Entering edit mode
22 months ago
akoussounadis
▴
10
Hi all
I was trying to update ExomeDepth R package in ubuntu 22, using R 4.1.2. Install is failing:
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: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’
Has anybody had similar experience or have a solution? Many thanks!
