Open AntonisSaphetor opened 2 years ago
Hi @vplagnol,
Is exomedepth compatible with R verson >4 in ubuntu 22? I have tried to run it, but it requested that I reinstall it, then failed:
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c CNV_estimate.cpp -o CNV_estimate.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ExomeDepth_init.c -o ExomeDepth_init.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c VP_gamma.c -o VP_gamma.o In file included from gsl_math.h:22, from VP_gamma.c:23: /usr/include/x86_64-linux-gnu/bits/mathcalls.h:85:1: error: expected ‘;’ before ‘extern’ 85 | MATHCALL_VEC (acosh,, (Mdouble __x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:87:1: error: expected ‘;’ before ‘extern’ 87 | MATHCALL_VEC (asinh,, (Mdouble x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:89:1: error: expected ‘;’ before ‘extern’ 89 | __MATHCALL_VEC (atanh,, (Mdouble x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:119:1: error: expected ‘;’ before ‘extern’ 119 | MATHCALL_VEC (expm1,, (Mdouble __x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:122:1: error: expected ‘;’ before ‘extern’ 122 | MATHCALL_VEC (log1p,, (Mdouble x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:147:1: error: expected ‘;’ before ‘extern’ 147 | __MATHCALL_VEC (hypot,, (Mdouble x, Mdouble y)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:85:1: error: expected ‘;’ before ‘extern’ 85 | __MATHCALL_VEC (acosh,, (Mdouble x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:87:1: error: expected ‘;’ before ‘extern’ 87 | MATHCALL_VEC (asinh,, (Mdouble __x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:89:1: error: expected ‘;’ before ‘extern’ 89 | MATHCALL_VEC (atanh,, (Mdouble x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:119:1: error: expected ‘;’ before ‘extern’ 119 | __MATHCALL_VEC (expm1,, (Mdouble x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:122:1: error: expected ‘;’ before ‘extern’ 122 | MATHCALL_VEC (log1p,, (Mdouble __x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:147:1: error: expected ‘;’ before ‘extern’ 147 | MATHCALL_VEC (hypot,, (Mdouble x, Mdouble y)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:85:1: error: expected ‘;’ before ‘extern’ 85 | MATHCALL_VEC (acosh,, (Mdouble __x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:87:1: error: expected ‘;’ before ‘extern’ 87 | MATHCALL_VEC (asinh,, (Mdouble x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:89:1: error: expected ‘;’ before ‘extern’ 89 | __MATHCALL_VEC (atanh,, (Mdouble x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:119:1: error: expected ‘;’ before ‘extern’ 119 | MATHCALL_VEC (expm1,, (Mdouble __x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:122:1: error: expected ‘;’ before ‘extern’ 122 | MATHCALL_VEC (log1p,, (Mdouble x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:147:1: error: expected ‘;’ before ‘extern’ 147 | __MATHCALL_VEC (hypot,, (Mdouble x, Mdouble __y)); | ^~~~~~ make: *** [/usr/lib/R/etc/Makeconf:168: VP_gamma.o] Error 1 ERROR: compilation failed for package ‘ExomeDepth’
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Hi @vplagnol,
Is exomedepth compatible with R verson >4 in ubuntu 22? I have tried to run it, but it requested that I reinstall it, then failed:
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c CNV_estimate.cpp -o CNV_estimate.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ExomeDepth_init.c -o ExomeDepth_init.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c VP_gamma.c -o VP_gamma.o In file included from gsl_math.h:22, from VP_gamma.c:23: /usr/include/x86_64-linux-gnu/bits/mathcalls.h:85:1: error: expected ‘;’ before ‘extern’ 85 | MATHCALL_VEC (acosh,, (Mdouble __x)); | ^
~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:87:1: error: expected ‘;’ before ‘extern’ 87 | MATHCALL_VEC (asinh,, (Mdouble x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:89:1: error: expected ‘;’ before ‘extern’ 89 | __MATHCALL_VEC (atanh,, (Mdouble x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:119:1: error: expected ‘;’ before ‘extern’ 119 | MATHCALL_VEC (expm1,, (Mdouble __x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:122:1: error: expected ‘;’ before ‘extern’ 122 | MATHCALL_VEC (log1p,, (Mdouble x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:147:1: error: expected ‘;’ before ‘extern’ 147 | __MATHCALL_VEC (hypot,, (Mdouble x, Mdouble y)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:85:1: error: expected ‘;’ before ‘extern’ 85 | __MATHCALL_VEC (acosh,, (Mdouble x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:87:1: error: expected ‘;’ before ‘extern’ 87 | MATHCALL_VEC (asinh,, (Mdouble __x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:89:1: error: expected ‘;’ before ‘extern’ 89 | MATHCALL_VEC (atanh,, (Mdouble x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:119:1: error: expected ‘;’ before ‘extern’ 119 | __MATHCALL_VEC (expm1,, (Mdouble x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:122:1: error: expected ‘;’ before ‘extern’ 122 | MATHCALL_VEC (log1p,, (Mdouble __x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:147:1: error: expected ‘;’ before ‘extern’ 147 | MATHCALL_VEC (hypot,, (Mdouble x, Mdouble y)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:85:1: error: expected ‘;’ before ‘extern’ 85 | MATHCALL_VEC (acosh,, (Mdouble __x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:87:1: error: expected ‘;’ before ‘extern’ 87 | MATHCALL_VEC (asinh,, (Mdouble x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:89:1: error: expected ‘;’ before ‘extern’ 89 | __MATHCALL_VEC (atanh,, (Mdouble x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:119:1: error: expected ‘;’ before ‘extern’ 119 | MATHCALL_VEC (expm1,, (Mdouble __x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:122:1: error: expected ‘;’ before ‘extern’ 122 | MATHCALL_VEC (log1p,, (Mdouble x)); | ^~~~~~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:147:1: error: expected ‘;’ before ‘extern’ 147 | __MATHCALL_VEC (hypot,, (Mdouble x, Mdouble __y)); | ^~~~~~ make: *** [/usr/lib/R/etc/Makeconf:168: VP_gamma.o] Error 1 ERROR: compilation failed for package ‘ExomeDepth’