -o thread_local_alloc.o >/dev/null 2>&1
  308. depbase=`echo pthread_start.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  309. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_start.lo -MD -MP -MF $depbase.Tpo -c -o pthread_start.lo pthread_start.c &&\
  310. mv -f $depbase.Tpo $depbase.Plo
  311. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_start.lo -MD -MP -MF .deps/pthread_start.Tpo -c pthread_start.c  -fPIC -DPIC -o .libs/pthread_start.o
  312. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_start.lo -MD -MP -MF .deps/pthread_start.Tpo -c pthread_start.c  -fPIC -DPIC -o pthread_start.o >/dev/null 2>&1
  313. depbase=`echo pthread_support.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  314. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_support.lo -MD -MP -MF $depbase.Tpo -c -o pthread_support.lo pthread_support.c &&\
  315. mv -f $depbase.Tpo $depbase.Plo
  316. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_support.lo -MD -MP -MF .deps/pthread_support.Tpo -c pthread_support.c  -fPIC -DPIC -o .libs/pthread_support.o
  317. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_support.lo -MD -MP -MF .deps/pthread_support.Tpo -c pthread_support.c  -fPIC -DPIC -o pthread_support.o >/dev/null 2>&1
  318. depbase=`echo pthread_stop_world.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  319. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -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 &&\
  320. mv -f $depbase.Tpo $depbase.Plo
  321. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_stop_world.lo -MD -MP -MF .deps/pthread_stop_world.Tpo -c pthread_stop_world.c  -fPIC -DPIC -o .libs/pthread_stop_world.o
  322. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_stop_world.lo -MD -MP -MF .deps/pthread_stop_world.Tpo -c pthread_stop_world.c  -fPIC -DPIC -o pthread_stop_world.o >/dev/null 2>&1
  323. depbase=`echo mach_dep.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
  324. /bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include   -fexceptions -g -O2 -fno-strict-aliasing -MT mach_dep.lo -MD -MP -MF $depbase.Tpo -c -o mach_dep.lo mach_dep.c &&\
  325. mv -f $depbase.Tpo $depbase.Plo
  326. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -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
  327. libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -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
  328. /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    mach_dep.lo -lpthread -ldl  -latomic_ops  
  329. 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 .libs/mach_dep.o   -lpthread -ldl -latomic_ops  -g -O2   -Wl,-soname -Wl,libgc.so.1 -o .libs/libgc.so.1.0.3
  330. /usr/bin/ld: .libs/alloc.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  331. /usr/bin/ld: .libs/blacklst.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  332. /usr/bin/ld: .libs/checksums.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  333. /usr/bin/ld: .libs/dbg_mlc.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  334. /usr/bin/ld: .libs/dyn_load.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  335. /usr/bin/ld: .libs/finalize.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  336. /usr/bin/ld: .libs/gc_dlopen.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  337. /usr/bin/ld: .libs/gcj_mlc.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  338. /usr/bin/ld: .libs/headers.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  339. /usr/bin/ld: .libs/malloc.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  340. /usr/bin/ld: .libs/mallocx.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  341. /usr/bin/ld: .libs/mark.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  342. /usr/bin/ld: .libs/mark_rts.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  343. /usr/bin/ld: .libs/misc.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  344. /usr/bin/ld: .libs/new_hblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  345. /usr/bin/ld: .libs/obj_map.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  346. /usr/bin/ld: .libs/os_dep.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  347. /usr/bin/ld: .libs/pcr_interface.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  348. /usr/bin/ld: .libs/ptr_chck.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  349. /usr/bin/ld: .libs/reclaim.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  350. /usr/bin/ld: .libs/specific.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  351. /usr/bin/ld: .libs/stubborn.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  352. /usr/bin/ld: .libs/typd_mlc.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  353. /usr/bin/ld: .libs/backgraph.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  354. /usr/bin/ld: .libs/thread_local_alloc.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  355. /usr/bin/ld: .libs/pthread_start.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  356. /usr/bin/ld: .libs/pthread_support.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  357. /usr/bin/ld: .libs/pthread_stop_world.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  358. /usr/bin/ld: .libs/mach_dep.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
  359. collect2: error: ld returned 1 exit status
  360. make[3]: *** [Makefile:1180: libgc.la] Error 1
  361. make[3]: Leaving directory '/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2'
  362. make[2]: *** [Makefile:1517: all-recursive] Error 1
  363. make[2]: Leaving directory '/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2'
  364. make[1]: *** [msaMakefile:5: build_gc] Error 2
  365. make[1]: Leaving directory '/tmp/RtmplXLLvZ/R.INSTALL27a5e6368f44d/msa/src/gc-7.2'
  366. make: *** [Makevars:12: build_gc] Error 2
  367. ERROR: compilation failed for package ‘msa’
  368. * removing ‘/home/freddie/R/x86_64-pc-linux-gnu-library/4.0/msa’
  369.  
  370. The downloaded source packages are in
  371.     ‘/tmp/RtmpbnQDKQ/downloaded_packages’
  372. Warning message:
  373. In install.packages(...) :
  374.  installation of package ‘msa’ had non-zero exit status
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