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UBod / msa

R package for multiple sequence alignment
https://github.com/UBod/msa
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compilation failed 1.20.0 #3

Closed drelo closed 3 years ago

drelo commented 4 years ago

Dear Ulrich,

I am having some trouble installing msa in R 4.0.2, currently using Fedora.

I tried to install it with

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("msa")

Here is the output I got 

> BiocManager::install("msa")
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.2 Patched (2020-08-23
  r79071)
Installing package(s) 'msa'
probando la URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/msa_1.20.0.tar.gz'
Content type 'application/x-gzip' length 3767459 bytes (3.6 MB)
==================================================
downloaded 3.6 MB

* installing *source* package ‘msa’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/opt/R/4.0.2.Patched/lib64/R/include" -DNDEBUG  -I'/home/andrespara/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I/usr/local/include  -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fpic  -g -O2  -c R_init_msa.cpp -o R_init_msa.o
En el fichero incluido desde ./Muscle/RMuscle.h:4,
                 desde R_init_msa.cpp:3:
./Muscle/muscle.h:54: aviso: «assert» redefinido
   54 | #define assert(exp)     ((void)0)
      | 
En el fichero incluido desde /usr/include/c++/10/cassert:44,
                 desde /home/andrespara/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp/utils/tinyformat/tinyformat.h:137,
                 desde /home/andrespara/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp/utils/tinyformat.h:40,
                 desde /home/andrespara/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/RcppCommon.h:70,
                 desde /home/andrespara/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp.h:27,
                 desde ./ClustalOmega/src/RClustalOmega.h:4,
                 desde R_init_msa.cpp:1:
/usr/include/assert.h:50: nota: esta es la ubicación de la definición previa
   50 | # define assert(expr)  (__ASSERT_VOID_CAST (0))
      | 
g++ -std=gnu++11 -I"/opt/R/4.0.2.Patched/lib64/R/include" -DNDEBUG  -I'/home/andrespara/R/x86_64-pc-linux-gnu-library/4.0/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
g++ -std=gnu++11 -I"/opt/R/4.0.2.Patched/lib64/R/include" -DNDEBUG  -I'/home/andrespara/R/x86_64-pc-linux-gnu-library/4.0/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
make --file=msaMakefile --directory=gc-7.2
make[1]: se entra en el directorio '/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2'
./configure --enable-cplusplus --enable-threads=pthreads --enable-shared --with-pic
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
checking GC version numbers... major=7 minor=2 
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking dependency style of gcc... gcc3
checking for inline... inline
checking for pthread_self in -lpthread... yes
configure: WARNING: "Explicit GC_INIT() calls may be required."
checking for xlc... no
checking whether gcc supports -fno-strict-aliasing... yes
checking for dlopen in -ldl... yes
checking whether to build shared libraries... yes
checking which machine-dependent code should be used... 
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... no
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether Solaris gcc optimization fix is necessary... no
checking sys/dg_sys_info.h usability... no
checking sys/dg_sys_info.h presence... no
checking for sys/dg_sys_info.h... no
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for ATOMIC_OPS... no
checking which libatomic_ops to use... internal
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating bdw-gc.pc
config.status: creating include/private/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
config.status: executing default commands
=== configuring in libatomic_ops (/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/libatomic_ops)
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=.
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for ranlib... ranlib
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for ANSI C header files... (cached) yes
checking for PIC compiler flag... -fPIC
checking whether gcc -fPIC causes __PIC__ definition... yes
checking for pthread_self in -lpthread... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating pkgconfig/atomic_ops.pc
config.status: creating pkgconfig/atomic_ops-uninstalled.pc
config.status: creating doc/Makefile
config.status: creating src/Makefile
config.status: creating src/atomic_ops/Makefile
config.status: creating src/atomic_ops/sysdeps/Makefile
config.status: creating tests/Makefile
config.status: creating src/config.h
config.status: executing depfiles commands
config.status: executing default commands
make
make[2]: se entra en el directorio '/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2'
make[3]: se entra en el directorio '/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2'
depbase=`echo allchblk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT allchblk.lo -MD -MP -MF .deps/allchblk.Tpo -c allchblk.c  -fPIC -DPIC -o .libs/allchblk.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT allchblk.lo -MD -MP -MF .deps/allchblk.Tpo -c allchblk.c  -fPIC -DPIC -o allchblk.o >/dev/null 2>&1
depbase=`echo alloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT alloc.lo -MD -MP -MF .deps/alloc.Tpo -c alloc.c  -fPIC -DPIC -o .libs/alloc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT alloc.lo -MD -MP -MF .deps/alloc.Tpo -c alloc.c  -fPIC -DPIC -o alloc.o >/dev/null 2>&1
depbase=`echo blacklst.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT blacklst.lo -MD -MP -MF .deps/blacklst.Tpo -c blacklst.c  -fPIC -DPIC -o .libs/blacklst.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT blacklst.lo -MD -MP -MF .deps/blacklst.Tpo -c blacklst.c  -fPIC -DPIC -o blacklst.o >/dev/null 2>&1
depbase=`echo checksums.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT checksums.lo -MD -MP -MF .deps/checksums.Tpo -c checksums.c  -fPIC -DPIC -o .libs/checksums.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT checksums.lo -MD -MP -MF .deps/checksums.Tpo -c checksums.c  -fPIC -DPIC -o checksums.o >/dev/null 2>&1
depbase=`echo dbg_mlc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dbg_mlc.lo -MD -MP -MF .deps/dbg_mlc.Tpo -c dbg_mlc.c  -fPIC -DPIC -o .libs/dbg_mlc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dbg_mlc.lo -MD -MP -MF .deps/dbg_mlc.Tpo -c dbg_mlc.c  -fPIC -DPIC -o dbg_mlc.o >/dev/null 2>&1
depbase=`echo dyn_load.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dyn_load.lo -MD -MP -MF .deps/dyn_load.Tpo -c dyn_load.c  -fPIC -DPIC -o .libs/dyn_load.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dyn_load.lo -MD -MP -MF .deps/dyn_load.Tpo -c dyn_load.c  -fPIC -DPIC -o dyn_load.o >/dev/null 2>&1
depbase=`echo finalize.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT finalize.lo -MD -MP -MF .deps/finalize.Tpo -c finalize.c  -fPIC -DPIC -o .libs/finalize.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT finalize.lo -MD -MP -MF .deps/finalize.Tpo -c finalize.c  -fPIC -DPIC -o finalize.o >/dev/null 2>&1
depbase=`echo gc_dlopen.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT gc_dlopen.lo -MD -MP -MF .deps/gc_dlopen.Tpo -c gc_dlopen.c  -fPIC -DPIC -o .libs/gc_dlopen.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT gc_dlopen.lo -MD -MP -MF .deps/gc_dlopen.Tpo -c gc_dlopen.c  -fPIC -DPIC -o gc_dlopen.o >/dev/null 2>&1
depbase=`echo gcj_mlc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT gcj_mlc.lo -MD -MP -MF .deps/gcj_mlc.Tpo -c gcj_mlc.c  -fPIC -DPIC -o .libs/gcj_mlc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT gcj_mlc.lo -MD -MP -MF .deps/gcj_mlc.Tpo -c gcj_mlc.c  -fPIC -DPIC -o gcj_mlc.o >/dev/null 2>&1
depbase=`echo headers.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT headers.lo -MD -MP -MF .deps/headers.Tpo -c headers.c  -fPIC -DPIC -o .libs/headers.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT headers.lo -MD -MP -MF .deps/headers.Tpo -c headers.c  -fPIC -DPIC -o headers.o >/dev/null 2>&1
depbase=`echo malloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT malloc.lo -MD -MP -MF .deps/malloc.Tpo -c malloc.c  -fPIC -DPIC -o .libs/malloc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT malloc.lo -MD -MP -MF .deps/malloc.Tpo -c malloc.c  -fPIC -DPIC -o malloc.o >/dev/null 2>&1
depbase=`echo mallocx.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mallocx.lo -MD -MP -MF .deps/mallocx.Tpo -c mallocx.c  -fPIC -DPIC -o .libs/mallocx.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mallocx.lo -MD -MP -MF .deps/mallocx.Tpo -c mallocx.c  -fPIC -DPIC -o mallocx.o >/dev/null 2>&1
depbase=`echo mark.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mark.lo -MD -MP -MF .deps/mark.Tpo -c mark.c  -fPIC -DPIC -o .libs/mark.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mark.lo -MD -MP -MF .deps/mark.Tpo -c mark.c  -fPIC -DPIC -o mark.o >/dev/null 2>&1
depbase=`echo mark_rts.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mark_rts.lo -MD -MP -MF .deps/mark_rts.Tpo -c mark_rts.c  -fPIC -DPIC -o .libs/mark_rts.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mark_rts.lo -MD -MP -MF .deps/mark_rts.Tpo -c mark_rts.c  -fPIC -DPIC -o mark_rts.o >/dev/null 2>&1
depbase=`echo misc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT misc.lo -MD -MP -MF .deps/misc.Tpo -c misc.c  -fPIC -DPIC -o .libs/misc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT misc.lo -MD -MP -MF .deps/misc.Tpo -c misc.c  -fPIC -DPIC -o misc.o >/dev/null 2>&1
depbase=`echo new_hblk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT new_hblk.lo -MD -MP -MF .deps/new_hblk.Tpo -c new_hblk.c  -fPIC -DPIC -o .libs/new_hblk.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT new_hblk.lo -MD -MP -MF .deps/new_hblk.Tpo -c new_hblk.c  -fPIC -DPIC -o new_hblk.o >/dev/null 2>&1
depbase=`echo obj_map.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT obj_map.lo -MD -MP -MF .deps/obj_map.Tpo -c obj_map.c  -fPIC -DPIC -o .libs/obj_map.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT obj_map.lo -MD -MP -MF .deps/obj_map.Tpo -c obj_map.c  -fPIC -DPIC -o obj_map.o >/dev/null 2>&1
depbase=`echo os_dep.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT os_dep.lo -MD -MP -MF .deps/os_dep.Tpo -c os_dep.c  -fPIC -DPIC -o .libs/os_dep.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT os_dep.lo -MD -MP -MF .deps/os_dep.Tpo -c os_dep.c  -fPIC -DPIC -o os_dep.o >/dev/null 2>&1
depbase=`echo pcr_interface.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pcr_interface.lo -MD -MP -MF .deps/pcr_interface.Tpo -c pcr_interface.c  -fPIC -DPIC -o .libs/pcr_interface.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pcr_interface.lo -MD -MP -MF .deps/pcr_interface.Tpo -c pcr_interface.c  -fPIC -DPIC -o pcr_interface.o >/dev/null 2>&1
depbase=`echo ptr_chck.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT ptr_chck.lo -MD -MP -MF .deps/ptr_chck.Tpo -c ptr_chck.c  -fPIC -DPIC -o .libs/ptr_chck.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT ptr_chck.lo -MD -MP -MF .deps/ptr_chck.Tpo -c ptr_chck.c  -fPIC -DPIC -o ptr_chck.o >/dev/null 2>&1
depbase=`echo real_malloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT real_malloc.lo -MD -MP -MF .deps/real_malloc.Tpo -c real_malloc.c  -fPIC -DPIC -o .libs/real_malloc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT real_malloc.lo -MD -MP -MF .deps/real_malloc.Tpo -c real_malloc.c  -fPIC -DPIC -o real_malloc.o >/dev/null 2>&1
depbase=`echo reclaim.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT reclaim.lo -MD -MP -MF .deps/reclaim.Tpo -c reclaim.c  -fPIC -DPIC -o .libs/reclaim.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT reclaim.lo -MD -MP -MF .deps/reclaim.Tpo -c reclaim.c  -fPIC -DPIC -o reclaim.o >/dev/null 2>&1
depbase=`echo specific.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT specific.lo -MD -MP -MF .deps/specific.Tpo -c specific.c  -fPIC -DPIC -o .libs/specific.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT specific.lo -MD -MP -MF .deps/specific.Tpo -c specific.c  -fPIC -DPIC -o specific.o >/dev/null 2>&1
depbase=`echo stubborn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT stubborn.lo -MD -MP -MF .deps/stubborn.Tpo -c stubborn.c  -fPIC -DPIC -o .libs/stubborn.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT stubborn.lo -MD -MP -MF .deps/stubborn.Tpo -c stubborn.c  -fPIC -DPIC -o stubborn.o >/dev/null 2>&1
depbase=`echo typd_mlc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT typd_mlc.lo -MD -MP -MF .deps/typd_mlc.Tpo -c typd_mlc.c  -fPIC -DPIC -o .libs/typd_mlc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT typd_mlc.lo -MD -MP -MF .deps/typd_mlc.Tpo -c typd_mlc.c  -fPIC -DPIC -o typd_mlc.o >/dev/null 2>&1
depbase=`echo backgraph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT backgraph.lo -MD -MP -MF .deps/backgraph.Tpo -c backgraph.c  -fPIC -DPIC -o .libs/backgraph.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT backgraph.lo -MD -MP -MF .deps/backgraph.Tpo -c backgraph.c  -fPIC -DPIC -o backgraph.o >/dev/null 2>&1
depbase=`echo thread_local_alloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT thread_local_alloc.lo -MD -MP -MF .deps/thread_local_alloc.Tpo -c thread_local_alloc.c  -fPIC -DPIC -o .libs/thread_local_alloc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT thread_local_alloc.lo -MD -MP -MF .deps/thread_local_alloc.Tpo -c thread_local_alloc.c  -fPIC -DPIC -o thread_local_alloc.o >/dev/null 2>&1
depbase=`echo pthread_start.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_start.lo -MD -MP -MF .deps/pthread_start.Tpo -c pthread_start.c  -fPIC -DPIC -o .libs/pthread_start.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_start.lo -MD -MP -MF .deps/pthread_start.Tpo -c pthread_start.c  -fPIC -DPIC -o pthread_start.o >/dev/null 2>&1
depbase=`echo pthread_support.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_support.lo -MD -MP -MF .deps/pthread_support.Tpo -c pthread_support.c  -fPIC -DPIC -o .libs/pthread_support.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_support.lo -MD -MP -MF .deps/pthread_support.Tpo -c pthread_support.c  -fPIC -DPIC -o pthread_support.o >/dev/null 2>&1
depbase=`echo pthread_stop_world.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_stop_world.lo -MD -MP -MF .deps/pthread_stop_world.Tpo -c pthread_stop_world.c  -fPIC -DPIC -o .libs/pthread_stop_world.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_stop_world.lo -MD -MP -MF .deps/pthread_stop_world.Tpo -c pthread_stop_world.c  -fPIC -DPIC -o pthread_stop_world.o >/dev/null 2>&1
depbase=`echo libatomic_ops/src/atomic_ops.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT libatomic_ops/src/atomic_ops.lo -MD -MP -MF libatomic_ops/src/.deps/atomic_ops.Tpo -c libatomic_ops/src/atomic_ops.c  -fPIC -DPIC -o libatomic_ops/src/.libs/atomic_ops.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT libatomic_ops/src/atomic_ops.lo -MD -MP -MF libatomic_ops/src/.deps/atomic_ops.Tpo -c libatomic_ops/src/atomic_ops.c  -fPIC -DPIC -o libatomic_ops/src/atomic_ops.o >/dev/null 2>&1
depbase=`echo mach_dep.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mach_dep.lo -MD -MP -MF .deps/mach_dep.Tpo -c mach_dep.c  -fPIC -DPIC -o .libs/mach_dep.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mach_dep.lo -MD -MP -MF .deps/mach_dep.Tpo -c mach_dep.c  -fPIC -DPIC -o mach_dep.o >/dev/null 2>&1
/bin/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 -ldl   
libtool: link: gcc -shared  -fPIC -DPIC  .libs/allchblk.o .libs/alloc.o .libs/blacklst.o .libs/checksums.o .libs/dbg_mlc.o .libs/dyn_load.o .libs/finalize.o .libs/gc_dlopen.o .libs/gcj_mlc.o .libs/headers.o .libs/malloc.o .libs/mallocx.o .libs/mark.o .libs/mark_rts.o .libs/misc.o .libs/new_hblk.o .libs/obj_map.o .libs/os_dep.o .libs/pcr_interface.o .libs/ptr_chck.o .libs/real_malloc.o .libs/reclaim.o .libs/specific.o .libs/stubborn.o .libs/typd_mlc.o .libs/backgraph.o .libs/thread_local_alloc.o .libs/pthread_start.o .libs/pthread_support.o .libs/pthread_stop_world.o libatomic_ops/src/.libs/atomic_ops.o .libs/mach_dep.o   -lpthread -ldl  -g -O2   -Wl,-soname -Wl,libgc.so.1 -o .libs/libgc.so.1.0.3
/usr/bin/ld: .libs/alloc.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/blacklst.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/checksums.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/dbg_mlc.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/dyn_load.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/finalize.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/gc_dlopen.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/gcj_mlc.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/headers.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/malloc.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/mallocx.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/mark.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/mark_rts.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/misc.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/new_hblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/obj_map.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/os_dep.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/pcr_interface.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/ptr_chck.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/reclaim.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/specific.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/stubborn.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/typd_mlc.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/backgraph.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/thread_local_alloc.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/pthread_start.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/pthread_support.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/pthread_stop_world.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/mach_dep.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:1180: libgc.la] Error 1
make[3]: se sale del directorio '/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2'
make[2]: *** [Makefile:1517: all-recursive] Error 1
make[2]: se sale del directorio '/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2'
make[1]: se sale del directorio '/tmp/RtmpV6iJfe/R.INSTALL2da8be70301f54/msa/src/gc-7.2'
make[1]: *** [msaMakefile:5: build_gc] Error 2
make: *** [Makevars:12: build_gc] Error 2
ERROR: compilation failed for package ‘msa’
* removing ‘/home/andrespara/R/x86_64-pc-linux-gnu-library/4.0/msa’

The downloaded source packages are in
    ‘/tmp/Rtmp0LCzA8/downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘msa’ had non-zero exit status
>

here is the output of sessionInfo()

sessionInfo()
R version 4.0.2 Patched (2020-08-23 r79071)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Generic 32 (Generic)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.10.so

locale:
 [1] LC_CTYPE=es_UY.UTF-8       LC_NUMERIC=C               LC_TIME=es_UY.UTF-8       
 [4] LC_COLLATE=es_UY.UTF-8     LC_MONETARY=es_UY.UTF-8    LC_MESSAGES=es_UY.UTF-8   
 [7] LC_PAPER=es_UY.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=es_UY.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] mgcv_1.8-33  nlme_3.1-149

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5          pillar_1.4.6        compiler_4.0.2      BiocManager_1.30.10
 [5] XVector_0.28.0      tools_4.0.2         zlibbioc_1.34.0     digest_0.6.25      
 [9] bit_4.0.4           tibble_3.0.3        lifecycle_0.2.0     RSQLite_2.2.0      
[13] memoise_1.1.0       lattice_0.20-41     pkgconfig_2.0.3     rlang_0.4.7        
[17] Matrix_1.2-18       cli_2.0.2           DBI_1.1.0           rstudioapi_0.11    
[21] parallel_4.0.2      dplyr_1.0.2         generics_0.0.2      Biostrings_2.56.0  
[25] S4Vectors_0.26.1    vctrs_0.3.4         globals_0.12.5      IRanges_2.22.2     
[29] tidyselect_1.1.0    stats4_4.0.2        bit64_4.0.5         grid_4.0.2         
[33] glue_1.4.2          R6_2.4.1            listenv_0.8.0       fansi_0.4.1        
[37] DECIPHER_2.16.1     purrr_0.3.4         blob_1.2.1          magrittr_1.5       
[41] ellipsis_0.3.1      codetools_0.2-16    splines_4.0.2       BiocGenerics_0.34.0
[45] assertthat_0.2.1    future_1.18.0       crayon_1.3.4

How could I fix this? Thanks in advance for any help.

UBod commented 3 years ago

Thanks for reporting this issue, Andres! (and sorry for the excessively long delay)

This issue is known. Unfortunately, I neither have the capacity nor the knowledge to fix it. I already asked the Bioc core team for help (https://stat.ethz.ch/pipermail/bioc-devel/2020-July/017033.html). However, they responded they do not have the capacity to maintain the package (https://stat.ethz.ch/pipermail/bioc-devel/2020-August/017071.html). Do you think you (or somebody you know) can dosomething about it? Your help would be gratefully appreciated!

drelo commented 3 years ago

Thanks for the reply, I would love to help but I don't have the knowledge atm, in the meantime I did a workaround with my dataset I 'just' needed to convert from one format to another, but I just did some cheat exporting and loading again the files in the required format.