zhizhi411
commented
4 months ago I solved it！So happy！please see “smartdenovo make error #18”。and https://github.com/ruanjue/smartdenovo/issues/18#issuecomment-1519060111 Changes in the Makefile as mentioned here Removing lines 95 to 97 and 832 to 834 in wtlay.h as mentioned here Add static before all five occurrences of inline (lines 491 to 518) in wtlay.h
Hi,I just tried to download and compile smartdenovo using your command lines: git clone https://github.com/ruanjue/smartdenovo.git cd smartdenovo make but, the compilation endend on:
gcc -W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 -o wtext file_reader.c ksw.c wtext.c -lm -lpthread gcc -W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 -o wtgbo file_reader.c ksw.c wtgbo.c -lm -lpthread gcc -W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 -o wtlay file_reader.c wtlay.c -lm -lpthread /tmp/ccXfrjCm.o：在函数‘merge_bubbles_strgraph’中： wtlay.c:(.text+0x9e43)：对‘cut_biedge_strgraph_core’未定义的引用 wtlay.c:(.text+0x9e5d)：对‘cut_biedge_strgraph_core’未定义的引用 wtlay.c:(.text+0x9e9e)：对‘cut_biedge_strgraph_core’未定义的引用 wtlay.c:(.text+0x9eb8)：对‘cut_biedge_strgraph_core’未定义的引用 collect2: 错误：ld 返回 1 make: *** [Makefile:48：wtlay] 错误 1
Please help me!
more other information:
gcc -v 使用内建 specs。 COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/8/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 目标：x86_64-redhat-linux 配置为：../configure --enable-bootstrap --enable-languages=c,c++,fortran,lto --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=https://bugs.rockylinux.org/ --enable-shared --enable-threads=posix --enable-checking=release --enable-multilib --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-gcc-major-version-only --with-linker-hash-style=gnu --enable-plugin --enable-initfini-array --with-isl --disable-libmpx --enable-offload-targets=nvptx-none --without-cuda-driver --enable-gnu-indirect-function --enable-cet --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux 线程模型：posix gcc 版本 8.5.0 20210514 (Red Hat 8.5.0-10) (GCC)
cpp -v 使用内建 specs。 COLLECT_GCC=cpp OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 目标：x86_64-redhat-linux 配置为：../configure --enable-bootstrap --enable-languages=c,c++,fortran,lto --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=https://bugs.rockylinux.org/ --enable-shared --enable-threads=posix --enable-checking=release --enable-multilib --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-gcc-major-version-only --with-linker-hash-style=gnu --enable-plugin --enable-initfini-array --with-isl --disable-libmpx --enable-offload-targets=nvptx-none --without-cuda-driver --enable-gnu-indirect-function --enable-cet --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux 线程模型：posix gcc 版本 8.5.0 20210514 (Red Hat 8.5.0-10) (GCC) COLLECT_GCC_OPTIONS='-E' '-v' '-mtune=generic' '-march=x86-64' /usr/libexec/gcc/x86_64-redhat-linux/8/cc1 -E -quiet -v - -mtune=generic -march=x86-64 忽略不存在的目录“/usr/lib/gcc/x86_64-redhat-linux/8/include-fixed” 忽略不存在的目录“/usr/lib/gcc/x86_64-redhat-linux/8/../../../../x86_64-redhat-linux/include”
include "..." 搜索从这里开始：
include <...> 搜索从这里开始：
/usr/lib/gcc/x86_64-redhat-linux/8/include /usr/local/include /usr/include 搜索列表结束