[Request for help] fastani
Hi,
src:fastani does not yet exist in the archive, this is a new one and exists here[1] at the moment. I wish to upload this to NEW after it gets cross-building.
It is using build compiler instead of the host one, so I tried $something[2] there which works, however the cross-build now ends with:
make[1]: Entering directory '/<<PKGBUILDDIR>>'
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -std=c++11 -Isrc -I /usr/local//include -fopenmp -include src/common/memcpyLink.h -Wl,--wrap=memcpy -Wdate-time -D_FORTIFY_SOURCE=2 src/cgi/core_genome_identity.cpp -o fastANI -L/usr/local//lib -lgsl -lgslcblas -lstdc++ -lz -lm -Wl,-z,relro -Wl,-z,now
/usr/lib/gcc-cross/aarch64-linux-gnu/10/../../../../aarch64-linux-gnu/bin/ld: /tmp/ccIOU1st.o: in function `ks_getuntil2(__kstream_t*, int, __kstring_t*, int*, int) [clone .constprop.0]':
/usr/aarch64-linux-gnu/include/bits/string_fortified.h:34: undefined reference to `memcpy@GLIBC_2.2.5'
/usr/lib/gcc-cross/aarch64-linux-gnu/10/../../../../aarch64-linux-gnu/bin/ld: /tmp/ccIOU1st.o: in function `memcpy':
/usr/aarch64-linux-gnu/include/bits/string_fortified.h:34: undefined reference to `memcpy@GLIBC_2.2.5'
/usr/lib/gcc-cross/aarch64-linux-gnu/10/../../../../aarch64-linux-gnu/bin/ld: /tmp/ccIOU1st.o: in function `std::char_traits<char>::copy(char*, char const*, unsigned long)':
/usr/aarch64-linux-gnu/include/c++/10/bits/char_traits.h:402: undefined reference to `memcpy@GLIBC_2.2.5'
/usr/lib/gcc-cross/aarch64-linux-gnu/10/../../../../aarch64-linux-gnu/bin/ld: /usr/aarch64-linux-gnu/include/c++/10/bits/char_traits.h:402: undefined reference to `memcpy@GLIBC_2.2.5'
/usr/lib/gcc-cross/aarch64-linux-gnu/10/../../../../aarch64-linux-gnu/bin/ld: /tmp/ccIOU1st.o: in function `kseq_read(kseq_t*)':
/usr/aarch64-linux-gnu/include/bits/string_fortified.h:34: undefined reference to `memcpy@GLIBC_2.2.5'
/usr/lib/gcc-cross/aarch64-linux-gnu/10/../../../../aarch64-linux-gnu/bin/ld: /tmp/ccIOU1st.o:/usr/aarch64-linux-gnu/include/bits/string_fortified.h:34: more undefined references to `memcpy@GLIBC_2.2.5' follow
collect2: error: ld returned 1 exit status
From my reading, it looks like this[3] file (one-liner) is the origin of this problem, but I have trouble figuring out a way to fix this one. Hence, any help is appreciated
[1]: https://salsa.debian.org/med-team/fastani
[2]: https://salsa.debian.org/med-team/fastani/-/blob/master/debian/patches/cross.patch
[3]: https://salsa.debian.org/med-team/fastani/-/blob/master/src/common/memcpyLink.h
Nilesh
Reply to: